Search

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with 18O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.

In this study, bacteriophages specific to Pseudomonas aeruginosa strains were isolated from wastewaters, and their potential to be used as a bioprotective in chicken meat was investigated. Then, among the 35 isolated bacteriophages, two phages (vB_PaeS-K10 and vB_PaeS-K13) with a wide host cell range and strong clear plaque formation were selected and their morphological, physical–chemical, and genetic properties and their inhibitory effects against the host cell in chicken meat were determined. As a consequence of the examination by TEM (transmission electron microscopy), vB_PaeS-K10 and vB_PaeS-K13 phages belong to the family Siphoviridae of the order Caudovirales. The genome size, multiplicity of infection value, latent period, burst time, and burst size of vB_PaeS-K10 phage were 54.20 kb, 10, 75 min, 30 min, and 34.86, respectively, whereas those of vB_PaeS-K13 phage were 44.06 kb, 0.01, 20 min, 35 min, and 35.95. Both of them were resistant to high temperature and entirely active between pH 3 and 12, and the rate of absorption of the phages against their host cells increased with Ca2+ ions. Lytic activity test revealed that both phages reduced host cell density in LB broth at 4 °C and 37 °C. Moreover, vB_PaeS-K10 and vB_PaeS-K13 phages lethally infect P. aeruginosa at 4 °C in chicken meat, and this situation is the evidence of their potential to be utilized as bioprotective in chicken meat. [ABSTRACT FROM AUTHOR]

Hosta species are abundant in northeastern Asia, offering significant ornamental and horticultural value due to their diverse foliage colors and textures, as well as their showy, fragrant flowers. Among the eight taxa naturally distributed in Korea, H. clausa is found in central and northern Korea, as well as northeastern China, providing valuable resources for developing and improving new varieties. Currently, four intraspecific taxa of H. clausa are recognized at the variety level based on reproductive (opened vs. closed perianth), vegetative (leaf shape), and habitat characteristics: var. clausa, var. normalis, var. ensata, and var. geumgangensis. Despite its horticultural and taxonomic importance, little is known about the degree of intraspecific chloroplast genome variation and relationships among the varieties of H. clausa. This could provide some valuable information for marker-assisted breeding programs and molecular cultivar identification. In this study, we investigated the complete plastid genome of 14 accessions of H. clausa, covering its native distribution range. We characterized genome size and features and performed comparative plastome analyses (frequency of codon usage, nucleotide diversity, mutation hotspots). Our analysis revealed highly conserved structures and gene content organization in H. clausa, along with significantly (two to three times) lower nucleotide diversity compared to intraspecific herbaceous and woody species. The phylogenetic analysis did not support the recognition of intraspecific taxa as currently delimited, and a broad-scale geographical structure of complete plastomes was not apparent. The asexual reproductive mode of H. clausa appears to contribute to the low plastome genetic diversity. A total of 72 polymorphic sites identified among 14 accessions of H. clausa and their phylogenetic relationships, in conjunction with their geographical distribution and morphological characteristics, will be a valuable resource for barcoding study, marker-assisted breeding programs, and developing conservation strategies for hosta species in East Asia. [ABSTRACT FROM AUTHOR]

Vigna radiata (L.) R. Wilczek var. radiata (mungbean) is a pulse crop important for both the global protein security and sustainable crop production. Here, to facilitate genomics-assisted breeding programs in mungbean, we present a high-quality reference genome originating from the crop's centre of origin, India. In this study, we present a significantly continuous genome assembly of V. radiata Indian cultivar, achieved through a combination of long-read PacBio HiFi sequencing and Hi-C sequencing. The total assembled genome size is ~596 Mb equating to ~98% of the predicted genome size complemented by a contig N50 value of 10.35 Mb and a BUSCO score of 98.5%. Around 502 Mb of the assembled genome is anchored on 11 pseudochromosomes conforming to the chromosome count in the crop with distinctly identified telomeres and centromeres. We predicted a total of 43,147 gene models of which 39,144 protein coding genes were functionally annotated. The present assembly was able to resolve several gaps in the genome and provides a high-quality genomic resource for accelerating mungbean breeding programs. [ABSTRACT FROM AUTHOR]

Background: Poplars are important woody plants, which are widely distributed in the forests from the subtropics to the north of the Northern Hemisphere. Poplars have high ecological and economic value. However, there are frequent interspecific and intraspecific hybrids in Populus, resulting in a large number of intermediate taxa, which makes the morphological identification of Populus very challenging. Plastid genome is an important tool to study the evolutionary relationship of plants. Therefore, comparison and phylogenetic analysis were carried out based on the population chloroplast genomes of 34 individuals from 7 taxa. Results: In this study, seven newly assembled and annotated chloroplast genomes of Populus were reported. They all had typical quadripartite structures with the same GC content (37.6%), but there were differences within the population, and the genome size ranged from 155,736 bp to 156,812 bp. In all Populus species, 134 genes were identified, including 88 protein coding genes (PCGs), 37 tRNA and 8 rRNA genes. The gene sequences alignment of different taxa showed that the gene sequences and content were relatively conservative, there was no gene rearrangement, and only 3 highly variable regions (psbZ-trnG, ndhC-trnV and trnN-trnR) were identified, which can be used as molecular markers. Most PCGs had high codon usage bias and 3 positive selection genes (rps7, rps12 and rpl16) have been identified. The analysis of population genetic structure and phylogeny showed that the chloroplast genomes supported that Populus was a monophyletic taxon, which could be divided into four sections (Abaso, Turanga, Populus and ATL (Aigeiros, Tacamahaca and Leucoides)). Among them, P. dafengensis, P. butuoensis and P. szechuanica had the closest genetic relationship, P. gonggaensis and P. cathayana had the closest genetic relationship, it was speculated that the taxa of Sect. Tacamahaca may be the main female parent of the three new taxa from Sect. Leucoides. Conclusion: In general, this study provides valuable insights for new species identification, phylogenetic relationships, breeding and resource development, and genetic diversity of Populus. [ABSTRACT FROM AUTHOR]

The complete genome of Legionella lytica PCM 2298 was sequenced and analyzed to provide insights into its genomic structure, virulence potential, and evolutionary position within the Legionella genus. The genome comprised a 3.2 Mbp chromosome and two plasmids, pLlyPCM2298_1 and pLlyPCM2298_2, contributing to a total genome size of 3.7 Mbp. Functional annotation identified 3,165 coding sequences, including genes associated with known virulence factors such as the major outer membrane protein (MOMP), the macrophage infectivity potentiator (Mip), and a comprehensive set of secretion systems (type II, type IVA, and type IVB Dot/Icm type IV secretion system). Notably, L. lytica contributed 383 unique genes to the Legionella pangenome, with 232 identified effector proteins, of which 35 were plasmid-encoded. The identification of unique genes, particularly those on plasmids, suggests an evolutionary strategy favoring horizontal gene transfer and niche adaptation. The effector repertoire included proteins with domains characteristic of host interaction strategies, such as ankyrin repeats and protein kinases. Comparative analyses showed that while L. lytica shares core virulence traits with other Legionella species, it has distinct features that may contribute to its adaptability and pathogenic potential. These findings underscore the genomic diversity within the genus and contribute to a deeper understanding of Legionella's ecological and clinical significance. A custom web application was developed using the R Shiny library, enabling users to interactively explore the expanded Legionella pangenome through UpSet plots. [ABSTRACT FROM AUTHOR]

Background: The sequencing of non-model species has increased exponentially in recent years, largely due to the advent of novel sequencing technologies. In this study, we construct the Reference Genome of the Spanish toothcarp (Aphanius iberus (Valenciennes, 1846)), a renowned euryhaline fish species. This species is native to the marshes along the Mediterranean coast of Spain and has been threatened with extinction as a result of habitat modification caused by urbanization, agriculture, and its popularity among aquarium hobbyists since the mid-twentieth century. It is also one of the first Reference Genome for Euro-Asian species within the globally distributed order Cyprinodontiformes. Additionally, this effort aims to enhance our comprehension of the species' evolutionary ecology and history, particularly its remarkable adaptations that enable it to thrive in diverse and constantly changing inland aquatic environments. Results: A hybrid assembly approach was employed, integrating PacBio long-read sequencing with Illumina short-read data. In addition to the assembly, an extensive functional annotation of the genome is provided by using AUGUSTUS, and two different approaches (InterProScan and Sma3s). The genome size (1.15 Gb) is consistent with that of the most closely related species, and its quality and completeness, as assessed with various methods, exceeded the suggested minimum thresholds, thus confirming the robustness of the assembly. When conducting an orthology analysis, it was observed that nearly all genes were grouped in orthogroups that included genes of genetically similar species. GO Term annotation revealed, among others, categories related with salinity regulation processes (ion transport, transmembrane transport, membrane related terms or calcium ion binding). Conclusions: The integration of genomic data with predicted genes presents future research opportunities across multiple disciplines, such as physiology, reproduction, disease, and opens up new avenues for future studies in comparative genomic studies. Of particular interest is the investigation of genes potentially associated with salinity adaptation, as identified in this study. Overall, this study contributes to the growing database of Reference Genomes, provides valuable information that enhances the knowledge within the order Cyprinodontiformes, and aids in improving the conservation status of threatened species by facilitating a better understanding of their behavior in nature and optimizing resource allocation towards their preservation. [ABSTRACT FROM AUTHOR]

The lifestyles of the order Geoglossales (Geoglossomycetes, Ascomycota) remain largely unknown. Recent observations support ericoid mycorrhizal lifestyles, especially in cultured Sarcoleotia-related species. However, the currently known genomes of geoglossoid fungi encode fewer carbohydrate-active enzymes (CAZymes) in Pezizomycotina, in contrast to the abundant CAZyme repertoires found in well-known ericoid mycorrhizal fungi. The absence of assembled genomes for cultured geoglossoid fungi hinders our understanding of the genomic features related to their lifestyles. We hypothesize that the genome of Sarcoleotia globosa, a putative ericoid mycorrhizal fungus, encodes abundant CAZymes, consistent with its culturability. General features, such as smaller genome size and smaller number of genes, are shared between the genome of S. globosa strain NBRC 116039 and other geoglossalean genomes. However, the former had the most extensive CAZyme repertoire, with several enzyme families involved in plant cell wall degradation. Some of these CAZymes are not found in Geoglossales and closely related lineages. Nonetheless, the number of CAZymes from S. globosa was notably smaller than that previously reported in ericoid mycorrhizal fungi. This inconsistency may highlight not only ecophysiological variation among ericoid root mycobionts but also the specific evolution of lifestyles in Geoglossales. [ABSTRACT FROM AUTHOR]

Rosa hugonis is widely distributed in the Hengduan Mountains, Qinling Mountains, and northern China. It is an important candidate species for ecological restoration, given its good adaptability. Here, we present the first high-quality chromosome-level assembly of R. hugonis based on HiFi reads and Hi-C data. The sequencing data were then assembled onto seven pseudochromosomes of R. hugonis. The genome sizes of R. hugonis is 337.92 Mb, with contig N50 length of 26.84 Mb. We annotated 36,218 protein-coding genes in R. hugonis. In summary, the high-quality genome sequences of R. hugonis provide a genetic roadmap for the study of its genetics and species relationships. This will facilitate future genomic comparative studies across more species within Rosa. [ABSTRACT FROM AUTHOR]

Mylabris sibirica is a hypermetamorphic insect that primarily feeds on oilseed rape during the adult stage. However, the limited availability of genomic resources hinders our understanding of the gene function, medical use, and ecological adaptation in M. sibirica. Here, a high-quality chromosome-level genome of M. sibirica was generated by PacBio, Illumina, and Hi-C technologies. Its genome size was 138.45 Mb, with a scaffold N50 of 13.84 Mb and 99.85% (138.25 Mb) of the assembly anchors onto 10 pseudo-chromosomes. BUSCO analysis showed this genome assembly had a high-level completeness of 100% (n = 1,367), containing 1,358 (99.4%) single-copy BUSCOs and 8 (0.6%) duplicated BUSCOs. In addition, a total of 11,687 protein-coding genes and 35.46% (49.10 Mb) repetitive elements were identified. The high-quality genome assembly offers valuable genomic resources for exploring gene function, medical use, and ecology. [ABSTRACT FROM AUTHOR]

C4 photosynthesis exemplifies convergent evolution of complex traits. Herein, we construct chromosome-scale genome assemblies and perform multi-omics analysis for five Flaveria species, which represent evolutionary stages from C3 to C4 photosynthesis. Chromosome-scale genome sequence analyses reveal a gradual increase in genome size during the evolution of C4 photosynthesis attributed to the expansion of transposable elements. Systematic annotation of genes encoding C4 enzymes and transporters identify additional copies of three C4 enzyme genes through retrotranspositions in C4 species. C4 genes exhibit elevated mRNA and protein abundances, reduced protein-to-RNA ratios, and comparable translation efficiencies in C4 species, highlighting a critical role of transcriptional regulation in C4 evolution. Furthermore, we observe an increased abundance of ethylene response factor (ERF) transcription factors and cognate cis-regulatory elements associated with C4 genes regulation. Altogether, our study provides valuable genomic resources for the Flaveria genus and sheds lights on evolutionary and regulatory mechanisms underlying C4 photosynthesis. C4 photosynthesis serves as a prominent example of convergent evolution in complex traits. Here, the authors construct chromosome-scale genome assemblies for five Flaveria species and investigate the genomic evolution of C4 photosynthesis. Their findings emphasize the roles of retrotransposition and transcriptional regulation in shaping C4 traits. [ABSTRACT FROM AUTHOR]

Background: Potentilla L. and Dasiphora L. are predominantly perennial herbs, occasionally manifesting as annuals or shrubs, primarily found in the northern temperate zone. However, taxonomic classification within this group remains contentious, particularly regarding genus boundaries and species delineation. Therefore, this study sequenced and analyzed the complete plastid genomes of 19 species from Potentilla and Dasiphora, comparing them with five previously published plastid sequences. Our objectives included reconstructing phylogenetic relationships within Potentilla and Dasiphora and investigating cytonuclear discordance among them. Results: These plastid genomes were highly conserved in structure, GC content, and overall genome composition, comprising 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Notably, all Dasiphora plastid genomes lacked the unique intron for rpl2. Comparative genomic analyses revealed that variations in plastid genome size were due to differences in the lengths of the LSC, SSC, and IR regions. The IR region was predominantly conserved, while non-coding regions exhibited higher variability than coding regions. We screened SSR and identified seven highly variable loci that serve as potential molecular markers, offering valuable insights into the intergeneric relationships between Potentilla and Dasiphora. Phylogenetic analyses based on nuclear (ITS, ETS) and cytoplasmic (plastid, mitochondrial) genes confirmed the monophyly of Potentilla and Dasiphora, with results largely consistent with previous studies and supported by robust reliability metrics. We identified cytonuclear conflicts within Potentilla, which frequently disrupt its monophyly. We hypothesize that these conflicts may result from interspecific hybridization or incomplete lineage sorting events during the evolutionary history of the genus. Conclusions: This study offers a theoretical foundation for advancing molecular identification and phylogenetic research on Potentilla and Dasiphora species. However, future work could benefit from greater detail on the criteria for selecting mitochondrial gene sequences and nrDNA datasets. [ABSTRACT FROM AUTHOR]

Ninety-eight actinomycetes isolates were screened for poly(lactic acid) (PLA)-degrading abilities using a minimal medium supplemented with emulsified PLA as the substrate. The isolate 8ER183 showed PLA degradation ability after incubation at ambient temperature (30 ± 2 °C) for 96 h. The 16S rRNA gene and whole-genome sequencing identified strain 8ER183 as Streptomyces rochei, and the genome size was 8.4 Mbp with an average G + C content of 72.39%. Genome mining revealed 5,689 proteins with functional assignments. The predicted degradation gene involving PLA-degrading enzymes such as protease and lipase was correlated with the phenotypic investigation. The enzymes involved in PLA degradation produced by 8ER183 strain were evaluated as protease and lipase. For enzyme production, cassava chips and peptone at 1.0 and 5.0 g/L yielded the highest PLA-degrading enzyme production (0.49 ± 0.02 U/mL) at 45 °C with pH 8.0. Scaling up enzyme production in a 3.0 L airlift bioreactor enhanced enzyme yield to 2.57 ± 0.12 U/mL, representing 5.25- and 32.12-fold increases compared to the optimized medium in shaking flasks and the unoptimized medium, respectively. The crude enzyme was most active at pH 9.0 and 50 °C. Electron microscopy and infrared spectroscopy revealed significant differences in the physical and chemical structures of PLA film after degradation by crude enzyme. This research identified and characterized a novel PLA-degrading actinomycetes strain as a solution to reduce bioplastic accumulation in the environment and contribute to a more sustainable future. [ABSTRACT FROM AUTHOR]

In the pregenomic era, scientists were puzzled by the observation that haploid genome size (the C-value) did not correlate well with organismal complexity. This phenomenon, called the "C-value paradox," is mostly explained by the fact that protein-coding genes occupy only a small fraction of eukaryotic genomes. When the first genome sequences became available, scientists were even more surprised by the fact that the number of genes (G-value) was also a poor predictor of complexity, which gave rise to the "G-value paradox." The proposed explanations usually invoke mechanisms that increase the information content of each individual gene (protein-protein interactions, intrinsic disorder, posttranslational modifications, alternative splicing, etc.). Less attention has been paid to mechanisms that increase the amount of genetic material but do not increase (or not to the same extent) the amount of information encoded in the genome, such as gene duplication and domain shuffling. Proteins belonging to the same family and/or sharing the same domains often carry out similar or even redundant functions. We thus hypothesized that an organism's number of different protein families and domains should be suitable predictors of organismal complexity. In agreement with our hypothesis, we observed that the number of protein families, clans, domains, and motifs increases from simple to progressively more complex organisms. In addition, these metrics correlate with the number of cell types better than and independently of the number of protein-coding genes and several previously proposed predictors of organismal complexity. Our observations have the potential to represent a resolution to the G-value paradox. [ABSTRACT FROM AUTHOR]

Malus niedzwetzkyana (MN) is the mother of Rosybloom hybrids, ornamental crabapples with red and purple flowers. We present a high-quality chromosome-scale genome for MN with a size of 672.64 Mb, anchored to 17 chromosomes and with a high BUSCO completeness score of 98.6%, reaching the 'gold standard' level. Moreover, our assembly has captured 28 telomeres. A total of 43,813 protein-coding genes was annotated in the MN genome. The assembled high quality provides a valuable opportunity to enhance our understanding of the genetic basis of flower colour and other ornamental traits in crabapples, thereby advancing the field of genetics and breeding. [ABSTRACT FROM AUTHOR]

Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. In Hainan and Guangzhou of China, the ST45-MRSA was mainly associated with t116. Methods: The MRSA strain SA2107 was isolated from the sputum of a 5-year-old child with pneumonia. The whole genome of SA2107 was sequence using Illumina (Novaseq 6000) and PacBio (Sequel IIe) sequencers, and the sequences were assembled using hybrid assembly. The carriage of antibiotic resistance genes, virulence genes, and mobile genetic elements were identified using bioinformatics tools. The comparative genomic analyses of MRSA strain SA2107 with other MRSA strains worldwide were performed. Findings: The genome size of ST45-SCC mec IVa (2B)-t116 MRSA strain SA2107 was ~2.9 Mb. Mobile genetic elements analysis of SA2107 revealed two plasmids (30,064-bp pSA2107-1 and 8,033-bp pSA2107-2), three prophages, two integrative and conjugative elements (ICEs), and two insertion sequences (ISs, IS 431 and IS 1272). The SCC mec IVa (2B) carried by SA2107 contained the class B mec gene complex (IS 431 - mecA -Δ mecR1 -IS 1272) and type 2 ccr gene complex (ccrA2 and ccrB2). Besides mecA , another beta-lactam resistance gene blaZ was found to located on six copies of bla complex (blaZ , blaR1 , and blaI) on the chromosome of SA2107. Three kinds of virulence factors were detected on the chromosome of SA2107, including genes encoding toxins, exoenzyme, and immune-modulating protein. Notably, the three prophages harbored by the chromosome of SA2107 all carried virulence genes. Conclusion: Thus far, only three complete genomes available for ST45-SCC mec IVa (2B)-t116 strain from United States, Germany, and Australia, respectively. The strain SA2107 was the first complete genome data (CP104559) from China for ST45-SCCmec IVa (2B)-t116 MRSA. [ABSTRACT FROM AUTHOR]

The dry forests of northern Peru are dominated by the legumous tree Neltuma pallida which is adapted to hot arid and semiarid conditions in the tropics. Despite having been successfully introduced in multiple other areas around the world, N. pallida is currently threatened in its native area, where it is invaluable for the dry forest ecosystem and human subsistence. A major tool for enhancing ecosystem conservation and understanding the adaptive properties of N. pallida to dry forest ecosystems is the construction of a reference genome sequence. Here, we report on a high-quality reference genome for N. pallida. The final genome assembly size is 403.7 Mb, consisting of 14 pseudochromosomes and 63 scaffolds with an N50 size of 26.2 Mb and a 34.3% GC content. Use of Benchmarking Universal Single Copy Orthologs revealed 99.2% complete orthologs. Long terminal repeat elements dominated the repetitive sequence content which was 51.2%. Genes were annotated using N. pallida transcripts, plant protein sequences, and ab initio predictions resulting in 22,409 protein-coding genes encoding 24,607 gene models. Comparative genomic analysis showed evidence of rapidly evolving gene families related to disease resistance, transcription factors, and signaling pathways. The chromosome-scale N. pallida reference genome will be a useful resource for understanding plant evolution in extreme and highly variable environments. [ABSTRACT FROM AUTHOR]

Nuclear genome sizes of 54 representative species from 44 genera of the monocot order Poales were investigated by flow cytometry. Small holoploid genomes with < 2 pg/2C are characteristic of the Poales; only some families have larger 2C values, although this is not consistently the case. The sizes of monoploid genomes as well as mean DNA content per chromosome (MC) show a similar pattern. A comparison of the genome size data with current molecular phylogenetic data suggests that small monoploid genomes (1Cx < 0.4 pg) and small chromosomes (MC ≤ 0.05 pg), as found in some families, are likely the ancestral features of the order Poales. Conspicuous increases in genome size occurred particularly in the Poaceae (grasses) and to a lesser extent in the xyrid clade and the Restionaceae. According to previous phylogenomic studies, the Poaceae are characterized by a whole-genome duplication (WGD) called ρ, which is absent in all other Poales families. However, it is clear from the 1Cx values that the ρ event is not, or no longer, associated with a significant increase in the minimum 1Cx genome sizes of grasses compared to other Poales families. Future studies need to clarify whether the smallest 1Cx values in the Poaceae are due to a secondary reduction of the nuclear genome after the ρ event and whether the relatively large minimal 1Cx values of the xyrid clade were caused by a further WGD within Poales. [ABSTRACT FROM AUTHOR]

The Alborz Mountains represent an area of endemism within the Irano-Turanian floristic region. They are particularly rich in the number of species belonging to Euphorbia subgenus Esula (leafy spurges). Here, we present a new annual leafy spurge discovered in the area. Morphologically and ecologically, it resembles annual Euphorbia szovitsii, the sole representative of Euphorbia sect. Szovitsiae, and Euphorbia arvalis from Euphorbia sect. Arvales. Phylogenetic analyses of the nuclear internal transcribed spacer sequences inferred its sister position to Euphorbia sect. Patellares, which includes perennials growing mostly in more mesic habitats; interestingly, the new species shares partly connate raylet-leaves with this section. Conversely, the plastid sequences indicated that it was most closely related to E. szovitsii. This suggests its hybrid origin, possibly including an allopolyploidisation event in its evolutionary history, indicated by an increased relative genome size compared to E. szovitsii. Based on our integrative approach we describe the new Alborz endemic as Euphorbia alborzensis and include it in E. sect. Szovitsiae. We provide a taxonomic treatment and discuss its morphological affinities with close relatives. Our study highlights the Alborz Mountains as an important area of endemism in the Irano-Turanian region and indicates that further in-depth studies are needed in this region. [ABSTRACT FROM AUTHOR]

Spirogyra is an extremely common, high-biomass, and species-rich green alga of freshwater ecosystems. Conjugating material with zygospores is traditionally required to achieve identification beyond genus. Although filament width classes have been related to habitat status elsewhere, the phylogenetic content of these classes is unknown. We report the results of a survey of 90 sites in New Zealand, designed to determine species distributions in contrasting stream habitats, using rbcL sequencing of microscopically separated filaments to resolve diversity. We found 22 phylospecies of Spirogyra inhabiting 51 sites, with traditional identification using fertile material where possible. Subgeneric resolution was obtained in essentially all samples (vs <30% in most studies relying on fertile material). Four phylospecies were relatively widespread, occurring in 4–10 of the sites examined. Older literature proposed the existence of widespread polyploid serialisation in Spirogyra, with implications for species-level diversity, and we found substantial variation in filament diameter and chloroplasts per cell within phylospecies. Environmental drivers of species distribution, chloroplasts per cell (inferred ploidy), and zygospore formation all differed. Mean summer temperature and pH were the strongest drivers of site occupancy by phylospecies. However, chloroplasts per cell, thought to reflect ploidal state, was mainly driven by habitat enrichment, resulting in larger forms being biased towards lowland waters. A long-standing hypothesis proposes that genome size is limited by nutrient availability, since nucleic acids demand high nitrogen and phosphorus; Spirogyra may offer an excellent experimental system to address this question. The width of zygospores, which are preserved in sediments and found during palaeoecological studies, is correlated with filament diameter and chloroplasts per cell, suggesting that these relationships with trophic status offer potentially useful palaeoecological information. Specimens of narrow (presumably haploid) phylotypes were encountered fertile far more often than were larger phylotypes; whether this reflects polyploidy-related incompatibilities or differences in population turnover rates are unknown. [ABSTRACT FROM AUTHOR]

The solitary bee Osmia excavata (Hymenoptera: Megachilidae) is a key pollinator managed on a large scale. It has been widely used for commercial pollination of fruit trees, vegetables, and other crops with high efficiency in increasing the crop seeding rate, yield, and seed quality in Northern hemisphere. Here, a high-quality chromosome-level genome of O. excavata was generated using PacBio sequencing along with Hi-C technology. The genome size was 207.02 Mb, of which 90.25% of assembled sequences were anchored to 16 chromosomes with a contig N50 of 9,485 kb. Approximately 186.83 Mb, accounting for 27.93% of the genome, was identified as repeat sequences. The genome comprises 12,259 protein-coding genes, 96.24% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of O. excavata and Osmia bicornis (Hymenoptera: Megachilidae) lived 8.54 million years ago. Furthermore, cytochrome P450 family might be involved in the responses of O. excavata to low-temperature stress.Taken together, the chromosome-level genome assembly of O. excavata provides in-depth knowledge and will be a helpful resource for the pollination biology research. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8–14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions. [ABSTRACT FROM AUTHOR]

Introduction: Heliconia , a genus within the Zingiberales order, is renowned for its diverse morphology, suggesting a rich genetic reservoir. However, genetic research on plants within the Heliconiaceae family has primarily focused on taxonomy and phylogenetics, with limited exploration into other genetic aspects, particularly the chloroplast genome. Given the significance of chloroplast genomes in evolutionary studies, a deeper understanding of their structure and diversity within Heliconia is essential. Methods: In this study, we sequenced and assembled the complete chloroplast genomes of four representative Heliconia species: Heliconia bihai, Heliconia caribaea, Heliconia orthotricha , and Heliconia tortuosa. The chloroplast genomes were analyzed for structure, gene content, and nucleotide diversity. We also performed comparative analysis with other species within the Zingiberales order to investigate structural and functional differences. Results: The assembled chloroplast genomes of the four Heliconia species exhibited a typical quadripartite structure and ranged in length from 161,680 bp to 161,913 bp. All genomes contained 86 protein-coding genes. Comparative analysis revealed that the chloroplast genome structures of the different Heliconia species were highly conserved, with minor variations. Notably, the chloroplast genome of Heliconia was slightly shorter than those of other Zingiberales species, primarily due to the reduced length of the inverted repeat region. In terms of nucleotide diversity, Heliconia species exhibited lower diversity in their chloroplast genomes compared to other families within the Zingiberales order. Discussion: This study provides valuable insights into the conserved nature of the chloroplast genome in Heliconia. The reduced chloroplast genome size, particularly the shortened inverted repeat region, marks a distinct feature of Heliconia within the Zingiberales family. Our findings also underscore the low nucleotide diversity within the chloroplast genomes of Heliconia species, which could be indicative of their evolutionary history and limited genetic differentiation. These results contribute to a broader understanding of chloroplast genome evolution in the Zingiberales and offer important genetic resources for future research on Heliconia and related species. [ABSTRACT FROM AUTHOR]

The article explores marine microorganisms in microbial mats from a Submarine Groundwater Discharge Site in Mabini, Batangas, Philippines. The study focuses on metagenome-assembled genomes (MAGs) recovered through shotgun metagenomics, providing insights into microbial diversity and functional potential. The research highlights the importance of these marine microorganisms in nutrient cycling, ecosystem functioning, and potential biotechnological applications. The study also identifies biosynthetic gene clusters (BGCs) in the MAGs, offering promising applications in medicine and biotechnology. The findings contribute to understanding microbial dimensions in SGD areas, providing a baseline for future research and highlighting the diversity of bioactive compounds from marine microbes. [Extracted from the article]

The cabbage aphid, Brevicoryne brassicae, is a major pest on Brassicaceae plants, causing significant yield losses annually. However, the lack of genomic resources has hindered progress in understanding this pest at the molecular level. Here, we present a high-quality, chromosomal-level genome assembly for B. brassicae, based on PacBio HiFi long-read sequencing and Hi-C data. The final assembled genome size was 429.99 Mb, with a scaffold N50 of 93.31 Mb. Notably, 96.19% of the assembled sequences were anchored to eight chromosomes. The genome covered 99.24% of BUSCO genes and 95.16% of CEGMA genes, indicating a high level of completeness. By integrating high-coverage transcriptome data, we annotated 22,671 protein-coding genes and 3,594 lncRNA genes. Preliminary comparative genomic analyses focused on genes related to host colonization, such as chemosensory- and detoxification-related genes, as well as cross-kingdom lncRNA Ya. In summary, this study presents a contiguous and complete genome for B. brassicae, which will advance our understanding of the molecular mechanisms underlying its host adaptation, pest behavior, and interaction with Brassicaceae plants. [ABSTRACT FROM AUTHOR]

Objectives: Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is frequently associated with multidrug resistance and global epidemic outbreaks, contributing significantly to morbidity and mortality in hospitalized patients. However, P. aeruginosa belonging to the sequence type (ST) 16 was rarely reported. Here, this report presents the complete genome sequence of YK01, a ST16 P. aeruginosa isolate from a patient with keratitis. The complete reference genome of P. aeruginosa YK01 is expected to provide valuable data for investigating its genomic population, enhancing understanding of genetic basis of P. aeruginosa species complex. Data description: A complete genome of 6.3 Mb was obtained for P. aeruginosa YK01 by combining Illumina 150-bp short reads and Nanopore long reads. The assembly is fully complete with chromosomal genome size of 6,183,266 bp, presenting a GC content of 66.7%, and a plasmid with the size of 46,067 bp, presenting GC content of 59.0%. Predicted chromosomal genomic features include 5,709 CDS, 12 rRNAs, 63 tRNAs, 4 ncRNAs, and 5,788 genes. To our knowledge, this genome data represents the first complete genome of P. aeruginosa ST16, providing crucial information for further comparative genome analysis. [ABSTRACT FROM AUTHOR]

Background: Frequent interspecific hybridization, unclear genetic backgrounds, and ambiguous evolutionary relationships within the genus Lycoris pose significant challenges to the identification and classification of hybrids, thereby impacting the application and development of Lycoris. This study utilizes karyotype structure, genome size, and fluorescent in situ hybridization (FISH) technology to explore the chromosomal evolution and hybrid identification of Lycoris employing three approaches at the cytogenetic level. Results: The findings indicate that species with a smaller basic chromosome number exhibit less asymmetry than those with a larger basic chromosome number, suggesting that species with different basic chromosome numbers may have followed different evolutionary pathways. Lycoris aurea has a more symmetrical karyotype, which may be the plesiomorphic state, reflecting an evolutionary transition from symmetry to asymmetry in Lycoris chromosomes. Systematic clustering of 18 Lycoris species is consistent with chromosomal karyotype classification, primarily dividing into two groups: species with M + T + A type an M + T type as one group, and A type as another group. The average nuclear genome size (C-value) of the Lycoris genus is 22.99 Gb, with the smallest genome being that of L. wulingensis (17.10 Gb) and the largest being L. squamigera (33.06 Gb). Chromosome length is positively correlated with the C-value, and the haploid genome size (Cx-value) decreases with an increase in basic chromosome number (x). The FISH technique can quickly identify and authenticate artificial hybrids, thus inferring the parentage of natural hybrids. Conclusion: The study reveals the genetic background and interspecific relationships of 18 Lycoris species, identifies the authenticity of artificial Lycoris hybrids, and infers the possible parentage of natural hybrids, offering technical insights for the identification, classification, and genomic projects of Lycoris. [ABSTRACT FROM AUTHOR]

Background: Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes. Results: Here, we conduct a size-fractioned (< 0.22 μm) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (≤ 41 years) and late stages (> 41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity. Conclusions: Overall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models. 36NkSuBhymqeFDHZtwigi8 Video Abstract [ABSTRACT FROM AUTHOR]

Chinese cherry belongs to the family Rosaceae, genus Prunus, and has high nutritional and economic value. 'Duiying' is a Chinese cherry variety local to Beijing, and has better performance than sweet cherry in terms of disease resistance. However, disease resistance resources of 'Duiying' have not been fully exploited partially due to the lack of a high-quality genome. In this study, we report a high-quality chromosome-scale genome assembly for Chinese cherry 'Duiying', by combining PacBio HiFi, Bionano and Hi-C sequencing data. The assembled genome has a size of 1035.19 Mb, with a scaffold N50 of 28.99 Mb, and 978.61 Mb (94.54%) assembled into 32 pseudochromosomes. A total of 547.16 Mb (52.86%) sequences were identified as repetitive sequences, and 114,451 protein-coding genes were annotated. Moreover, a total of 1635 microRNA (miRNA), 6637 transfer RNA (tRNA), 38,258 ribosomal RNA (rRNA), and 169 small nuclear RNAs (snRNA) genes were identified. The genome assembly presented here provides valuable genomic resources to enhance our understanding of genetic and molecular basis of Chinese cherry. [ABSTRACT FROM AUTHOR]

Meteorus pulchricornis Wesmael (Hymenoptera: Braconidae) is an important parasitoid of lepidopteran insects. So far, only three scaffold-level genomes have been published for the genus Meteorus. In this study, we present a high-quality, chromosome-level genome assembly of M. pulchricornis, characterized by high accuracy and contiguity. This assembly was achieved using Oxford Nanopore Technologies long-read, MGI-SEQ short-read, and Hi-C sequencing methods. The final assembly was 158.5 Mb in genome size, with 153.8 Mb (97.03%) assigned to ten pseudochromosomes. The scaffold N50 length reached 17.51 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 99.3%. The genome contains 28.29 Mb of repetitive elements, accounting for 18.39% of the total genome size. We identified 12,342 protein-coding genes, of which 12,308 genes were annotated functionally. Our investigation into gene family evolution in M. pulchricornis showed that 563 gene families expanded, 1,739 contracted, and 58 underwent rapid evolution. The high-quality genome assembly we report here is advantageous for further research on parasitoid wasps and provides a foundational data resource for natural enemy studies. [ABSTRACT FROM AUTHOR]

Cyperus iria is an aggressive weed of rice throughout the world. Until now, the reference genome of C. iria has not been published. Here, we completed the chromosome-level genome assembly of C. iria based on Illumina, PacBio and Hi-C reads. The assembled genome size of C. iria was 479.08 Mb with a contig N50 of 7.02 Mb. 68 pseudochromosomes were produced using Hi-C scaffolding, accounting for 99.65% of the assembled genome. The number of predicted protein-coding genes is 47,395, of which 93.26% were annotated, and 37.69% repetitive sequences were identified. Our study provided a valuable genomic resource for the molecular biology research and the management of C. iria. [ABSTRACT FROM AUTHOR]

Rubiaceae plants are globally widespread and possess significant economic and medicinal value. Such as the globally important crop of coffee, and Cinchona calisaya Wedd., which is rich in alkaloids, is an important medicinal resource for treating malaria. In recent years, several genome resources of Rubiaceae have been reported. However, the comprehensive phylogenetic relationships of Rubiaceae are still unknown. In this study, we present a nearly complete diploid genome assembly of C. calisaya, characterized by a genome size of 869.93 Mb, and contig N50 length of 44.34 Mb. Notably, 99.75% of the sequences have been successfully anchored to 17 chromosomes, with only 12 gaps remaining. BUSCO assessment indicates that 97.40% of complete core genes are present in the assembly. We identified a total of 42,741 protein-coding genes, among which 38,022 (89.00%) have received functional annotation. The high continuity and integrity of the C. calisaya genome provide a robust foundation for functional genomics research, varietal improvement, and the conservation of genomic resources in medicinal plants. [ABSTRACT FROM AUTHOR]

The bluespotted cornetfish (Fistularia commersonii), a Lessepsian sprinter species, is distributed in the inter-tropical zone across the entire Indo-Pacific, ranging from the Tropical Eastern Pacific to the Red Sea. In this study, we achieve assembly of a chromosome-level genome for F. commersonii by harnessing the precision of PacBio HiFi sequencing in conjunction with the sophistication of Hi-C sequencing technologies. The assembly yields a size of 638.75 Mb, achieving a distribution rate of 99.35% across 36 chromosomes. Notably, the contig N50 value stands at 15.67 Mb, while the scaffold N50 value reaches an impressive 18.69 Mb. BUSCO analysis demonstrates a genome completeness of 96.9% for F. commersonii. Repetitive elements constitute approximately 29.61% of the genome's size. A total of 20,961 protein-coding genes are predicted, with 95.97% of them having functional annotations. This high-quality assembly provides crucial resources for future studies on the invasion mechanisms of F. commersonii, as well as for comparative genomics research on seahorses and pipefish. [ABSTRACT FROM AUTHOR]

Arhopalus unicolor is a carrier of the pine wood nematode (PWN), which causes pine wilt disease, killing pine trees and causing considerable economic and environmental losses. While the A. unicolor mitochondrial genome has been published, a high-quality genome assembly and annotation of A. unicolor is not yet available. To address this, we assembled a chromosome-level reference genome assembly of A. unicolor with a combination of Illumina, PacBio, and Hi-C sequencing technologies. The final genome size was determined to be 1268.11 Mb, with a GC% of 32.44%, and the scaffold N50 value was 19.30 Mb. A total of 98.77% of the assembled sequences mapped to 10 pseudochromosomes, and BUSCO analysis revealed high completeness, with 97.15% gene coverage. Furthermore, the genome contains 71.74% repeat elements and encompasses 16,450 predicted protein-coding genes. This genome sequence of A. unicolor will be a valuable resource for understanding the genetics and evolutionary history of this species and for developing effective management strategies for this PWN carrier. [ABSTRACT FROM AUTHOR]

Chromosomes, as carriers of genes, are the fundamental units of heredity, with the eukaryotic genome divided into multiple chromosomes. Each species typically has a consistent number of chromosomes within its lineage. Ants, however, display remarkable diversity in chromosome numbers, and previous studies have shown that this variation may correlate with ant diversity. As ants evolved, various karyotypes emerged, primarily through chromosomal fissions, leading to an increase in chromosome number and a decrease in chromosome size. In this study, we investigate chromosome evolution in ants from a phylogenetic perspective using ancestral reconstruction. Our analysis indicates that the most recent common ancestor of ants had an ancestral haploid chromosome number of 11, likely composed of biarmed chromosomes. The bimodal distribution of karyotypes and the trend toward increased chromosome numbers align with previous assumptions. However, both dysploidy and ploidy changes have been indicated as likely mechanisms of chromosome number evolution. Descending dysploidy occurs consistently throughout the phylogeny, while changes in ploidy are believed to occur occasionally within the subfamilies during genus diversification. We propose, based on our results and previous evidence (e.g., genome size in ants), that both fusions and fissions contribute equally to karyotype changes in Formicidae. Additionally, changes in ploidy should not be fully ignored, as they can occur across specific lineages. [ABSTRACT FROM AUTHOR]

Bougainvillea glabra Choisy, a common perennial shrub or climbing vine in tropical and subtropical areas, has significant ornamental and ecological value due to its showy floriferous blooms and adaptability to multiple environmental stresses. In this study, based on PacBio and Hi-C sequencing data, we presented the haplotype-resolved, and chromosome-level assembled genomes for B. glabra (2n = 34). We obtained two haplotypes with genome size of 2,855,692,602 bp and 2,889,511,499 bp, N50 of 165 Mbp and 167 Mbp, and both anchored to 17 chromosomes with anchor ratio of 97.07% and 97.55%, respectively. Through the BUSCO evaluation process, the two assembled haplotypes both exhibited the high score of 96%. By combining the high-confidence different evidence of genome structure annotation pipeline we annotated each haplotype containing ~33,000 predicted genes, of which 86% were functionally annotated by different databases. These high-quality haplotypes assembly and annotation results will serve as a great genomic resource to explore the ornamental traits and environmental adaptability and accelerate improvement in future. [ABSTRACT FROM AUTHOR]

Summary: Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well‐understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression.We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment.Utilizing fitness assays, flow cytometry, and RNA‐Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression‐level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression‐level dominance and a pattern of 'functional dominance' from the haploid parent was observed.Despite major genomic and nucleo‐cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems. [ABSTRACT FROM AUTHOR]

The funarioid moss species Physcomitrium eurystomum, which is threatened with extinction, was the subject of this study. The riparian habitat type of this species is often under the influence of contaminated water, and, therefore, we tested the influence of selected potentially toxic elements (PTEs), namely zinc and copper, on the development, physiological features, and survival of the species on two different accessions (German and Croatian). The results obtained showed the different resilience of the two accessions to the PTEs. Flow cytometry analyses revealed that the two accessions differ significantly in terms of genome size. However, the different amplitude of resilience to the tested PTEs, the divergence in physiological responses, and survival within two accessions of the same species are confirmed, as well as the dissimilarity of their genome size, likely associated with ploidy level difference and possibly distinct hybrid origin. [ABSTRACT FROM AUTHOR]

Strain TE5 was isolated from a wheat (Triticum turgidum L. subsp. durum) rhizosphere grown in a commercial field of wheat in the Yaqui Valley in Mexico. In this work, we present strain TE5 as a promising biological control agent against Bipolaris sorokiniana. First, after its genome sequencing through Illumina NovaSeq, this strain showed a genome size of 4,262,927 bp, with a 43.74% G + C content, an N50 value of 397,059 bp, an L50 value of 4 bp, and 41 contigs (>500 bp). Taxonomical affiliation was carried out by using overall genome relatedness indexes (OGRIs) and the construction of a phylogenomic tree based on the whole genome. The results indicated that strain TE5 identifies with Bacillus cabrialesii subsp. cabrialesii. Genomic annotation using Rapid Annotation Using Subsystems Technology (RAST) and Rapid Prokaryotic Genome Annotation (Prokka) indicated the presence of 4615 coding DNA sequences (CDSs) distributed across 330 subsystems, which included gene families associated with biocontrol, stress response, and iron competition. Furthermore, when the antiSMASH 7.1 platform was used for genome mining, the results indicated the presence of seven putative biosynthetic gene clusters related to the production of biocontrol metabolites, namely subtilosin A, bacillibactin, fengycin, bacillaene, bacilysin, surfactin, and rhizocticin A. Moreover, the antifungal activity of strain TE5 and its cell-free extract (CFE) was evaluated against Bipolaris sorokiniana, an emergent wheat pathogen. The results of in vitro dual confrontation showed fungal growth inhibition of 67% by strain TE5. Additionally, its CFE almost completely inhibited (93%) the growth of the studied phytopathogenic fungus on liquid media. Further observations of the impact of these bacterial metabolites on fungal spore germination exhibited inhibition of fungal spores through degrading the germinative hypha, avoiding mycelium development. Finally, the protective effect of strain TE5 against Bipolaris sorokiniana was evaluated for wheat seedlings. The results showed a significant decrease (83%) in disease severity in comparison with the plant infection without inoculation of the biological control agent. Thus, this work proposes Bacillus cabrialesii subsp. cabrialesii strain TE5 as a promising biological control agent against the wheat pathogen Bipolaris sorokiniana while suggesting lipopeptides as the potential mode of action, together with plant growth and defense stimulation. [ABSTRACT FROM AUTHOR]

Fat greenling (Hexagrammos otakii Jordan & Starks, 1895) is a valuable marine fish species, crucial for aquaculture in Northern China due to its high-quality meat and significant economic value. However, the aquaculture industry faces challenges such as trait degradation, early sexual maturity, and disease susceptibility, necessitating advanced genomic interventions for sustainable cultivation. This study presents the first chromosomal-level genome assembly of H. otakii, achieved using PacBio long-read sequencing and Hi-C technology. The assembly yielded a genome size of 682.43 Mb with a contig N50 size of 2.39 Mb and a scaffold N50 size of 27.83 Mb. The completeness of genome assessed by BUSCO is 96.99%. A total of 22,334 protein-coding genes were predicted, with 21,619 (96.80%) functionally annotated across various protein databases. This genomic resource is a step forward in supporting the breeding, germplasm conservation, and enhancement of H. otakii, facilitating genetic studies and the development of strategies for disease resistance and growth optimization in aquaculture. [ABSTRACT FROM AUTHOR]

Riccia sorocarpa Bisch., commonly known as common crystalwort, is a plant belonging to the Marchantiales order with a cosmopolitan distribution among a wide range of habitats: fields, gardens, waste ground, on paths, cliff tops, and thin soil over rocks or by water bodies. However, research into the genetic aspects of this species is limited. In this study, the chromosome-scale telomere-to-telomere genome of R. sorocarpa was assembled exclusively by Oxford Nanopore long-read sequencing and Pore-C technology. A high-quality chromosomal-scale assembly was obtained with a final genome size of 376.690 Mbp, contig N50 of 49.132 Mbp and 97.02% of the assembled contigs associated with the eight chromosomes. Genome assembly completeness was confirmed by BUSCO analysis accounting 91.8%. Among 27,626 total genes, 23,562 (85.29%) were functionally annotated. Moreover, collinearity of Marchantiales was analyzed as well as gene family evolution and DNA methylation profile. The availability of this genome, which is the second telomere-to-telomere liverwort assembly, opens up new avenues for in-depth analysis of R. sorocarpa genetic diversity and genomic characteristics. [ABSTRACT FROM AUTHOR]

Copyright of Food & Fermentation Industries is the property of Food & Fermentation Industries and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far. Results: Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens. Analyses disclosed considerable inter- and intra-species genomic variabilities, with genome sizes that can vary by twice as much. Phylogenetic analysis based on concatenated orthologous genes revealed that avian mycoplasmas fell into either Hominis or Pneumoniae groups within the Mollicutes and could split into various clusters. No host co-evolution of avian mycoplasmas can be inferred from the proposed phylogenetic scheme. With 3,237 different gene clusters, the avian mycoplasma group under study proved diverse enough to have an open pan genome. However, a set of 150 gene clusters was found to be shared between all avian mycoplasmas, which is likely encoding essential functions. Comparison of energy metabolism pathways showed that avian mycoplasmas rely on various sources of energy. Superposition between phylogenetic and energy metabolism groups revealed that the glycolytic mycoplasmas belong to two distinct phylogenetic groups (Hominis and Pneumoniae), while all the arginine-utilizing mycoplasmas belong only to Hominis group. This can stand for different evolutionary strategies followed by avian mycoplasmas and further emphasizes the diversity within this group. Virulence determinants survey showed that the involved gene arsenals vary significantly within and between species, and could even be found in species often reported apathogenic. Immunoglobulin-blocking proteins were detected in almost all avian mycoplasmas. Although these systems are not exclusive to this group, they seem to present some particular features making them unique among mycoplasmas. Conclusion: This comparative genomic study uncovered the significant variable nature of avian mycoplasmas, furthering our knowledge on their biological attributes and evoking new hallmarks. [ABSTRACT FROM AUTHOR]

Background: The genus Astragalus is the largest and one of the most diverse genera of flowering plants, particularly in the Northern Hemisphere, with a significant concentration of species in the Irano-Turanian region. Within this genus, section Hymenostegis is notable for its complexity and high levels of endemism, especially in northwestern Iran. During recent field explorations in West Azarbaijan province, a distinct population of Astragalus was identified, differing from known species within section Hymenostegis. This study aimes to describe and analyze this new species and clarify its relationship with closely related taxa using an integrative approach. Results: Astragalus kuzehrashensis sp. nov. is described following detailed morphological comparisons with its closest relatives, A. chehreganii and A. hakkianus. The new species is distinguished by unique stipule characteristics, leaflet shape, inflorescence structure, and seed micromorphology. Molecular phylogenetic analysis using ITS and ycf1 sequences reveals that A. kuzehrashensis forms a clade with A. chehreganii and A. hakkianus, although it exhibits genetic differences. Genome size estimation confirms that A. kuzehrashensis is hexaploid (2n = 6x = 48), aligning it more closely with A. hakkianus than with the tetraploid A. chehreganii. The distinct morphological characters and genomic data support recognizing A. kuzehrashensis as a new species within section Hymenostegis. Conclusions: The identification of A. kuzehrashensis underscores the importance of an integrative taxonomic approach, combining morphological, molecular, and cytogenetic data to resolve species boundaries within complex groups like Astragalus section Hymenostegis. This study highlights the rich biodiversity of the Irano-Turanian floristic region, emphasizing the need for ongoing exploration and conservation efforts, particularly in areas of high endemism. Our findings contribute to a deeper understanding of the taxonomy and evolutionary relationships within the genus Astragalus. [ABSTRACT FROM AUTHOR]

Yerba mate (YM, Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here, we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large YM genome size is partly due to a whole-genome duplication (Ip-α) during the early evolutionary history of Ilex, in addition to the hexaploidization event (γ) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in YM and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the X-ray diffraction data suggest structural constraints are minimal for the convergent evolution of individual reactions. [ABSTRACT FROM AUTHOR]