Genomics最新文献

{"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":"Multiomics reveals blood differential metabolites and differential genes in the early onset of ketosis in dairy cows","authors":"Sha Ping ,&nbsp;Ma Xuehu ,&nbsp;Hu Chunli,&nbsp;Feng Xue,&nbsp;An Yanhao,&nbsp;Ma Yun,&nbsp;Ma Yanfen","doi":"10.1016/j.ygeno.2024.110927","DOIUrl":"10.1016/j.ygeno.2024.110927","url":null,"abstract":"<div><p>Ketosis—a metabolic state characterized by elevated levels of ketone bodies in the blood or urine—reduces the performance and health of dairy cows and causes substantial economic losses for the dairy industry. Currently, beta-hydroxybutyric acid is the gold standard for determining ketosis in cows; however, as this method is only applicable postpartum, it is not conducive to the early intervention of ketosis in dairy cows. In this study, the sera of dry, periparturient, postpartum ketotic, and healthy cows were analyzed by both transcriptomics and metabolomics techniques. Moreover, changes of gene expression and metabolites were observed, and serum physiological and biochemical indexes were detected by ELISA. The purpose was to screen biomarkers that can be used to detect the incidence of dry or periparturient ketosis in cows. The results showed that ketotic cows had increased levels of glycolipid metabolism indexes, oxidizing factors, and inflammatory factors during dry periods and liver damage, which could be used as early biomarkers to predict the onset of ketosis. Transcriptomic results yielded 20 differentially expressed genes (DEGs) between ketotic and healthy cows during dry, peripartum, and postpartum periods. GO and KEGG enrichment analyses indicated that these DEGs were involved in amino acid metabolism, energy metabolism, and disease-related signaling pathways. The metabolomics sequencing results showed that ketotic cows mainly showed enrichment in tricarboxylic acid cycle, butyric acid metabolism, carbon metabolism, lysine degradation, fatty acid degradation, and other signaling pathways. Metabolites differed between ketotic and healthy cows in dry, pre-parturition, and post-parturition periods. Combined transcriptomics and metabolomics analyses identified significant enrichment in the glucagon signaling pathway and the lysine degradation signaling pathway in dry, periparturient, and postpartum ketotic cows. PRKAB2 and SETMAR—key DEGs of the glucagon signaling pathway and lysine degradation signaling pathway, respectively—can be used as key marker genes for determining the early onset of ketosis in dairy cows.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001484/pdfft?md5=f2af94bc739c0e96aa8aa24e6438e6cd&pid=1-s2.0-S0888754324001484-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142072452","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":"STRIP2 is regulated by the transcription factor Sp1 and promotes lung adenocarcinoma progression via activating the PI3K/AKT/mTOR/MYC signaling pathway","authors":"Junfan Pan ,&nbsp;Yuan Zhang ,&nbsp;Liu He ,&nbsp;Yue Wu ,&nbsp;Weijin Xiao ,&nbsp;Jing Zhang ,&nbsp;Yiquan Xu","doi":"10.1016/j.ygeno.2024.110923","DOIUrl":"10.1016/j.ygeno.2024.110923","url":null,"abstract":"<div><h3>Background</h3><p>Patients with lung adenocarcinoma (LUAD) generally have poor prognosis. The role of striatin-interacting protein 2 (STRIP2) in LUAD remain unclear.</p></div><div><h3>Methods</h3><p>Liquid chromatography-mass spectrometry analyses were used to screen the STRIP2-binding proteins and co-immunoprecipitation verified these interactions. A dual luciferase reporter assay explored the transcription factor activating STRIP2 transcription. Xenograft and lung metastasis models assessed STRIP2's role in tumor growth and metastasis <em>in vivo</em>.</p></div><div><h3>Results</h3><p>STRIP2 is highly expressed in LUAD tissues and is linked to poor prognosis. STRIP2 expression in LUAD cells significantly promoted cell proliferation, invasion, and migration <em>in vitro</em> and <em>in vivo</em>. Mechanistically, STRIP2 boosted the PI3K/AKT/mTOR/MYC cascades by binding AKT. In addition, specificity protein 1, potently activated STRIP2 transcription by binding to the STRIP2 promoter. Blocking STRIP2 reduces tumor growth and lung metastasis in xenograft models.</p></div><div><h3>Conclusions</h3><p>Our study identifies STRIP2 is a key driver of LUAD progression and a potential therapeutic target.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001447/pdfft?md5=fb3dd61a38bea2281d1d30458eab77d1&pid=1-s2.0-S0888754324001447-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142079945","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":null,"pages":null},"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":null,"pages":null},"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}

{"title":"Whole-genome sequence of Sclerotium delphinii, a pathogenic fungus of Dendrobium officinale southern blight","authors":"Yu-Jie Chen ,&nbsp;Qiao Liu ,&nbsp;Yong-Jing Zhang,&nbsp;Zhi-Li Jiang,&nbsp;Hai-Lan Fu,&nbsp;Hui Wu,&nbsp;Ming-Jie Liu,&nbsp;Ji-Hong Jiang,&nbsp;Lu-Dan Li","doi":"10.1016/j.ygeno.2024.110932","DOIUrl":"10.1016/j.ygeno.2024.110932","url":null,"abstract":"<div><p><em>Dendrobium officinale</em> is a rare and precious medicinal plant. Southern blight is a destructive disease in the artificial cultivation of <em>D. officinale</em>, and one of its pathogens is <em>Sclerotium delphinii</em>. <em>S. delphinii</em> is a phytopathogenic fungus with a wide host range with extremely strong pathogenicity. In this study, <em>S. delphinii</em> was isolated from <em>D. officinale</em> with southern blight. Subsequently, this specific strain underwent thorough whole-genome sequencing using the PacBio Sequel II platform, which employed single-molecule real-time (SMRT) technology. Comprehensive annotations were obtained through functional annotation of protein sequences using various publicly available databases. The genome of <em>S. delphinii</em> measures 73.66 Mb, with an N90 contig size of 2,707,110 bp, and it contains 18,506 putative predictive genes. This study represents the first report on the genome size assembly and annotation of <em>S. delphinii</em>, making it the initial species within the <em>Sclerotium</em> genus to undergo whole-genome sequencing, which can provide solid data and a theoretical basis for further research on the pathogenesis, omics of <em>S. delphinii</em>.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001538/pdfft?md5=bbf26dfea948a36db04297732ebddada&pid=1-s2.0-S0888754324001538-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142096758","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":"Structural analysis of the mitochondrial genome of Santalum album reveals a complex branched configuration","authors":"Guang-Hua Liu ,&nbsp;You-Wei Zuo ,&nbsp;Yuanyu Shan ,&nbsp;Jie Yu ,&nbsp;Jia-Xi Li ,&nbsp;Ying Chen ,&nbsp;Xin-Yi Gong ,&nbsp;Xiao-Min Liao","doi":"10.1016/j.ygeno.2024.110935","DOIUrl":"10.1016/j.ygeno.2024.110935","url":null,"abstract":"<div><h3>Background</h3><p><em>Santalum album</em> L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value.</p></div><div><h3>Results</h3><p>In this study, the complete mitochondrial genome of <em>S. album</em> were assembled and annotated, which could be descried by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in <em>S. album</em> mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52 % of the plastome, 6.37 % of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between <em>S. album</em> and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between <em>S. album</em> and other angiosperms.</p></div><div><h3>Conclusions</h3><p>We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001563/pdfft?md5=f8c9aae391b32e116113b9fb2e29933f&pid=1-s2.0-S0888754324001563-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145519","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}