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Earthworms belong to the main groups of soil-dwelling invertebrates and are an important element for soil biota. The ecological importance of earthworms on terrestrial ecosystem is mainly attributed to their close synergistic interaction with soil biota. Among earthworms, Eisenia fetida has been considered as preferred for vermiculture and vermicomposting practices due to their reproductive potentials, short life cycle and wide temperature and density pressure tolerances. Although the genome and transcriptome data for E. fetida are available, the EST-SSRs composition and frequency of this species, which used for phylogenetic studies, genus-level taxonomy and population genetics, remain poorly defined. In current study, we mined publicly available transcriptome data and characterised genome-wide EST-SSR markers for this epigeic species. A total of 13,060 EST-SSRs were identified from 162,609 contigs. The most abundant EST-SSR types were found to be trimeric repeats (5,998, 46%) followed by dimeric (4,762, 36%), tetrameric (1,716, 13%), pentameric (478, 4%) and hexameric repeats (106, 1%). For SSR motifs, the most prevalent motifs were AC/GT (14.72%), followed by AT/AT (13.20%), ATC/ATG (13.03%), AAT/ATT (12.30%) and AG/CT (8.46%). Following validation of the species using COI sequences and to test the designed primer pairs, the eight primer pairs were designed, but only six of them were successfully amplified. Although EST-SSR information is scarce for annelids, the EST-SSR patterns of E. fetida seem to be similar to annelids. Overall, the EST-SSR markers help in taxonomic resolution of Eisenia genus from other earthworm genera and in studying the population structure and geographic distributions of E. fetida.

The present study evaluated fatty acid (FA) metabolism in juvenile gilthead sea bream (Sparus aurata, 60.4 ± 4.9 g) fed diets with camelina seed oil and chia oil which totally (CSO and CO diets, respectively) or 60% (60CSO and 60CO diets, respectively) replaced fish oil (FO diet) for 90 days. Analysis of the expression of genes was carried out to determine the effects of the diets on some of the major genes involved in fatty acid metabolism in fish. Good growth performance was recorded in all fish although lower growth (P

WOS: 000443307900005, PubMed ID: 30155366, Background. Extraintestinal pathogenic Escherichia coli (ExPEC) is an important bacterium and responsible for many bloodstream infections, including urinary tract infections and even fatal bacteremia. The aim of this research was to investigate whether ExPEC strains isolated from Turkish blood cultures have a relationship between 16S rRNA based phylogenetic clusters and antibiotic resistance profiles, virulence factors or clonal lineages. Methods. Phenotypically identified ExPEC blood culture isolates (n = 104) were included in this study. The 16S rRNA partial sequence analysis was performed for genotypic identification of ExPEC isolates. Antibiotic susceptibility and Extended Spectrum beta-Lactamase testing of isolates were performed. Phylogenetic classification (A, B1, B2 and D), Multi Locus Sequence Typing analysis and virulence-associated genes were investigated. Results. Based on 16S rRNA partial sequence analysis, 97 out of 104 (93.26%) ExPEC isolates were confirmed as E. coli. Ampicillin (74.22%) and cefuroxime axetil (65.97%) resistances had the highest frequencies among the ExPEC isolates. In terms of phylogenetic classification of ExPEC, D (38.14%, 37/97) was the most prevalent group after A (29.89%, 29/97), B2 (20.61%, 20/97), and B1 (11.34%, 11/97). The sequence types of the 20 ExPEC isolates belonging to the B2 phylogenetic group were analyzed by Multi Locus Sequence Typing. Ten isolates out of 20 (50.0%) were identified as ST131. The other STs were ST95 (n=1), ST14 (n=1), ST10 (n=1), ST69 (n=1), ST1722 (n=2), ST141 (n=1), ST88 (n=1), ST80 (n=1), and ST998 (n=1). Of the ST131 strains, six (60%, 6/10) represented serogroup O25. The most common virulence factor genes were serum resistance factor gene, traT (55.7%) aerobactin siderophore receptor and yersiniabactin encoding genes iutA (45.3%) and fyuA (50.5%), respectively. In addition, PAI (41.2%), iroN (23.7%), hlyA (15.4%), kpsII (13.4%), ompT (13.4%), papG (12.4%), iss (9.3%), cnf1 (7.2%), ibeA (2.06%), and sfaS (2.06%) genes were present in the ExPEC isolates. Conclusion. The 16S rRNA-based phylogenetic relationship tree analysis showed that a large cluster was present among 97 ExPEC isolates along with related reference strains. There were 21 main clusters with 32 closely related subclusters. Based on our findings, different clonal lineages of ExPEC can display different antibiotic susceptibilities and virulence properties. We also concluded that virulence factors were not distributed depending on phylogenetic groups (A, B1, B2, and D). The ExPEC isolates belonging to the same phylogenetic group and sequence type could display different resistance and virulence characteristics., Scientific Research Unit of the Istanbul University [FUA-2016-20386, BYP-2016-2305], This study was supported by The Scientific Research Unit of the Istanbul University with project ID: FUA-2016-20386 and ID: BYP-2016-2305. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

European anchovy has considerable economic and ecological importance due to its high reproduction capacity and growth rate. As one of the largest source of wild marine protein, an increasing muscle mass strength has a major contribution to this growth rate during transition from subadult to adult stage. In the present study, using Illumina sequencing technology (HiSeq2000) accompanied with appropriate bioinformatics softwares; we have sequenced, assembled and annotated the transcriptome of wild subadult and adult anchovy muscles. A total of 131,081,776 high-quality reads were assembled into 125,506 contigs with an average length of 709.35 bp and N50 length of 1159 bp. Functional annotations of assembled contigs have been summarized according to 3325 GO terms, 3370 PFAM domains and 378 predicted KEGG metabolic pathways. About 11% of all contigs had at least one type of SSR motif in their sequences. According to the sequence homology analysis by BlasTN it was concluded that the assembled contigs include 16 skeletal muscle-expressed miRNAs, 14 ncRNAs and most of sarcomeric/myofibrillar genes. We hope that the sequence information regarding the muscle transcriptome of anchovy can provide some insight into the understanding of genome-wide transcriptome profile of teleost muscle tissue and give useful information in fish muscle development. (C) 2015 Elsevier B.V. All rights reserved.

Hyperhydricity is a morphophysiological disorder of plants in tissue culture characterized morphologically by the presence of translucent, thick, curled, and fragile leaves as a result of excessive water intake. Since clonal propagation is a major in vitro technique for multiplying plants vegetatively, the emergence of hyperhydricity-related symptoms causes significant economic losses to agriculture and horticulture. Although numerous efforts have been hitherto devoted to the morphological and anatomical responses of plants to hyperhydricity, the underlying molecular mechanism remains largely unknown. Here, a genome-wide transcriptome analysis was performed to identify differentially expressed genes in hyperhydric and nonhyperhydric leaves of peach [Prunus persica (L.) Batsch]. The RNA sequencing (RNA-Seq) analysis showed that the expression of >300 transcripts was altered between control and hyperhydric leaf cells. The top 30 differentially expressed transcripts (DETs) were related to the posttranscriptional regulators of organelle gene expression and photosynthesis, cellular elimination, plant cuticle development, and abiotic stress response processes. The expression of 10 DETs was also conformed by quantitative real-time polymerase chain reaction (RT-qPCR) in hyperhydric and nonhyperhydric leaves. As a complex biological process, hyperhydricity alters the expression of various transcripts including transcription factor (Myb2), RNA binding protein (pentatricopeptide, PPR), transporter protein (ABC), and Laccase3. Thus, this genome-wide transcriptome profiling study may help elucidate the molecular mechanism of hyperhydricity.

Alburnus istanbulensis (Thracian shemaya) is an endemic fish species to the northwestern region of Turkey. Alburnus istanbulensis has a remarkably limited geographic distribution, and no genetic data have been available on this species until now. The mitogenome (16,612 bp) had the typical mitochondrial characteristics of other Leuciscinae fishes. This mitogenome sequence can help to further resolve phylogenetic relationships among Cyprinidae.

bZIP proteins are one of the largest transcriptional regulators playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of recently published draft genome sequence of Cucumis sativus, no comprehensive investigation of these family members has been presented for cucumber. We have identified 64 bZIP transcription factor-encoding genes in the cucumber genome. Based on structural features of their encoded proteins, CsbZIP genes could be classified into 6 groups. Cucumber bZIP genes were expanded mainly by segmental duplication rather than tandem duplication. Although segmental duplication rate of the CsbZIP genes was lower than that of Arabidopsis, rice and sorghum, it was observed as a common expansion mechanism. Some orthologous relationships and chromosomal rearrangements were observed according to comparative mapping analysis with other species. Genome-wide expression analysis of bZIP genes indicated that 64 CsbZIP genes were differentially expressed in at least one of the ten sampled tissues. A total of 4 CsbZIP genes displayed higher expression values in leaf, flowers and root tissues. The in silico micro-RNA (miRNA) and target transcript analyses identified that a total of 21 CsbZIP genes were targeted by 38 plant miRNAs. CsbZIP20 and CsbZIP22 are the most targeted by miR165 and miR166 family members, respectively. We also analyzed the expression of ten CsbZIP genes in the root and leaf tissues of drought-stressed cucumber using quantitative RT-PCR. All of the selected CsbZIP genes were measured as increased in root tissue at 24th h upon PEG treatment. Contrarily, the down-regulation was observed in leaf tissues of all analyzed CsbZIP genes. CsbZIP12 and CsbZIP44 genes showed gradual induction of expression in root tissues during time points. This genome-wide identification and expression profiling provides new opportunities for cloning and functional analyses, which may be used in further studies for improving stress tolerance in plants.

Boron stress is an environmental factor affecting plant development and production. Recently, microRNAs (miRNAs) have been found to be involved in several plant processes such as growth regulation and stress responses. In this study, miRNAs associated with boron stress were identified and characterized in barley. miRNA profiles were also comparatively analyzed between root and leave samples. A total of 31 known and 3 new miRNAs were identified in barley; 25 of them were found to respond to boron treatment. Several miRNAs were expressed in a tissue specific manner; for example, miR156d, miR171a, miR397, and miR444a were only detected in leaves. Additionally, a total of 934 barley transcripts were found to be specifically targeted and degraded by miRNAs. In silico analysis of miRNA target genes demonstrated that many miRNA targets are conserved transcription factors such as Squamosa promoter-binding protein, Auxin response factor (ARF), and the MYB transcription factor family. A majority of these targets were responsible for plant growth and response to environmental changes. We also propose that some of the miRNAs in barley such as miRNA408 might play critical roles against boron exposure. In conclusion, barley may use several pathways and cellular processes targeted by miRNAs to cope with boron stress.

Peach (Prunus persica L.) is one of the most important worldwide fresh fruits. Since fruit growth largely depends on adequate water supply, drought stress is considered as the most important abiotic stress limiting fleshy fruit production and quality in peach. Plant responses to drought stress are regulated both at transcriptional and post-transcriptional level. As post-transcriptional gene regulators, miRNAs (miRNAs) are small (19-25 nucleotides in length), endogenous, non-coding RNAs. Recent studies indicate that miRNAs are involved in plant responses to drought. Therefore, Illumina deep sequencing technology was used for genome-wide identification of miRNAs and their expression profile in response to drought in peach. In this study, four sRNA libraries were constructed from leaf control (LC), leaf stress (LS), root control (RC) and root stress (RS) samples. We identified a total of 531, 471, 535 and 487 known mature miRNAs in LC, LS, RC and RS libraries, respectively. The expression level of 262 (104 up-regulated, 158 down-regulated) of the 453 miRNAs changed significantly in leaf tissue, whereas 368 (221 up-regulated, 147 down-regulated) of the 465 miRNAs had expression levels that changed significantly in root tissue upon drought stress. Additionally, a total of 197, 221, 238 and 265 novel miRNA precursor candidates were identified from LC, LS, RC and RS libraries, respectively. Target transcripts (137 for LC, 133 for LS, 148 for RC and 153 for RS) generated significant Gene Ontology (GO) terms related to DNA binding and catalytic activites. Genome-wide miRNA expression analysis of peach by deep sequencing approach helped to expand our understanding of miRNA function in response to drought stress in peach and Rosaceae. A set of differentially expressed miRNAs could pave the way for developing new strategies to alleviate the adverse effects of drought stress on plant growth and development. Citation: Eldem V, Celikkol Akcay U, Ozhuner E, Bakir Y, Uranbey S, et al. (2012) Genome-Wide Identification of miRNAs Responsive to Drought in Peach (Prunus persica) by High-Throughput Deep Sequencing. PLoS ONE 7(12): e50298. doi:10.1371/journal.pone.0050298

Alburnus tarichi is the only vertebrate species that can survive in Lake Van, the largest soda lake on Earth, which is characterized by extremely high pH and salinity. The circular mitogenomes of A. tarichi was 16,602 base pairs in size, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 major non-coding control regions (D-Loop and OL). Congurence was observed between the Alburnus mtDNAs in terms of genome organization, base composition, gene arrangement, and tRNA structure. Mitogenome sequences may be useful for conservation efforts of this endangered species.