Genomics最新文献

{"title":"Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer","authors":"Hao Chen ,&nbsp;Meizi Zeng ,&nbsp;Syeda Sundas Batool ,&nbsp;Yiming Zhao ,&nbsp;Zheng Yu ,&nbsp;Jumei Zhou ,&nbsp;Ke Liu ,&nbsp;Jing Huang","doi":"10.1016/j.ygeno.2024.110951","DOIUrl":"10.1016/j.ygeno.2024.110951","url":null,"abstract":"<div><div>Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110951"},"PeriodicalIF":3.4,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration analysis of transcriptome and metabolome revealed the potential mechanism of spermatogenesis in Tibetan sheep (Ovis aries) at extreme high altitude","authors":"Miaoshu Zhang ,&nbsp;Xuejiao An ,&nbsp;Chao Yuan ,&nbsp;Tingting Guo ,&nbsp;Binpeng Xi ,&nbsp;Jianbin Liu ,&nbsp;Zengkui Lu","doi":"10.1016/j.ygeno.2024.110949","DOIUrl":"10.1016/j.ygeno.2024.110949","url":null,"abstract":"<div><div>Testis has an indispensable function in male reproduction of domestic animals. Numerous genes and metabolites were related to testicular development and spermatogenesis. However, little is known about the biological regulation pathways associated with fecundity in male Tibetan sheep. In this study, Testes were collected from Huoba Tibetan sheep (HB, 4614 m) and Gangba Tibetan sheep (GB, 4401 m) at extreme high altitude, and Alpine Merino sheep (AM, 2500 m, control group) at medium-high altitude, investigating the genes and metabolites levels of them. The histological analysis of testicular tissue using hematoxylin-eosin (HE) staining was performed for Tibetan sheep and Alpine Merino sheep, and the testes of them were analyzed by transcriptomics and metabolomics to explore the potential mechanism of testicular development and spermatogenesis. The statistical results showed that the cross-sectional area of testicular seminiferous tubules, diameter of seminiferous tubules, and spermatogenic epithelium thickness were significantly smaller in HB and GB than in AM (<em>P</em> &lt; 0.05). Overall, 5648 differentially expressed genes (DEGs) and 336 differential metabolites (DMs) were identified in three sheep breeds, which were significantly enriched in spermatogenesis and other related pathways. According to integrated metabolomic and transcriptomic analysis, glycolysis/gluconeogenesis, AMPK signaling pathway, and TCA cycle, were predicted to have dramatic effects on the spermatogenesis of Tibetan sheep. Several genes (including <em>Wnt2</em>, <em>Rab3a</em>, <em>Sox9</em>, <em>Hspa8</em>, and <em>Slc38a2</em>) and metabolites (including L-histidinol, Glucose, Fumaric acid, Malic acid, and Galactose) were significantly enriched in pathways related to testicular development and spermatogenesis, and might affect the reproduction of Tibetan sheep by regulating the acrosome reaction, meiotic gene expression, and the production of sex hormones. Our results provide further understanding of the key genes and metabolites involved in testicular development and spermatogenesis in Tibetan sheep.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110949"},"PeriodicalIF":3.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of genetic evolutionary differences among four Tibetan pig populations in China","authors":"Yiting Yang ,&nbsp;Mailin Gan ,&nbsp;Chengming Liu ,&nbsp;Zhongwei Xie ,&nbsp;Meng Wang ,&nbsp;Chengpeng Zhou ,&nbsp;Wenqiang Cheng ,&nbsp;Lei Chen ,&nbsp;Shunhua Zhang ,&nbsp;Ye Zhao ,&nbsp;Lili Niu ,&nbsp;Yan Wang ,&nbsp;Jingyong Wang ,&nbsp;Linyuan Shen ,&nbsp;Li Zhu","doi":"10.1016/j.ygeno.2024.110950","DOIUrl":"10.1016/j.ygeno.2024.110950","url":null,"abstract":"<div><div>Tibetan pigs are a locally bred domestic pig breed originating from the Tibetan Plateau in China. They can be categorized into four distinct groups based on their geographical locations: Sichuan Tibetan pigs, Tibetan pigs from Tibet, Yunnan Tibetan pigs, and Gansu Tibetan pigs. This study aimed to explore population diversity, genetic structure and selection signals among Tibetan pigs in four Chinese national nature reserves. The results show that there is different observed heterozygosity among Tibetan pig populations (0.1957–0.1978). Ratio of runs of homozygosity (F_roh) calculation of four Tibetan pig populations by runs of homozygosity (ROH) revealed the presence of inbreeding within the population (0.0336–0.0378). Analysis of the genetic structure demonstrated distinct population stratification among the four Tibetan pig populations, with each showing relatively independent evolutionary directions. Furthermore, Five methods (FST, Piratio, ROD, Tajima's D, XP-CLR) were used to artificially select evolutionary trajectories. The results mainly involved processes such as DNA repair, immune regulation, muscle fat deposition and adaptation to hypoxia. In conclusion, this study enhances our understanding of the genetic characteristics of Tibetan pig populations and provides a theoretical reference for the conservation of resources across different populations of Tibetan pigs.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110950"},"PeriodicalIF":3.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptome analysis and identification of candidate bZIP transcription factors involved in anthraquinone biosynthesis in Rheum officinale Baill","authors":"Jing Tang ,&nbsp;Yi-min Li ,&nbsp;Yan Wang ,&nbsp;Feng Yan ,&nbsp;Zhao Feng ,&nbsp;Rui-hua LV ,&nbsp;Jing Gao ,&nbsp;Liang Peng ,&nbsp;Xiao-chen Hu ,&nbsp;Gang Zhang","doi":"10.1016/j.ygeno.2024.110948","DOIUrl":"10.1016/j.ygeno.2024.110948","url":null,"abstract":"<div><div>Rhubarb is a traditional medicinal plant in China, whose pharmacological effects derive mainly from its anthraquinones. However, the regulatory mechanism affecting anthraquinone biosynthesis in <em>R. officinale</em> remains poorly understood. We assembled a high-quality, full-length transcriptome using single-molecule real-time (SMRT) sequencing. 274 unigenes potentially involved in the biosynthesis of anthraquinones, including those in the shikimate, polyketide, MVA and MEP pathways, were identified based on full-length transcriptome. Differentially expressed genes (DEGs) induced by MeJA treatment and DEGs between different tissues were identified through next-generation sequencing (NGS), revealing the genes that may be involved in the biosynthesis of anthraquinones. The basic leucine zipper (bZIP) transcription factors of <em>R. officinale</em> were systematically identified. Key genes such as <em>RobZIP50</em> and <em>RobZIP53</em> were systematically identified and found to be associated with anthraquinone biosynthesis in <em>R. officinale</em> through differential expression, co-expression and protein interaction analyses. <em>RobZIP50</em> and <em>RobZIP53</em> were highly expressed in roots and rhizomes, and significantly increased after 12 h of MeJA treatment. Additionally, both RobZIP50 and RobZIP53 were localized exclusively in the nucleus, with RobZIP53 showing significant transcriptional activity. Taken together, our results suggest that RobZIP53 may play a role in regulating anthraquinone biosynthesis in <em>R. officinale</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110948"},"PeriodicalIF":3.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The molecular regulated mechanism of METTL3 and FTO in lipid metabolism of Hu sheep","authors":"Bowen Chen ,&nbsp;Chao Yuan ,&nbsp;Tingting Guo ,&nbsp;Jianbin Liu ,&nbsp;Bohui Yang ,&nbsp;Zengkui Lu","doi":"10.1016/j.ygeno.2024.110945","DOIUrl":"10.1016/j.ygeno.2024.110945","url":null,"abstract":"<div><h3>Background</h3><div>Balanced lipid metabolism can improve the growth performance and meat quality of livestock. The m6A methylation-related genes <em>METTL3</em> and <em>FTO</em> play important roles in animal lipid metabolism; however, the mechanism through which they regulate lipid metabolism in sheep is unclear.</div></div><div><h3>Results</h3><div>We established lipid deposition models of hepatocytes and preadipocytes in Hu sheep. In the hepatocyte lipid deposition model, the genes expression levels of <em>FABP4</em>, Accα, <em>ATGL</em> and <em>METTL3</em>, <em>METTL14</em>, and <em>FTO</em>—were significantly up-regulated after lipid deposition (<em>P</em> &lt; 0.05). Transcriptomic and metabolomic analyses showed that lipid deposition had a significant effect on MAPK, steroid biosynthesis, and glycerophospholipid metabolism pathway in hepatocytes. The m6A methylation level decreased but the difference was not significant after <em>METTL3</em> interference, and the expression levels of <em>FABP4</em> and <em>ATGL</em> increased significantly (<em>P</em> &lt; 0.05); the m6A methylation level significantly increased following <em>METTL3</em> overexpression, and <em>LPL</em> and <em>ATGL</em> expression levels significantly decreased (<em>P</em> &lt; 0.05), indicating that overexpression of <em>METTL3</em> inhibited the expression of lipid deposition-related genes in a m6A-dependent manner. The m6A methylation level was significantly increased, <em>ATGL</em> expression was significantly decreased (<em>P</em> &lt; 0.05), and <em>LPL</em>, <em>FABP4</em>, and <em>Accα</em> expression was not significantly changed following <em>FTO</em> interference (<em>P</em> &gt; 0.05); the m6A methylation level was significantly decreased after <em>FTO</em> overexpression, and <em>LPL</em>, <em>FABP4</em>, and <em>ATGL</em> expression was significantly increased (<em>P</em> &lt; 0.05), indicating that <em>FTO</em> overexpression increased the expression of lipid deposition-related genes in a m6A-dependent manner. Transcriptomic and metabolomic analyses showed that m6A methylation modification mainly regulated lipid metabolism through triglyceride metabolism, adipocytokine signaling, MAPK signaling, and fat digestion and absorption in hepatocytes. In the lipid deposition model of preadipocytes, the regulation of gene expression is the same as that in hepatocytes.</div></div><div><h3>Conclusions</h3><div><em>METTL3</em> significantly inhibited the expression of lipid deposition-related genes, whereas <em>FTO</em> overexpression promoted lipid deposition. Our study provides a theoretical basis and reference for accurately regulating animal lipid deposition by mastering <em>METTL3</em> and <em>FTO</em> genes to promote high-quality animal husbandry.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110945"},"PeriodicalIF":3.4,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Definition of regulatory elements and transcription factors controlling porcine immune cell gene expression at single cell resolution using single nucleus ATAC-seq","authors":"Pengxin Yang ,&nbsp;Ryan Corbett ,&nbsp;Lance Daharsh ,&nbsp;Juber Herrera Uribe ,&nbsp;Kristen A. Byrne ,&nbsp;Crystal L. Loving ,&nbsp;Christopher Tuggle","doi":"10.1016/j.ygeno.2024.110944","DOIUrl":"10.1016/j.ygeno.2024.110944","url":null,"abstract":"<div><div>The transcriptome of porcine peripheral blood mononuclear cells (PBMC) at single cell (sc) resolution is well described, but little is understood about the cis-regulatory mechanism behind scPBMC gene expression. Here, we profiled the open chromatin landscape of porcine PBMC that define cis-regulatory elements and mechanism contributing to the transcription using single nucleus ATAC sequencing (snATAC-seq). Approximately 22 % of the identified peaks overlapped with annotated transcription start sites (TSS). Using clustering based on open chromatin pattern similarity, we demonstrate that cell type annotations using snATAC-seq are highly concordant to that reported for sc RNA sequencing (scRNA-seq). The differentially accessible peaks (DAPs) for each cell type were characterized and the pattern of accessibility of the DAPs near cell type markers across cell types was similar to that of the average gene expression level of corresponding marker genes. Additionally, we found that peaks identified in snATAC-seq have the potential power to predict the cell type specific transcription starting site (TSS). We identified both transcription factors (TFs) whose binding motif were enriched in cell type DAPs of multiple cell types and cell type specific TFs by conducting transcription factor binding motif (TFBM) analysis. Furthermore, we identified the putative enhancer or promoter regions bound by TFs for each differentially expressed gene (DEG) with a DAP that overlapped with its TSS by generating cis-co-accessibility networks (CCAN). To predict the regulators of such DEGs, TFBM analysis was performed for each CCAN. The regulator TF-target DEG pairs predicted in this way were largely consistent with the results reported in the ENCODE Transcription Factor Targets Dataset (TFTD). This snATAC-seq approach provides insights into the regulation of chromatin accessibility landscape of porcine PBMCs and enables discovery of TFs predicted to control DEG through binding regulatory elements whose chromatin accessibility correlates with the DEG promoter region.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110944"},"PeriodicalIF":3.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Key role of CYP17A1 in Leydig cell function and testicular development in Qianbei Ma goats.","authors":"Tang Wen, Zhang Yuan, Wang Zhong, Guo Wei, Chen Jiajing, Ji Quan, Wang Yanfei, Li Ruiyang, Xu Houqiang, Chen Xiang","doi":"10.1016/j.ygeno.2024.110937","DOIUrl":"10.1016/j.ygeno.2024.110937","url":null,"abstract":"<p><p>Reproductive traits are vital economic parameters in goat production, and boosting the reproductive capacity of breeding rams is crucial for enhancing the profitability of goat farming. Currently, research on the reproductive performance of Qianbei Ma goats mainly centers on investigating mechanisms associated with prolificacy and estrous ovulation in ewes, with limited emphasis on ram reproductive aspects. This study used scanning electron microscopy and enzyme-linked immunosorbent assay (ELISA) to profile the morphology of testis and the dynamic changes of Luteinizing Hormone (LH), Follicle-Stimulating Hormone (FSH), and Testosterone (T) in serum at different developmental stages of Qianbei Ma goats. Meanwhile, transcriptome sequencing technology was used to investigate the mRNA expression patterns in testicular tissues at different developmental stages: newborn (0 M), puberty (6 M), sexual maturity (12 M), and physical maturity (18 M). The results showed that the diameter, circumference, and area of the testicular seminiferous tubules gradually increased with age. The levels of T and LH in serum significantly increased from 0 to 6 months after birth (p < 0.05), followed by a stabilization of T levels and a significant decrease in LH levels (p < 0.05). Meanwhile, FSH shows a decreasing trend between 0 and 18 months after birth. A total of 26,437 differentially expressed genes were identified in 6 comparison groups, which involve various biological processes such as immunity, growth, metabolism, development, and reproduction, and are significantly enriched in signaling pathways related to testicular development and spermatogenesis. WGCNA analysis identified 6 regions significantly associated with testicular development and spermatogenesis, and selected 320 genes for constructing a PPI network. Ten candidate genes related to testicular development and spermatogenesis were identified, including TP53, PLK4, RPS9, PFN4, ACTB, CYP17A1, GPX4, CLDN1, AMH and DHH. Of these, the CYP17A1 gene promotes interstitial cell proliferation, and promotes T synthesis. This study provides a theoretical basis and data support for promoting efficient breeding of goats and early breeding of excellent male goats.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110937"},"PeriodicalIF":3.4,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome resequencing and RNA-seq analysis implicates GPR75 as a potential genetic basis related to retarded growth in South China carp (Cyprinus carpio rubrofuscus)","authors":"Zaixuan Zhong ,&nbsp;Jiajia Fan ,&nbsp;Yuanyuan Tian ,&nbsp;Minhui Lin ,&nbsp;Huaping Zhu ,&nbsp;Dongmei Ma","doi":"10.1016/j.ygeno.2024.110934","DOIUrl":"10.1016/j.ygeno.2024.110934","url":null,"abstract":"<div><div>The south China carp (<em>Cyprinus carpio rubrofuscus</em>) is an indigenous and important fish species, widely cultured in south China. However, part of individuals experienced retarded growth, the genetic basis of which has yet to be elucidated. In this study, whole-genome resequencing of 35 fast-growing and 35 retarded-growing south China carp were conducted to identify promising genes associated with retarded growth. Twelve candidate SNPs were detected and annotated to the <em>Gpr75</em> gene, which has been reported to be related with body weight through regulating insulin homeostasis. RNA-seq analysis of muscle suggested that differentially expressed genes were significantly enriched in the insulin signaling pathway. Additionally, the fasting serum insulin level was significantly lower while the blood glucose level was significantly higher in the retarded-growing group. Our preliminary study provides insights into the genetic basis underlying the retarded growth and may facilitate further genetic improvement of south China carp.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110934"},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001551/pdfft?md5=4c7052715cbf8b411b873ffe9df72f49&pid=1-s2.0-S0888754324001551-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper","authors":"Julie Blommaert ,&nbsp;Jonathan Sandoval-Castillo ,&nbsp;Luciano B. Beheregaray ,&nbsp;Maren Wellenreuther","doi":"10.1016/j.ygeno.2024.110929","DOIUrl":"10.1016/j.ygeno.2024.110929","url":null,"abstract":"<div><p>Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (<em>Chrysophrys auratus</em>). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110929"},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001502/pdfft?md5=ee0dd278a894eb470d4f5bad6982cefa&pid=1-s2.0-S0888754324001502-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow–Bohai seas","authors":"Yushun Yong ,&nbsp;Shunxin Hu ,&nbsp;Mingyu Zhong ,&nbsp;Yun Wen ,&nbsp;Yue Zhou ,&nbsp;Ruixue Ma ,&nbsp;Xiangyang Jiang ,&nbsp;Quansheng Zhang","doi":"10.1016/j.ygeno.2024.110940","DOIUrl":"10.1016/j.ygeno.2024.110940","url":null,"abstract":"<div><div>Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of <em>Ruppia sinensis</em> were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of <em>cp-rpl19</em> genes in Zosteraceae, most <em>cp-ndh</em> genes in Hydrocharitaceae, and <em>mt-rpl</em> and <em>mt-rps</em> genes in all seagrasses, except for the <em>mt-rpl16</em> gene in <em>Phyllospadix iwatensis</em>. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of <em>Zostera</em> containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in <em>R. sinensis</em>. Moreover, four positively selected genes (<em>atp8</em>, <em>nad5</em>, <em>atp4</em>, and <em>ccmFn</em>) and five variable regions (<em>matR</em>, <em>atp4</em>, <em>atp8</em>, <em>rps7</em>, and <em>ccmFn</em>) were identified.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 5","pages":"Article 110940"},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001617/pdfft?md5=a51dacc1d10603ce7d6a0dd7945a1a21&pid=1-s2.0-S0888754324001617-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}