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In wine grape, the multi-functional cytochrome P450 enzyme VvCYP76F14 sequentially catalyzes the formation of linalool-derived compounds, including (E)-8-hydroxylinalool, (E)-8-oxolinalool, and (E)-8-carboxylinalool, which are crucial precursors for the wine bouquet. However, molecular basis towards VvCYP76F14 in regulating the wine bouquet precursor production remain unknown. In this study, both wine bouquet precursor contents and catalytic activities of VvCYP76F14s varied among the three different wine bouquet type varieties. Subcellular localization analysis revealed that VvCYP76F14s are predominantly localized in the endoplasmic reticulum. Notably, a maltosebinding protein (MBP) fusion-tag was added to each of the three VvCYP76F14 proteins in the Escherichia coli expression system, significantly induced the concentration of the MBP-VvCYP76F14 fusion proteins. Site-directed mutation of 4 amino acid residues (I120L, L298V, E378G, and T389A) in VvCYP76F14 resulted in a significant decrease in VvCYP76F14 enzymatic activities, respectively. Furthermore, the transient expression of VvCYP76F14 cloned from 'Yanniang No.2' significantly increased the levels of (E)-8-hydroxylinalool, 8-oxolinalool, and (E)-8-carboxylinalool compounds in the transformed 'Yanniang No.2', 'Italian Riesling', and 'Marselan' berries, respectively. In conclusion, VvCYP76F14 dominates the production of wine bouquet precursors and could be a fingerprint marker for screening superior hybrid offspring with desired levels of wine bouquet precursors. [ABSTRACT FROM AUTHOR]

Background: Understanding the genetic control of pod shatter resistance and its association with pod length is crucial for breeding improved pod shatter resistance and reducing pre-harvest yield losses due to extensive shattering in cultivars of Brassica species. In this study, we evaluated a doubled haploid (DH) mapping population derived from an F1 cross between two Brassica carinata parental lines Y-BcDH64 and W-BcDH76 (YWDH), originating from Ethiopia and determined genetic bases of variation in pod length and pod shatter resistance, measured as rupture energy. The YWDH population, its parental lines and 11 controls were grown across three years for genetic analysis. Results: By using three quantitative trait loci (QTL) analytic approaches, we identified nine genomic regions on B02, B03, B04, B06, B07 and C01 chromosomes for rupture energy that were repeatedly detected across three growing environments. One of the QTL on chromosome B07, flanked with DArTseq markers 100,046,735 and 100,022,658, accounted for up to 27.6% of genetic variance in rupture energy. We observed no relationship between pod length and rupture energy, suggesting that pod length does not contribute to variation in pod shatter resistance. Comparative mapping identified six candidate genes; SHP1 on B6, FUL and MAN on chromosomes B07, IND and NST2 on B08, and MAN7 on C07 that mapped within 0.2 Mb from the QTL for rupture energy. Conclusion: The results suggest that favourable alleles of stable QTL on B06, B07, B08 and C01 for pod shatter resistance can be incorporated into the shatter-prone B. carinata and its related species to improve final seed yield at harvest. [ABSTRACT FROM AUTHOR]

Introduction: Short Tandem Repeats (STRs) are highly valuable genetic markers in forensic science. However, the conventional PCR-CE technique has limitations, and the emergence of massively parallel sequencing (MPS) technology presents new opportunities for STR analysis. Yet, there is limited research on Chinese population diversity using MPS. Methods: In this study, we obtained genotype data for 52 A-STRs and 81 Y-STRs from the Hakka population in Meizhou, Guangdong, China, using the Forensic Analysis System Multiplecues SetB Kit on the MGISEQ-2000 platform. Results: Our findings demonstrate that these 133 STRs are highly efficient for forensic applications within the Meizhou Hakka population. Statistical analysis revealed Hobs values ranging from 0.61306 to 0.91083 and Hexp values ranging from 0.59156 to 0.91497 for A-STRs based on length polymorphism. For sequence polymorphism, Hobs values ranged from 0.61306 to 0.94586, and Hexp values fluctuated between 0.59156 and 0.94487. The CPE values were 1-5.0779620E-21 and 1-3.257436E-24 for length and sequence polymorphism, respectively, while the CPD values were 1-1.727007E-59 and 1-5.517015E-66, respectively. Among the 80 Y-STR loci, the HD values for length and sequence polymorphism were 0.99764282 and 0.99894195, respectively. The HMP values stood at 0.00418102 and 0.00288427, respectively, and the DC values were 0.75502742 and 0.83363803, respectively. For the 52 A-STR loci, we identified 554 and 989 distinct alleles based on length and sequence polymorphisms, respectively. For the 81 Y-STR loci, 464 and 652 unique alleles were detected at the length and sequence level, respectively. Population genetic analysis revealed that the Meizhou Hakka population has a close kinship relationship with the Asian populations THI and KOR based on length polymorphism data of A-STRs. Conversely, based on length polymorphism data of Y-STRs, the Meizhou Hakka population has the closest kinship relationship with the Henan Han population. Discussion: Overall, the variation information of repeat region sequences significantly enhances the forensic identification efficacy of STR genetic markers, providing an essential database for forensic individual and paternity testing in this region. Additionally, the data generated by our study will serve as a vital resource for research into the genetic structure and historical origins of the Meizhou Hakka population. [ABSTRACT FROM AUTHOR]

The technology based on CRISPR/Cas9, one of the potential solutions recognized for addressing the worsening situation of fusarium wilt caused by Fusarium oxysporum f. sp. cubense 'Tropical Race 4' (TR4) plaguing the Philippine banana industry, still lacks information on its use to target host resistance in Philippine bananas. This study reports the elucidation of the gene sequence of chitinase homologs chit6 and chac in the leading Philippine dessert banana varieties, „Lakatan' and „Latundan,' and the design, selection, and pre-validation of sgRNAs using in vitro cleavage assay. Multiple sequence alignment revealed the conserved sites, SNPs, and indels. Evolutionary analysis disclosed that the pattern of nucleotide substitution resulted in an overall bias in favor of adenine and thymine changing to cytosine and guanine. It said transitions outnumber transversions typical of clonally propagated crops. The in silico prediction initially identified a total of 58 sgRNAs for chit6 and 68 sgRNAs for chac, with 58.62% and 58.97% found across „Latundan' and 'Lakatan'/„Mapilak' backgrounds, respectively. A design criteria imposition for plants and consideration of the predicted efficiency and localization of sgRNAs along the targets narrowed down the sgRNAs. Four selected efficient sgRNAs were demonstrated to cleave all targets under in vitro assay with Cas9, showing its potential for gene editing by the SDN-1 or SDN-2 mechanism. With unavailable protocols for embryogenic cell suspension and corresponding delivery systems for these varieties, this in vitro approach provides a strategy to identify potential sgRNAs to streamline resources for the gene-editing pipeline and a guide to employing CRISPR/Cas9 for elucidation of the functional role of chit6 and chac in host resistance response to TR4 in bananas. [ABSTRACT FROM AUTHOR]

To determine the structure and sequence variation of the chloroplast genome of genus Aucuba and to reveal their interspecies relationship, the chloroplast genomes of six Aucuba species including A. chinensis and A. japonica var. variegata as well as Garrya buxifolia were sequenced using next-generation sequencing technology. The chloroplast genomes were assembled and annotated using bioinformatics software. The genome characteristics, sequence comparison and phylogeny were analyzed based on the chloroplast genomes. The results were as follows: (1) Six Aucuba species chloroplast genomes exhibited typical quadripartite circular structure (i.e., LSC, SSC, IRB and IRA) and were between 157 891-158 325 bp in length. A total of 114 genes were annotated (except the duplicate genes on IRs), including 80 protein-coding genes (CDS), 30 tRNA genes and 4 rRNA genes. (2) A total of 29 high-frequency codons prefer ending in A/U, and a total of 100 optimal codons of these six sequences were filtered out, including 12 were shared by six Aucuba species. (3) A total of 270 interspersed repeats, 133 tandem repeats and 412 SSR loci were detected in the six Aucuba chloroplast genomes. (4) Comparative analysis result of six Aucuba species revealed a highly conserved chloroplast genome sequence. (5) Ten highly divergent regions were identified based on nucleotide diversity analysis. (6) The phylogenetic trees were constructed using maximum likelihood (ML) and Bayesian (BI) showing a similar topology. The results supported that genus Aucuba was monophyletic with high support rate, as a sister to genus Garrya. The complete chloroplast genomes of these five Aucuba species and one Garrya species is firstly sequenced in the study. The results reveal the interspecies relationships and the taxonomic status of genus Aucuba, and provide references for the classification, identification and phylogeny of the genus Aucuba.

Phase separation (PS) is an important mechanism underlying the formation of biomolecular condensates. Physiological condensates are associated with numerous biological processes, such as transcription, immunity, signaling, and synaptic transmission. Changes in particular amino acids or segments can disturb the protein’s phase behavior and interactions with other biomolecules in condensates. It is thus presumed that variations in the phase-separating-prone domains can significantly impact the properties and functions of condensates. The dysfunction of condensates contributes to a number of pathological processes. Pharmacological perturbation of these condensates is proposed as a promising way to restore physiological states. In this review, we characterize the variations observed in PS proteins that lead to aberrant biomolecular compartmentalization. We also showcase recent advancements in bioinformatics of membraneless organelles (MLOs), focusing on available databases useful for screening PS proteins and describing endogenous condensates, guiding researchers to seek the underlying pathogenic mechanisms of biomolecular condensates.

To determine the structure and sequence variation of the chloroplast genome of genus Aucuba and to reveal their interspecies relationship, the chloroplast genomes of six Aucuba species including A. chinensis and A. japonica var. variegata as well as Garrya buxifolia were sequenced using next-generation sequencing technology. The chloroplast genomes were assembled and annotated using bioinformatics software. The genome characteristics, sequence comparison and phylogeny were analyzed based on the chloroplast genomes. The results were as follows: (1) Six Aucuba species chloroplast genomes exhibited typical quadripartite circular structure (i.e., LSC, SSC, IRB and IRA) and were between 157 891-158 325 bp in length. A total of 114 genes were annotated(except the duplicate genes on IRs), including 80 protein-coding genes (CDS), 30 tRNA genes and 4 rRNA genes.(2) A total of 29 high-frequency codons prefer ending in A/U, and a total of 100 optimal codons of these six sequences were filtered out, including 12 were shared by six Aucuba species.(3)A total of 270 interspersed repeats, 133 tandem repeats and 412 SSR loci were detected in the six Aucuba chloroplast genomes.(4)Comparative analysis result of six Aucuba species revealed a highly conserved chloroplast genome sequence. (5) Ten highly divergent regions were identified based on nucleotide diversity analysis. (6) The phylogenetic trees were constructed using maximum likelihood(ML)and Bayesian(BI)showing a similar topology. The results supported that genus Aucuba was monophyletic with high support rate, as a sister to genus Garrya. The complete chloroplast genomes of these five Aucuba species and one Garrya species is firstly sequenced in the study. The results reveal the interspecies relationships and the taxonomic status of genus Aucuba, and provide references for the classification, identification and phylogeny of the genus Aucuba. [ABSTRACT FROM AUTHOR]

Saussurea plants are widely distributed in Asia and Europe; however, their complex phylogenetic relationships have led to many difficulties in phylogenetic studies and interspecific identification. In this study, we assembled, annotated, and analyzed the chloroplast genomes of three Saussurea plants: Saussurea katochaete, Saussurea superba, and Saussurea stella. The results showed that the full-length sequences of the three Saussurea plants were 152,561 bp, 151,452 bp, and 152,293 bp, respectively, which represent the typical quadripartite structure, and the genomes were relatively conserved. The gene annotation results showed that the chloroplast genomes of S. katochaete, S. superba, and S. stella were annotated with 128, 124, and 127 unique genes, respectively, which included 83, 80, and 83 protein-coding genes (PCGs), respectively, 37, 36, and 36 tRNA genes, respectively, and 8 rRNA genes. Moreover, 46, 45, and 43 SSR loci, respectively, and nine highly variable regions (rpl32-trnL-UAG, rpl32, ndhF-rpl32, ycf1, trnC-GCA-petN, trnC-GCA, rpcL, psbE-petL, and rpl16-trnG-UUG) were identified and could be used as potential molecular markers for population identification and phylogenetic study of Saussurea plants. Phylogenetic analyses strongly support the sisterhood of S. katochaete with S. superba and S. stella, and are all clustered with S. depsagensis, S. inversa, S. medusa, and S. gossipihora, of which S. gossipiphora is most closely related. Additionally, the phylogenetic results indicate a high frequency of differentiation among different species of Saussurea plants, and many different species or genera are morphologically very different from each other, which may be related to certain genetic material in the chloroplasts. This study provides an important reference for the identification of Saussurea plants and studies their evolution and phylogenetics. [ABSTRACT FROM AUTHOR]

Abstract Background Current proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus, protein sequence database and the corresponding softwares should also be improved to solve this issue. Results We developed a state-of-the-art toolkit (SeqWiz) for constructing next-generation sequence databases and performing proteomic-centric sequence analyses. First, we proposed two derived data formats: SQPD (a well-structured and high-performance local sequence database based on SQLite), and SET (an associated list of selected entries based on JSON). The SQPD format follows the basic standards of the emerging PEFF format, which also aims to facilitate the search of complex proteoform. The SET format is designed for generating subsets with with high-efficiency. These formats are shown to greatly outperform the conventional FASTA or PEFF formats in time and resource consumption. Then, we mainly focused on the UniProt knowledgebase and developed a collection of open-source tools and basic modules for retrieving species-specific databases, formats conversion, sequence generation, sequence filter, and sequence analysis. These tools are implemented by using the Python language and licensed under the GNU General Public Licence V3. The source codes and distributions are freely available at GitHub ( https://github.com/fountao/protwiz/tree/main/seqwiz ). Conclusions SeqWiz is designed to be a collection of modularized tools, which is friendly to both end-users for preparing easy-to-use sequence databases as well as bioinformaticians for performing downstream sequence analysis. Besides the novel formats, it also provides compatible functions for handling the traditional text based FASTA or PEFF formats. We believe that SeqWiz will promote the implementing of complementary proteomics for data renewal and proteoform analysis to achieve precision proteomics. Additionally, it can also drive the improvement of proteomic standardization and the development of next-generation proteomic softwares.

Pod shatter is a trait of agricultural relevance that ensures plants dehisce seeds in their native environment and has been subjected to domestication and selection for non-shattering types in several broadacre crops. However, pod shattering causes a significant yield reduction in canola (Brassica napus L.) crops. An interspecific breeding line BC95042 derived from a B. rapa/B. napus cross showed improved pod shatter resistance (up to 12-fold than a shatter-prone B. napus variety). To uncover the genetic basis and improve pod shatter resistance in new varieties, we analysed F2 and F2:3 derived populations from the cross between BC95042 and an advanced breeding line, BC95041, and genotyped with 15,498 DArTseq markers. Through genome scan, interval and inclusive composite interval mapping analyses, we identified seven quantitative trait loci (QTLs) associated with pod rupture energy, a measure for pod shatter resistance or pod strength, and they locate on A02, A03, A05, A09 and C01 chromosomes. Both parental lines contributed alleles for pod shatter resistance. We identified five pairs of significant epistatic QTLs for additive x additive, additive dominance and dominance x dominance interactions between A01/C01, A03/A07, A07/C03, A03/C03, and C01/C02 chromosomes for rupture energy. QTL effects on A03/ A07 and A01/C01 were in the repulsion phase. Comparative mapping identified several candidate genes (AG, ABI3, ARF3, BP1, CEL6, FIL, FUL, GA2OX2, IND, LATE, LEUNIG, MAGL15, RPL, QRT2, RGA, SPTand TCP10) underlying main QTL and epistatic QTL interactions for pod shatter resistance. Three QTLs detected on A02, A03, and A09 were near the FUL (FRUITFULL) homologues BnaA03g39820D and BnaA09g05500D. Focusing on the FUL, we investigated putative motifs, sequence variants and the evolutionary rate of its homologues in 373 resequenced B. napus accessions of interest. BnaA09g05500D is subjected to purifying selection as it had a low Ka/Ks ratio compared to other FUL homologues in B. napus. This study provides a valuable resource for genetic improvement for yield through an understanding of the genetic mechanism controlling pod shatter resistance in Brassica species. [ABSTRACT FROM AUTHOR]

Background: Yersinia pestis, a Gram-negative bacterium, is the causative agent of plague. Y. pestis is a zoonotic pathogen that occasionally infects humans and became endemic in the western United States after spreading from California in 1899. Methods: To better understand evolutionary patterns in Y. pestis from the southwestern United States, we sequenced and analyzed 22 novel genomes from New Mexico. Analytical methods included, assembly, multiple sequences alignment, phylogenetic tree reconstruction, genotype-phenotype correlation, and selection pressure. Results: We identified four genes, including Yscp and locus tag YPO3944, which contained codons undergoing negative selection. We also observed 42 nucleotide sites displaying a statistically significant skew in the observed residue distribution based on the year of isolation. Overall, the three genes with the most statistically significant variations that associated with metadata for these isolates were sapA, fliC, and argD. Phylogenetic analyses point to a single introduction of Y. pestis into the United States with two subsequent, independent movements into New Mexico. Taken together, these analyses shed light on the evolutionary history of this pathogen in the southwestern US over a focused time range and confirm a single origin and introduction into North America. [ABSTRACT FROM AUTHOR]

Background: Cinnamomum verum (true cinnamon) and Cinnamomum cassia (cassia cinnamon) are two important species belonging to family Lauraceae. These species are recognized by morphological, chemical composition and essential oil contents. The appropriate identification of species would be considerably improved by a genetic method. The main objective of the present study was to develop molecular markers distinguishing between C. verum and C. cassia. Methods and results: A total 71 ISSR (Inter simple sequence repeat) and four universal barcoding (ITS, rbcL, matK, and psbA-trnH) genes were used to distinguish both the species. No sequence variation was observed between the two species for any DNA barcode gene. However, one ISSR i.e. ISSR-37 showed a clear distinction between the species and produced 570 bp and 746 bp amplicons in C. verum and C. cassia, respectively. The polymorphic bands were converted into species-specific SCAR markers. The SCAR-CV was specific to C. verum and amplified 190 bp band, however there was no amplification seen in the C. cassia samples. Conclusion: The SCAR marker generated in this study can be employed as efficient, economical, and reliable molecular tool for the identification of C. verum. [ABSTRACT FROM AUTHOR]

Candida albicans (C. albicans) is an opportunistic pathogen increasingly causing candidiasis worldwide. This study aims to investigate the pattern of systemic immune responses triggered by C. albicans with disease associated variation of Sap2, identifying the novel evasion strategies utilized by clinical isolates. Specifically, a variation in clinical isolates is identified at nucleotide position 817 (G to T). This homozygous variation causes the 273rd amino acid exchange from valine to leucine, close to the proteolytic activation center of Sap2. The mutant (Sap2‐273L) generated from SC5314 (Sap2‐273V) background carrying the V273L variation within Sap2 displays higher pathogenicity. In comparison to mice infected with Sap2‐273V strain, mice infected with Sap2‐273L exhibit less complement activation indicated by less serum C3a generation and weaker C3b deposition in the kidney. This inhibitory effect is mainly achieved by Sap2273L‐mediated stronger degradation of C3 and C3b. Furthermore, mice infected with Sap2‐273L strain exhibit more macrophage phenotype switching from M0 to M2‐like and more TGF‐β release which further influences T cell responses, generating an immunosuppressed cellular microenvironment characterized by more Tregs and exhausted T cell formation. In summary, the disease‐associated sequence variation of Sap2 enhances pathogenicity by complement evasion and M2‐like phenotype switching, promoting a more efficient immunosuppressed microenvironment. [ABSTRACT FROM AUTHOR]

Sweet potato [Ipomoea batatas (L.) Lam.] is an important food and industrial crop. Its storage root is rich in starch, which is present in the form of granules and represents the principal storage carbohydrate in plants. Starch content is an important trait of sweet potato controlling the quality and yield of industrial products. Vacuolar invertase encoding gene Ibbfruct2 was supposed to be a key regulator of starch content in sweet potato, but its function and regulation were unclear. In this study, three Ibbfruct2 gene members were detected. Their promoters displayed differences in sequence, activity, and cis-regulatory elements and might interact with different transcription factors, indicating that the three Ibbfruct2 family members are governed by different regulatory mechanisms at the transcription level. Among them, we found that only Ibbfruct2-1 show a high expression level and promoter activity, and encodes a protein with invertase activity, and the conserved domains and three conserved motifs NDPNG, RDP, and WEC are critical to this activity. Only two and six amino acid residue variations were detected in sequences of proteins encoded by Ibbfruct2-2 and Ibbfruct2-3, respectively, compared with Ibbfruct2-1; although not within key motifs, these variations affected protein structure and affinities for the catalytic substrate, resulting in functional deficiency and low activity. Heterologous expression of Ibbfruct2-1 in Arabidopsis decreased starch content but increased glucose content in leaves, indicating Ibbfruct2-1 was a negative regulator of starch content. These findings represent an important advance in understanding the regulatory and functional divergence among duplicated genes in sweet potato, and provide critical information for functional studies and utilization of these genes in genetic improvement. [ABSTRACT FROM AUTHOR]

Rustrela virus (RusV; species Rubivirus strelense , family Matonaviridae) was discovered in different zoo animal species affected by fatal encephalitis. Simultaneous RusV RNA detection in multiple yellow-necked field mice (Apodemus flavicollis) suggested this rodent as a reservoir of RusV. Here, we investigated 1,264 yellow-necked field mice and sympatric other small mammals from different regions in Germany for RusV RNA using an optimized reverse transcription-quantitative polymerase chain reaction (RT-qPCR) protocol and high-throughput sequencing. The investigation resulted in the detection of RusV RNA exclusively in 50 of 396 (12.6 per cent) yellow-necked field mice but absence in other sympatric species. RT-qPCR-determined tissue distribution of RusV RNA revealed the highest viral loads in the central nervous system, with other tissues being only very rarely affected. The histopathological evaluation did not reveal any hints of encephalitis in the brains of infected animals despite the detection of viral RNA in neurons by in situ hybridization (ISH). The positive association between the body mass of yellow-necked field mice and RusV RNA detection suggests a persistent infection. Phylogenetic analysis of partial E1 and full-genome sequences showed a high diversification with at least four RusV lineages (1A–1D) in northeastern Germany. Moreover, phylogenetic and isolation-by-distance analyses indicated evolutionary processes of RusV mostly in local reservoir populations. A comparison of complete genome sequences from all detected RusV lineages demonstrated a high level of amino acid and nucleotide sequence variability within a part of the p150 peptide of the non-structural polyprotein and its coding sequence, respectively. The location of this region within the RusV genome and its genetic properties were comparable to the hypervariable region of the rubella virus. The broad range of detected RusV spillover hosts in combination with its geographical distribution in northeastern Germany requires the assessment of its zoonotic potential and further analysis of encephalitis cases in mammals. Future studies have to prove a putative co-evolution scenario for RusV in the yellow-necked field mouse reservoir. [ABSTRACT FROM AUTHOR]

Introduction: Each population has its own unique genotype. Genotyping data on Indian cardiomyopathy patients is lacking. Methods: We aimed to create and analyse a database of sequence variations in Indian patients with primary cardiomyopathies. This included all data of the cardiomyopathy cohort at the Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh. In addition, all published papers in Pubmed containing sequence variations in Indian cardiomyopathy patients till December 2020 using specific search terms were included. Affected genes and sequence variations, methodologies and quality of clinical data was analysed. Novel sequence variations were documented. Results: A database of 493 datasets including 417 different sequence variations was created. Of these, the PGIMER database had 137 datasets consisting of 94 different variants. Only 63 publications included genotyping data of Indian cardiomyopathy cohort from 2000 to 2020 reporting 335 sequence variations. Five (7.9%) studies were from institutions abroad. Of published variations, 35.1% were novel. Most studies carried out selective genotyping. Comprehensive genotyping using cardiomyopathy panels or whole exome sequencing was reported in only 9 (14.3%) publications. Conclusion: Database of 417 different sequence variations in Indian cardiomyopathy patients was analysed. Over a third of all reported sequence variations in Indians were novel.

Background: Current proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus, protein sequence database and the corresponding softwares should also be improved to solve this issue. Results: We developed a state-of-the-art toolkit (SeqWiz) for constructing next-generation sequence databases and performing proteomic-centric sequence analyses. First, we proposed two derived data formats: SQPD (a well-structured and high-performance local sequence database based on SQLite), and SET (an associated list of selected entries based on JSON). The SQPD format follows the basic standards of the emerging PEFF format, which also aims to facilitate the search of complex proteoform. The SET format is designed for generating subsets with with high-efficiency. These formats are shown to greatly outperform the conventional FASTA or PEFF formats in time and resource consumption. Then, we mainly focused on the UniProt knowledgebase and developed a collection of open-source tools and basic modules for retrieving species-specific databases, formats conversion, sequence generation, sequence filter, and sequence analysis. These tools are implemented by using the Python language and licensed under the GNU General Public Licence V3. The source codes and distributions are freely available at GitHub (https://github.com/fountao/protwiz/tree/main/seqwiz). Conclusions: SeqWiz is designed to be a collection of modularized tools, which is friendly to both end-users for preparing easy-to-use sequence databases as well as bioinformaticians for performing downstream sequence analysis. Besides the novel formats, it also provides compatible functions for handling the traditional text based FASTA or PEFF formats. We believe that SeqWiz will promote the implementing of complementary proteomics for data renewal and proteoform analysis to achieve precision proteomics. Additionally, it can also drive the improvement of proteomic standardization and the development of next-generation proteomic softwares. [ABSTRACT FROM AUTHOR]

Background Yersinia pestis, a Gram-negative bacterium, is the causative agent of plague. Y. pestis is a zoonotic pathogen that occasionally infects humans and became endemic in the western United States after spreading from California in 1899. Methods To better understand evolutionary patterns in Y. pestis from the southwestern United States, we sequenced and analyzed 22 novel genomes from New Mexico. Analytical methods included, assembly, multiple sequences alignment, phylogenetic tree reconstruction, genotype-phenotype correlation, and selection pressure. Results We identified four genes, including Yscp and locus tag YPO3944, which contained codons undergoing negative selection. We also observed 42 nucleotide sites displaying a statistically significant skew in the observed residue distribution based on the year of isolation. Overall, the three genes with the most statistically significant variations that associated with metadata for these isolates were sapA, fliC, and argD. Phylogenetic analyses point to a single introduction of Y. pestis into the United States with two subsequent, independent movements into New Mexico. Taken together, these analyses shed light on the evolutionary history of this pathogen in the southwestern US over a focused time range and confirm a single origin and introduction into North America.

Pod shatter is a trait of agricultural relevance that ensures plants dehisce seeds in their native environment and has been subjected to domestication and selection for non-shattering types in several broadacre crops. However, pod shattering causes a significant yield reduction in canola (Brassica napus L.) crops. An interspecific breeding line BC95042 derived from a B. rapa/B. napus cross showed improved pod shatter resistance (up to 12-fold than a shatter-prone B. napus variety). To uncover the genetic basis and improve pod shatter resistance in new varieties, we analysed F2 and F2:3 derived populations from the cross between BC95042 and an advanced breeding line, BC95041, and genotyped with 15,498 DArTseq markers. Through genome scan, interval and inclusive composite interval mapping analyses, we identified seven quantitative trait loci (QTLs) associated with pod rupture energy, a measure for pod shatter resistance or pod strength, and they locate on A02, A03, A05, A09 and C01 chromosomes. Both parental lines contributed alleles for pod shatter resistance. We identified five pairs of significant epistatic QTLs for additive x additive, additive dominance and dominance x dominance interactions between A01/C01, A03/A07, A07/C03, A03/C03, and C01/C02 chromosomes for rupture energy. QTL effects on A03/A07 and A01/C01 were in the repulsion phase. Comparative mapping identified several candidate genes (AG, ABI3, ARF3, BP1, CEL6, FIL, FUL, GA2OX2, IND, LATE, LEUNIG, MAGL15, RPL, QRT2, RGA, SPT and TCP10) underlying main QTL and epistatic QTL interactions for pod shatter resistance. Three QTLs detected on A02, A03, and A09 were near the FUL (FRUITFULL) homologues BnaA03g39820D and BnaA09g05500D. Focusing on the FUL, we investigated putative motifs, sequence variants and the evolutionary rate of its homologues in 373 resequenced B. napus accessions of interest. BnaA09g05500D is subjected to purifying selection as it had a low Ka/Ks ratio compared to other FUL homologues in B. napus. This study provides a valuable resource for genetic improvement for yield through an understanding of the genetic mechanism controlling pod shatter resistance in Brassica species.

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Triticale regeneration via anther culture faces many difficulties, e.g., a low percentage of regenerated plants and the presence of albinos. Plant regeneration may be affected by abiotic stresses and by ingredients added to the induction medium. The latter influences biochemical pathways and plant regeneration efficiency. Among such ingredients, copper and silver ions acting as cofactors for enzymatic reactions are of interest. However, their role in plant tissue cultures and relationships with biochemical pathways has not been studied yet. The study evaluated relationships between DNA methylation, changes in DNA sequence variation, and green plant regeneration efficiency influenced by copper and silver ions during triticale plant regeneration. For this purpose, a biological model based on donor plants and their regenerants, a methylation-sensitive amplified fragment length polymorphism, and structural equation modeling were employed. The green plant regeneration efficiency varied from 0.71 to 6.06 green plants per 100 plated anthers. The values for the components of tissue culture-induced variation related to cytosine methylation in a CHH sequence context (where H is A, C, or T) were 8.65% for sequence variation, 0.76% for DNA demethylation, and 0.58% for de novo methylation. The proposed model states that copper ions affect the regeneration efficiency through cytosine methylation and may induce mutations through, e.g., oxidative processes, which may interfere with the green plant regeneration efficiency. The linear regression confirms that the plant regeneration efficiency rises with increasing copper ion concentration in the absence of Ag ions in the induction medium. The least absolute shrinkage and selection operator regression shows that de novo methylation, demethylation, and copper ions may be involved in the green plant regeneration efficiency. According to structural equation modeling, copper ions play a central role in the model determining the regeneration efficiency. [ABSTRACT FROM AUTHOR]

Abstract The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.

Plumeria rust fungi caused by Coleosporium plumeriae is one of emerging diseases which is currently fast distributed over the world. The pathogen is also listed as an invasive plant pathogen species. This research aimed to identify Plumeria Rust Fungi from five regencies in Yogyakarta, Indonesia based on Rust2inv and LR6 Primers, which was developed from 5.8S subunit, ITS2 and 28S LSU regions to get more accurate identification of C. plumeriae. The results showed that uredospores of each specimen had variation in shape and verrucose spore walls thickness. All five specimens, which were collected from Plumeria rubra and P. alba, were identified as C. plumeriae based on homology sequences from BLAST NCBI and phylogenetic tree. Visualisation of nucleotides sequence alignment confirmed that those five specimens contain some nucleotides variations. Especially, BL specimen showed nucleotides insertions and substitutions, different from other sequences. The result performed a basic significant information for further study about genetic variations and pathogen evolution of C. plumeriae. Each specimen sequence in this study was deposited into the GenBank with accession No. OM780189- OM78019. [ABSTRACT FROM AUTHOR]

Malaria rapid diagnosis test (RDT) is crucial for managing the disease, and the effectiveness of detection depends on parameters such as sensitivity and specificity of the RDT. Several factors can affect the performance of RDT. In this study, we focused on the pfhrp2 sequence variation and its impact on RDTs targeted by antigens encoded by Plasmodium falciparum histidine-rich protein 2 (pfhrp2). Field samples collected during cross-sectional surveys in Tanzania were sequenced to investigate the pfhrp2 sequence diversity and evaluate the impact on HRP2-based RDT performance. We observed significant mean differences in amino acid repeats between current and previous studies. Several new amino acid repeats were found to occur at different frequencies, including types AAY, AHHAHHAAN, and AHHAA. Based on the abundance of types 2 and 7 amino acid repeats, the binary predictive model was able to predict RDT insensitivity by about 69% in the study area. About 85% of the major epitopes targeted by monoclonal antibodies (MAbs) in RDT were identified. Our study suggested that the extensive sequence variation in pfhrp2 can contribute to reduced RDT sensitivity. The correlation between the different combinations of amino acid repeats and the performance of RDT in different malaria transmission settings should be investigated further. [ABSTRACT FROM AUTHOR]

Eggplant is a widely consumed vegetable, with significant nutritional value and high antioxidant content, mainly due to its phenolic constituents. Our goal was to determine the levels of carbohydrates, proteins, total phenolics, anthocyanins, flavonoids, chlorogenic acid, and the antioxidant capacity in thirteen eggplant cultivars cultivated in Greece and to identify sequence polymorphisms in key regulating genes of the phenylpropanoid pathway (C4H, HCT, HQT, C3H, F3H, ANS, MYB1), which might relate to the phytochemical content of those cultivars. The carbohydrates' content differs among and within cultivars, while the rest of the phytochemicals differ only among cultivars. The cultivars 'EMI' and 'Lagkada' scored higher than the rest in phenolics, anthocyanins, ascorbic acid, caffeoylquinic acid, and antioxidant capacity. Moreover, significant correlations were observed between various ingredients and the antioxidant capacity (FRAP and DPPH). Sequence analysis revealed several SNPs in C4H, HQT, F3H, ANS, and MYB1 among the cultivars studied. According to chi-square and logistic regression analyses, the missense mutation C4H4-108 correlates significantly with flavonoids, anthocyanins, and proteins; the synonymous mutation HQT-105 correlates with anthocyanins and ascorbic acid; the missense mutation HQT-438 correlates with flavonoids and chlorogenic acid, while the missense mutation ANS1-65 correlates with anthocyanins and sugars. These polymorphisms can be potentially utilized as molecular markers in eggplant breeding, while our data also contribute to the study of eggplant's secondary metabolism and antioxidant properties. [ABSTRACT FROM AUTHOR]

The bread wheat (Triticum aestivum) pangenome is a patchwork of variable regions, including translocations and introgressions from progenitors and wild relatives. Although a large number of these have been documented, it is likely that many more remain unknown. To map these variable regions and make them more traceable in breeding programs, wheat accessions need to be genotyped or sequenced. The wheat genome is large and complex and consequently, sequencing efforts are often targeted through exome capture. In this study, we employed exome capture prior to sequencing 12 wheat varieties; 10 elite T. aestivum cultivars and two T. aestivum landrace accessions. Sequence coverage across chromosomes was greater toward distal regions of chromosome arms and lower in centromeric regions, reflecting the capture probe distribution which itself is determined by the known telomere to centromere gene gradient. Superimposed on this general pattern, numerous drops in sequence coverage were observed. Several of these corresponded with reported introgressions. Other drops in coverage could not be readily explained and may point to introgressions that have not, to date, been documented. [ABSTRACT FROM AUTHOR]

The bread wheat (Triticum aestivum) pangenome is a patchwork of variable regions, including translocations and introgressions from progenitors and wild relatives. Although a large number of these have been documented, it is likely that many more remain unknown. To map these variable regions and make them more traceable in breeding programs, wheat accessions need to be genotyped or sequenced. The wheat genome is large and complex and consequently, sequencing efforts are often targeted through exome capture. In this study, we employed exome capture prior to sequencing 12 wheat varieties; 10 elite T. aestivum cultivars and two T. aestivum landrace accessions. Sequence coverage across chromosomes was greater toward distal regions of chromosome arms and lower in centromeric regions, reflecting the capture probe distribution which itself is determined by the known telomere to centromere gene gradient. Superimposed on this general pattern, numerous drops in sequence coverage were observed. Several of these corresponded with reported introgressions. Other drops in coverage could not be readily explained and may point to introgressions that have not, to date, been documented.

The genus Actinidia, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species' relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species' phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes' sequences derived from 25 Actinidia taxa. The average genome size is 156,673.38 bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in Actinidia were revealed to be the causal agent leading to the chloroplast genome size expansion. The clpP gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in Actinidia species. Comprehensive sequence analyses indicated the distinct variation at the clpP gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e., rps16 ~ trnQ-UUG, rps4 ~ trnT-UGU, petA ~ psbJ, and rps12 ~ psbB) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying rps12 ~ psbB (including clpP gene and its up/downstream noncoding sequence) were identified as variation hot spots in Actinidia species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25 Actinidia taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in Actinidia. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among Actinidia species. [ABSTRACT FROM AUTHOR]

Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD). It provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ~60.44 M SNPs, ~6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map, using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.

Abstract Background Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-synonymous Single Nucleotide Variants – missense SNVs or nsSNVs) for particular proteins. We assembled SAV annotations from 22 different DMS experiments and normalized the effect scores to evaluate variant effect prediction methods. Three trained on traditional variant effect data (PolyPhen-2, SIFT, SNAP2), a regression method optimized on DMS data (Envision), and a naïve prediction using conservation information from homologs. Results On a set of 32,981 SAVs, all methods captured some aspects of the experimental effect scores, albeit not the same. Traditional methods such as SNAP2 correlated slightly more with measurements and better classified binary states (effect or neutral). Envision appeared to better estimate the precise degree of effect. Most surprising was that the simple naïve conservation approach using PSI-BLAST in many cases outperformed other methods. All methods captured beneficial effects (gain-of-function) significantly worse than deleterious (loss-of-function). For the few proteins with multiple independent experimental measurements, experiments differed substantially, but agreed more with each other than with predictions. Conclusions DMS provides a new powerful experimental means of understanding the dynamics of the protein sequence space. As always, promising new beginnings have to overcome challenges. While our results demonstrated that DMS will be crucial to improve variant effect prediction methods, data diversity hindered simplification and generalization.

Abstract Background Impaired proteostatic regulation of proteins with prion-like domains (PrLDs) is associated with a variety of human diseases including neurodegenerative disorders, myopathies, and certain forms of cancer. For many of these disorders, current models suggest a prion-like molecular mechanism of disease, whereby proteins aggregate and spread to neighboring cells in an infectious manner. The development of prion prediction algorithms has facilitated the large-scale identification of PrLDs among “reference” proteomes for various organisms. However, the degree to which intraspecies protein sequence diversity influences predicted prion propensity has not been systematically examined. Results Here, we explore protein sequence variation introduced at genetic, post-transcriptional, and post-translational levels, and its influence on predicted aggregation propensity for human PrLDs. We find that sequence variation is relatively common among PrLDs and in some cases can result in relatively large differences in predicted prion propensity. Sequence variation introduced at the post-transcriptional level (via alternative splicing) also commonly affects predicted aggregation propensity, often by direct inclusion or exclusion of a PrLD. Finally, analysis of a database of sequence variants associated with human disease reveals a number of mutations within PrLDs that are predicted to increase prion propensity. Conclusions Our analyses expand the list of candidate human PrLDs, quantitatively estimate the effects of sequence variation on the aggregation propensity of PrLDs, and suggest the involvement of prion-like mechanisms in additional human diseases.

We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities. The unique functionalities of ribosome populations within a cell can become central in situations of stress where they may preferentially translate mRNAs coding for proteins better suited to contributing to survival of the cell. In model systems where this concept has been developed, the engagement of initiation factors and elongation factors to account for variation in the translation machinery of the cell in response to stresses provided the precedents. The polyploid nature of wheat adds extra variation at each step of the synthesis and assembly of the rRNAs and RPs which can, as a result, potentially enhance its response to changing environments and disease threats. [ABSTRACT FROM AUTHOR]

A data set of promoter and 5′UTR sequences of homoeo‐alleles of 459 wheat genes that contribute to agriculturally important traits in 95 ancestral and commercial wheat cultivars is presented here. The high‐stringency myBaits technology used made individual capture of homoeo‐allele promoters possible, which is reported here for the first time. Promoters of most genes are remarkably conserved across the 83 hexaploid cultivars used with <7 haplotypes per promoter and 21% being identical to the reference Chinese Spring. InDels and many high‐confidence SNPs are located within predicted plant transcription factor binding sites, potentially changing gene expression. Most haplotypes found in the Watkins landraces and a few haplotypes found in Triticum monococcum, germplasms hitherto not thought to have been used in modern wheat breeding, are already found in many commercial hexaploid wheats. The full data set which is useful for genomic and gene function studies and wheat breeding is available at https://rrescloud.rothamsted.ac.uk/index.php/s/DMCFDu5iAGTl50u/authenticate. [ABSTRACT FROM AUTHOR]

The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is the cause of the novel coronavirus disease 2019 (COVID-19) pandemic. Its diagnosis relies on the molecular detection of the viral RNA by polymerase chain reaction (PCR) while newer rapid CRISPR-based diagnostic tools are being developed. As molecular diagnostic assays rely on the detection of unique sequences of viral nucleic acid, the target regions must be common to all coronavirus SARS-CoV-2 circulating strains, yet unique to SARS-CoV-2 with no cross-reactivity with the genome of the host and other normal or pathogenic organisms potentially present in the patient samples. This stage 1 protocol proposes in silico cross-reactivity and inclusivity analysis of the recently developed CRISPR-based diagnostic assays. Cross-reactivity will be analyzed through comparison of target regions with the genome sequence of the human, seven coronaviruses and 21 other organisms. Inclusivity analysis will be performed through the verification of the sequence variability within the target regions using publicly available SARS-CoV-2 sequences from around the world. The absence of cross-reactivity and any mutations in target regions of the assay used would provide a higher degree of confidence in the CRISPR-based diagnostic tests being developed while the presence could help guide the assay development efforts. We believe that this study would provide potentially important information for clinicians, researchers, and decision-makers. [ABSTRACT FROM AUTHOR]

We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities. The unique functionalities of ribosome populations within a cell can become central in situations of stress where they may preferentially translate mRNAs coding for proteins better suited to contributing to survival of the cell. In model systems where this concept has been developed, the engagement of initiation factors and elongation factors to account for variation in the translation machinery of the cell in response to stresses provided the precedents. The polyploid nature of wheat adds extra variation at each step of the synthesis and assembly of the rRNAs and RPs which can, as a result, potentially enhance its response to changing environments and disease threats.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is the cause of the novel coronavirus disease 2019 (COVID-19) pandemic. Its diagnosis relies on the molecular detection of the viral RNA by polymerase chain reaction (PCR) while newer rapid CRISPR-based diagnostic tools are being developed. As molecular diagnostic assays rely on the detection of unique sequences of viral nucleic acid, the target regions must be common to all coronavirus SARS-CoV-2 circulating strains, yet unique to SARS-CoV-2 with no cross-reactivity with the genome of the host and other normal or pathogenic organisms potentially present in the patient samples. This stage 1 protocol proposes in silico cross-reactivity and inclusivity analysis of the recently developed CRISPR-based diagnostic assays. Cross-reactivity will be analyzed through comparison of target regions with the genome sequence of the human, seven coronaviruses and 21 other organisms. Inclusivity analysis will be performed through the verification of the sequence variability within the target regions using publicly available SARS-CoV-2 sequences from around the world. The absence of cross-reactivity and any mutations in target regions of the assay used would provide a higher degree of confidence in the CRISPR-based diagnostic tests being developed while the presence could help guide the assay development efforts. We believe that this study would provide potentially important information for clinicians, researchers, and decision-makers.

Barley is an economically important cereal crop grown under diverse environmental conditions and ranked fourth in terms of production volume. Barley is a diploid self-fertilizing plant with seven chromosomes, and has a 5.1 Gbp genome with more than 80% repeat sequences. Whole genome re-sequencing (WGR) has provided substantial information on sequence variation distributed on all chromosomes, such as single nucleotide polymorphisms, insertions, and deletions, which are used in the development of DNA markers. In this study, we performed WGR to detect sequence variations among six Korean malting varieties. An average of 92,552 insertions and deletions (InDels) were detected in these varieties in comparison to the high-quality reference genome sequences. The InDel density of the six Korean malting varieties ranged from 17 to 19 InDel/1Mbp with an average of 18 InDel/1Mbp. No InDel could be detected in 193 regions in all chromosomes except chr. unassigned. One interval with high-density InDel, more than 150 InDel/1Mbp, was located on the 1H, 3H, 6H, and 7H chromosomes. A total of 145 InDel markers were developed using 225 large-InDel markers, longer than 50 bp. Seventeen large-InDel makers showed polymorphisms among 31 malting barley varieties. These 31 malting barley varieties were divided into four groups based on phylogenetic analysis. These results presented a development method of agarose-resolvable large-InDel markers using WGR. Seventeen polymorphic large-InDel markers were used to conserve and identify barley germplasms. This vast information on sequence variation in six Korean malting barleys could be used for the development of DNA markers and marker-assisted selection. [ABSTRACT FROM AUTHOR]

Introduction and Objectives: The hepatitis B virus (HBV) surface antigen (HBsAg) variations suggested having some effects on infection outcome. Due to some controversial issues, the aim of this study was to compare the pattern of HBsAg variation between asymptomatic carriers and HCC/cirrhosis patients. Materials and methods: In this cross-sectional study, 19 HCC/cirrhotic and 26 asymptomatic patients were enrolled. After viral DNA extraction, HBs gene was amplified using an in-house nested-PCR. Then, PCR products were introduced into bi-directional Sanger sequencing. The retrieved sequences were compared with references, to investigate the variation of immunologic sites, major hydrophilic region (MHR) of HBsAg as well as reverse transcriptase (RT), and also to determine genotype/subtype. Results: The analysis of MHR and epitopes on HBsAg showed dozens of substitution, which occurred more prevalently in I110, P120, Y134, G159, S193, Y206, S207, I208, L213 and P214 positions. However, Y134N/F/L (P = 0.04) and P120T/S (P = 0.009) were significantly detected in MHR and B-cell epitope of HCC/Cirrhotic group. A number of truncation-related mutations were higher in HCC/Cirrhotic group (P > 0.001), albeit only C69* stop codon was statistically significant (P = 0.003). In RT, some potentially resistant substitutions such as Q215S, V191I and V214A, were revealed. Phylogenetic analysis showed that all of isolates belonged to genotype D, and the major serotype was ayw1. Conclusion: The higher frequency of substitutions in MHR and immune epitopes at positions such as Y134 and P120 as well as stop codons such as C69* in HCC/cirrhotic group might candidate them as predictive factors for infection outcome.

Relying on their polymorphic nature, short tandem repeats (STRs) have been extensively studied and routinely utilized as human identity markers in forensic genetics. However, even the most comprehensive STR multiplexes in use today are limited in their ability to determine the number and appropriation of component contributor alleles in DNA mixtures. The difficulty in parsing out individuals in DNA mixtures is a consequence of overlapping length‐based alleles genotyped using the polymerase chain reaction (PCR) coupled with capillary electrophoresis (CE). Many challenges exist in the resolution of minor alleles (i.e., the alleles originating from a minor contributor) from stutter and stochastic effects (e.g., inherent heterozygote peak imbalance, undetected alleles [drop out]) in a given DNA profile, in addition to the complex statistical models and algorithms necessary to render DNA mixtures interpretable from a forensic casework standpoint. Therefore, we can either adapt to complex interpretation methods, or pursue new bench science approaches to DNA mixture deconvolution. One promising area of research includes the incorporation of additional highly polymorphic STR loci to compliment current marker multiplexes and offer great potential to improve the forensic genetic analysis of DNA mixtures. This article is categorized under:Forensic Biology > Forensic DNA TechnologiesForensic Biology > Interpretation of Biological EvidenceForensic Biology > Ethical and Social Implications [ABSTRACT FROM AUTHOR]

Non-alcoholic or recently re-defined metabolic associated fatty liver disease (MAFLD), a spectrum of progressive hepatic disease, has become a public health issue in obese children and adolescents. MAFLD is a complex metabolic disease strongly associated with obesity and insulin resistance. It is not known why not every obese subject will develop MAFLD. Different ethnic/racial groups display differences in MAFLD prevalence, indicating genetic factor plays a role. In the past two decades, sequence variations in genetic loci, including PNPLA3, TM6SF2, GCKR, MBOAT7, HSD17B13, etc. have been shown to confer susceptibility to MAFLD in children and adults. This review article provides an updated viewpoint of genetic predictors related to pediatric MAFLD. We discuss whether these susceptible genes can be clinically used for risk stratification and personalized care. Understanding human genetics and molecular mechanisms can give important information not only for prediction of risk but also on how to design drugs. In view of current epidemic of MAFLD worldwide, it is necessary to identify which children with MAFLD progress rapidly and need earlier intervention. In the future, a comprehensive analysis of individualized genetic and environmental factors may help assess the risk of children with MAFLD and personalize their treatment.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This study conducted a reassessment of published diagnostic PCR assays, including those recommended by the World Health Organization (WHO), through the evaluation of mismatches with publicly available viral sequences. An exhaustive evaluation of the sequence variability within the primer/probe target regions of the viral genome was performed using more than 17 000 viral sequences from around the world. The analysis showed the presence of mutations/mismatches in primer/probe binding regions of 7 assays out of 27 assays studied. A comprehensive bioinformatics approach for in silico inclusivity evaluation of PCR diagnostic assays of SARS-CoV-2 was validated using freely available software programs that can be applied to any diagnostic assay of choice. These findings provide potentially important information for clinicians, laboratory professionals and policy-makers.

Peroxisome proliferator-activated receptor alpha (PPARA) is a member of the nuclear receptor superfamily that regulates key proteins involved in fatty acid oxidation and extracellular lipid metabolism. Given the importance of PPARA in modulating energy metabolism, PPARA may be a suitable candidate gene for assessing economic traits in cattle. In the present study, the genetic diversity of the PPARA gene in Chinese cattle breeds and its effects on growth traits in the Nanyang and Jiaxian breeds were investigated. First, the transcript profiles for PPARA were determined in eight adult cattle tissue types. Next, polymorphisms were identified in the coding and predicted promoter regions of the bovine PPARA gene in 424 animals. Finally, an association study was carried out to evaluate the relationship between PPARA and the development of cattle. Based on quantitative real-time polymerase chain reaction, PPARA was mainly expressed in the kidney and liver. Nine single nucleotide polymorphisms (SNPs) were identified in Chinese domestic cattle, including one novel SNP. Haplotype frequencies and linkage disequilibrium were also investigated. Four SNPs (g.17148558A>T, g.117195348A>G, g.117228160T>C, and g.117233248A>G) showed significant associations with growth traits in NY and JX cattle, including body weight, average daily gain, and hipbone width. These results confirmed the importance of PPARA as a candidate gene for marker-assisted selection for growth traits in cattle.

ATP‐binding cassette (ABC) proteins are found in every sequenced genome and evolved deep in the phylogenetic tree of life. ABC proteins form one of the largest homologous protein families, with most being involved in substrate transport across biological membranes, and a few cytoplasmic members regulating in essential processes like translation. The predominant ABC protein classification scheme is derived from human members, but the increasing number of fully sequenced genomes permits to reevaluate this paradigm in the light of the evolutionary history the ABC‐protein superfamily. As we study the diversity of substrates, mechanisms, and physiological roles of ABC proteins, knowledge of the evolutionary relationships highlights similarities and differences that can be attributed to specific branches in protein divergence. While alignments and trees built on natural sequence variation account for the evolutionary divergence of ABC proteins, high‐throughput experiments and next‐generation sequencing creating experimental sequence variation are instrumental in identifying functional constraints. The combination of natural and experimentally produced sequence variation allows a broader and more rational study of the function and physiological roles of ABC proteins. [ABSTRACT FROM AUTHOR]

Coffee is a popular beverage in the world and a valuable agricultural export commodity for several developing countries. Coffea arabica is one of the widely cultivated species and is believed to have originated from Ethiopia. Currently, a large number of C. arabica accessions are conserved ex situ in field gene banks in Ethiopia. However, there is no useful molecular barcoding to identify the conserved accessions, which presents a challenge to sustainable utilization of this economic species. To identify polymorphic chloroplast markers for the use in various studies, the complete chloroplast genome sequences of 24 C. arabica accessions were assembled and screened for variable regions in this study. The total length of the individual chloroplast genome sequence varied from 155,059 to 155,192 bp. Genome annotation revealed a total of 114 unique genes, consisting of 80 protein-coding, 30 tRNA, and four rRNA genes in all the 24 genomes. Twenty-four polymorphic regions were identified and developed. Most (71%) of the variable regions were found in non-coding sequence, and 54% of the variations detected are single base pairs. Three non-synonymous SNPs were found in accD, rpoA, and ycf1 genes. The markers developed were able to cluster the majority of the coffee accessions according to their geographical regions of collection. Five out of 24 newly developed markers were validated by assessing the diversity levels that were assessed in five original regions. The southwest region displayed the highest genetic diversity (HE = 0.224; I = 0.370) and might become a potential coffee genetic resource bank. Overall, the polymorphic markers developed and validated in this study could be a useful genomic resource for molecular breeding, identification, and biogeography studies of this commercially important crop. [ABSTRACT FROM AUTHOR]

Rapid and accurate detection of contagium virus is a key tool for controlling the outbreak. As the number of patients infected with 2019 novel coronavirus (SARS-CoV-2) pneumonia is increasing and the epidemic is spreading, many hospitals, laboratories and pharmaceutical companies have developed diagnostic reagents that can detect SARS-CoV-2. Currently, genome sequencing or real-time PCR is a method for detecting SARS-CoV-2. However, there have been reported cases of negative results by nucleic acid detection but confirmed on the radiological CT scan. How to improve the diagnostic efficiency and the sensitivity of molecular detection remains to be solved. To analyze the variations in viral genomic sequence may be helpful in guiding the prevention and treatment of diseases infected by SARS-CoV-2. At present, controversy still exists over the source of SARS-CoV-2 even though the probable origin is bat in nature. This article summarizes the recent findings of SARS-CoV-2 from genetic, virological and evolutionary biological perspectives. By comparing the genomic variations among SARSCoV- 2 infected patients, we hope the findings can be used in the viral detection and potential antiviral therapy. Also, it will be great if we can trace the spread of the virus from one person to another, which will be an much effective way to predict and control the spread from the virus-carrier without symptoms at the incubation period to the others. [ABSTRACT FROM AUTHOR]

In higher plants, sexual and asexual reproductions through seeds (apomixis) have evolved as alternative strategies. Evolutionary advantages leading to coexistence of both reproductive modes are currently not well understood. It is expected that accumulation of deleterious mutations leads to a rapid elimination of apomictic lineages from populations. In this line, apomixis originated repeatedly, likely from deregulation of the sexual pathway, leading to alterations in the development of reproductive lineages (germlines) in apomicts as compared with sexual plants. This potentially involves mutations in genes controlling reproduction. Increasing evidence suggests that RNA helicases are crucial regulators of germline development. To gain insights into the evolution of 58 members of this diverse gene family in sexual and apomictic plants, we applied target enrichment combined with next-generation sequencing to identify allelic variants from 24 accessions of the genus Boechera , comprising sexual, facultative, and obligate apomicts. Interestingly, allelic variants from apomicts did not show consistently increased mutation frequency. Either sequences were highly conserved in any accession, or allelic variants preferentially harbored mutations in evolutionary less conserved C- and N-terminal domains, or presented high mutation load independent of the reproductive mode. Only for a few genes allelic variants harboring deleterious mutations were only identified in apomicts. To test if high sequence conservation correlates with roles in fundamental cellular or developmental processes, we analyzed Arabidopsis thaliana mutant lines in VASA-LIKE (VASL), and identified pleiotropic defects during ovule and reproductive development. This indicates that also in apomicts mechanisms of selection are in place based on gene function. [ABSTRACT FROM AUTHOR]

Background: Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-synonymous Single Nucleotide Variants – missense SNVs or nsSNVs) for particular proteins. We assembled SAV annotations from 22 different DMS experiments and normalized the effect scores to evaluate variant effect prediction methods. Three trained on traditional variant effect data (PolyPhen-2, SIFT, SNAP2), a regression method optimized on DMS data (Envision), and a naïve prediction using conservation information from homologs. Results: On a set of 32,981 SAVs, all methods captured some aspects of the experimental effect scores, albeit not the same. Traditional methods such as SNAP2 correlated slightly more with measurements and better classified binary states (effect or neutral). Envision appeared to better estimate the precise degree of effect. Most surprising was that the simple naïve conservation approach using PSI-BLAST in many cases outperformed other methods. All methods captured beneficial effects (gain-of-function) significantly worse than deleterious (loss-of-function). For the few proteins with multiple independent experimental measurements, experiments differed substantially, but agreed more with each other than with predictions. Conclusions: DMS provides a new powerful experimental means of understanding the dynamics of the protein sequence space. As always, promising new beginnings have to overcome challenges. While our results demonstrated that DMS will be crucial to improve variant effect prediction methods, data diversity hindered simplification and generalization. [ABSTRACT FROM AUTHOR]