Genomics最新文献

{"title":"A systematic comparison of natural product potential, with an emphasis on RiPPs, by Mining of Bacteria of three large ecosystems","authors":"Yunhai Yi ,&nbsp;Lifeng Liang ,&nbsp;Anne de Jong ,&nbsp;Oscar P. Kuipers","doi":"10.1016/j.ygeno.2024.110880","DOIUrl":"10.1016/j.ygeno.2024.110880","url":null,"abstract":"<div><p>The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001010/pdf?md5=5014b7315893fc3280940055e17b776b&pid=1-s2.0-S0888754324001010-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300433","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 metabolomics and transcriptomics analyses provide insights into branching changes induced by heterografting in Pinus massoniana seedlings","authors":"Feng Xiao ,&nbsp;Yayan Zhu ,&nbsp;Yao Yang ,&nbsp;Xiurong Wang ,&nbsp;Xueyan Jian ,&nbsp;Yang Zhao","doi":"10.1016/j.ygeno.2024.110882","DOIUrl":"10.1016/j.ygeno.2024.110882","url":null,"abstract":"<div><p>The investigation of dwarfing rootstocks for the establishment of high-generation seed orchards is a prospective avenue of research. In this investigation, <em>Pinus massoniana</em>, <em>Pinus yunnanensis</em> var. <em>pygmaea</em> (<em>P. pygmaea</em>), and <em>P. elliottii</em> seedlings were used as rootstocks for grafting with <em>P. massoniana</em> scions. Grafting <em>P. massoniana</em> onto <em>P. pygmaea</em> rootstock resulted in observable phenotypic alterations in lateral branches, apical buds, and needle length. Certain characteristic metabolites of rootstocks, such as fatty acyls, pregnenolones, steroids, and steroid derivatives, were found to be highly expressed in scions after grafting. RNA-seq analysis revealed <em>MYB-related</em>, <em>SBP</em>, and <em>bHLH</em> demonstrating a significant positive correlation, while <em>C2H2</em> and <em>Orphans</em> exhibited negative correlations with the differential intensity of metabolites related to lipids and lipid-like molecules. This study offers valuable insights for the establishment of rootstock breeding programs.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001034/pdfft?md5=b710119b88ddae2f7361de19428972b3&pid=1-s2.0-S0888754324001034-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300434","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":"Transcriptome and metabolome analyses reveal chlorogenic acid accumulation in pigmented potatoes at different altitudes","authors":"Qiu-Ju Dong,&nbsp;Xiao-Yu Xu,&nbsp;Cai-Xia Fan,&nbsp;Ji-Ping Xiao","doi":"10.1016/j.ygeno.2024.110883","DOIUrl":"10.1016/j.ygeno.2024.110883","url":null,"abstract":"<div><p>Pigmented potato tubers are abundant in chlorogenic acids (CGAs), a metabolite with pharmacological activity. This article comprehensively analyzed the transcriptome and metabolome of pigmented potato Huaxingyangyu and Jianchuanhong at four altitudes of 1800 m, 2300 m, 2800 m, and 3300 m. A total of 20 CGAs and intermediate CGA compounds were identified, including 3-o-caffeoylquinic acid, 4-o-caffeoylquinic acid, and 5-o-caffeoylquinic acid. CGA contents in Huaxinyangyu and Jianchuanhong reached its maximum at an altitude of 2800 m and slightly decreased at 3300 m. 48 candidate genes related to the biosynthesis pathway of CGAs were screened through transcriptome analysis. Weighted gene co-expression network analysis (WGCNA) identified that the structural genes of phenylalanine deaminase <em>(PAL),</em> coumarate-3 hydroxylase <em>(C3H),</em> cinnamic acid 4-hydroxylase <em>(C4H)</em> and the transcription factors of MYB and bHLH co-regulate CGA biosynthesis. The results of this study provide valuable information to reveal the changes in CGA components in pigmented potato at different altitudes.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001046/pdfft?md5=7e616c69140258b9a44765b5295f125a&pid=1-s2.0-S0888754324001046-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300435","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":"Comprehensive analysis of circRNA-miRNA-mRNA regulatory network and novel potential biomarkers in eutopic endometrium of adenomyosis","authors":"Zhengchen Guo ,&nbsp;Qi Lin ,&nbsp;Yanan Chang ,&nbsp;Yuanyuan An ,&nbsp;Hua Duan","doi":"10.1016/j.ygeno.2024.110877","DOIUrl":"10.1016/j.ygeno.2024.110877","url":null,"abstract":"<div><p>Adenomyosis (ADS) is a common gynecological disorder, and its pathogenesis remains unclear. This study explores the functions of circRNAs in the eutopic endometrium of ADS and their diagnostic efficacy for ADS. High-throughput RNA sequencing was performed on 12 eutopic endometrial samples from ADS patients and 3 control endometrial samples. Additionally, circRNAs were analyzed in conjunction with clinical features. A competitive endogenous RNA network was established based on bioinformatics analysis, comprising 3 circRNAs, 1 miRNA, and 13 mRNAs. In the ADS group, the expression levels of hsa_circ_0008959 and SLC15A4 were significantly reduced, while hsa-miR-124-3p expression was increased. SLC15A4 was associated with cell proliferation and invasion. Decreased expression of hsa_circ_0008959 and SLC15A4, along with high VAS scores and elevated hsa-miR-124-3p levels, were identified as risk factors for ADS development. The combination of hsa_circ_0008959 and VAS scores demonstrated the highest diagnostic value for ADS.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000983/pdfft?md5=e832701764e4ff63e50a13f3decc6188&pid=1-s2.0-S0888754324000983-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141295889","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":"Comprehensive analysis of differentially expressed mRNAs, circRNAs, and miRNAs and their ceRNA network in the testis of cattle–yak, yak, and cattle","authors":"Mengli Cao ,&nbsp;Lin Xiong ,&nbsp;Xingdong Wang ,&nbsp;Shaoke Guo ,&nbsp;Liyan Hu ,&nbsp;Yandong Kang ,&nbsp;Xiaoyu Wu ,&nbsp;Pengjia Bao ,&nbsp;Min Chu ,&nbsp;Chunnian Liang ,&nbsp;Jie Pei ,&nbsp;Xian Guo","doi":"10.1016/j.ygeno.2024.110872","DOIUrl":"10.1016/j.ygeno.2024.110872","url":null,"abstract":"<div><p>Cattle–yak is a hybrid offspring resulting from the crossbreeding of yak and cattle, and it exhibits substantial heterosis in production performance. However, male sterility in cattle–yak remains a concern. Reports suggest that noncoding RNAs are involved in the regulation of spermatogenesis. Therefore, in this study, we comprehensively compared testicular transcription profiles among cattle, yak, and cattle–yak. Numerous differentially expressed genes (DEGs), differentially expressed circRNAs (DECs), and differentially expressed miRNAs (DEMs) were identified in the intersection of two comparison groups, namely cattle versus cattle–yak and yak versus cattle–yak, with the number of DEGs, DECs, and DEMs being 4968, 360, and 59, respectively. The DEGs in cattle–yaks, cattle, and yaks were mainly associated with spermatogenesis, male gamete generation, and sexual reproduction. Concurrently, GO and KEGG analyses indicated that DEC host genes and DEM source genes were involved in the regulation of spermatogenesis. The construction of a potential competing endogenous RNA network revealed that some differentially expressed noncoding RNAs may be involved in regulating the expression of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, and miR-15b, as well as previously unreported miR-6123 and miR-1306, along with various miRNA–circRNA interaction pairs. This study serves as a valuable reference for further investigations into the mechanisms underlying male sterility in cattle–yaks.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000934/pdfft?md5=c76db2348bd7bb333bad9967516e5fbe&pid=1-s2.0-S0888754324000934-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288002","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":"Transcriptomic responses of peripheral blood leukocytes to cardiac surgery after acute inflammation, and three months recovery","authors":"Eric A. Lewallen ,&nbsp;Da Liu ,&nbsp;Jake Karwoski ,&nbsp;Wilson Y. Szeto ,&nbsp;Andre J. van Wijnen ,&nbsp;Krzysztof Laudanski","doi":"10.1016/j.ygeno.2024.110878","DOIUrl":"10.1016/j.ygeno.2024.110878","url":null,"abstract":"<div><p>Traumatic perioperative conditions may trigger early systemic responses, activate leukocytes and reprogram the immune system. We hypothesize that leukocyte activation may not revert to pre-surgical states, and that protracted activation may emerge with increased risks of comorbidities. We tested this concept by examining the transcriptomes of monocytes and T cells in a representative observational cohort of patients (<em>n</em> = 13) admitted for elective cardiac surgery. Transcriptomes in T cells and monocytes were compared from before surgery (t₀), and monocytes were analyzed longitudinally after acute (t_24hr), and convalescent (t_3m) time points. Monocytes and T cells expressed distinct transcriptomes, reflected by statistically significant differential expression of 558 T cell related genes. Monocytes expressed genes related to protein degradation and presented atypical activation of surface markers and cytoplasmic functions over time. Additionally, monocytes exhibited limited transcriptomic heterogeneity prior to surgery, and long-term patterns of gene expression associated with atherosclerosis showed three temporally distinct signatures. These data establish that post-cardiac surgery transcriptomes of monocytes differ even at three months compared to baselines, which may reflect latent (‘smoldering’) inflammation and persistent progression of tissue degenerative processes that should inform clinical care.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000995/pdfft?md5=a5b2c12cccfc9e240403fae674871ae2&pid=1-s2.0-S0888754324000995-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293315","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":"Apoptosis and NETotic cell death affect diabetic nephropathy independently: An study integrative study encompassing bioinformatics, machine learning, and experimental validation","authors":"Huilian Cai ,&nbsp;Yi Zeng ,&nbsp;Dongqiang Luo ,&nbsp;Ying Shao ,&nbsp;Manting Liu ,&nbsp;Jiayu Wu ,&nbsp;Xiaolu Gao ,&nbsp;Jiyuan Zheng ,&nbsp;Lisi Zhou ,&nbsp;Feng Liu","doi":"10.1016/j.ygeno.2024.110879","DOIUrl":"10.1016/j.ygeno.2024.110879","url":null,"abstract":"<div><h3>Objective</h3><p>Although programmed cell death (PCD) and diabetic nephropathy (DN) are intrinsically conneted, the interplay among various PCD forms remains elusive. In this study, We aimed at identifying independently DN-associated PCD pathways and biomarkers relevant to the related pathogenesis.</p></div><div><h3>Methods</h3><p>We acquired DN-related datasets from the GEO database and identified PCDs independently correlated with DN (DN-PCDs) through single-sample Gene Set Enrichment Analysis (ssGSEA) as well as, univariate and multivariate logistic regression analyses. Subsequently, applying differential expression analysis, weighted gene co-expression network analysis (WGCNA), and Mfuzz cluster analysis, we filtered the DN-PCDs pertinent to DN onset and progression. The convergence of various machine learning techniques ultimately spotlighted hub genes, substantiated through dataset meta-analyses and experimental validations, thereby confirming hub genes and related pathways expression consistencies.</p></div><div><h3>Results</h3><p>We harmonized four DN-related datasets (GSE1009, GSE142025, GSE30528, and GSE30529) post-batch-effect removal for subsequent analyses. Our differential expression analysis yielded 709 differentially expressed genes (DEGs), comprising 446 upregulated and 263 downregulated DEGs. Based on our ssGSEA as well as univariate and multivariate logistic regressions, apoptosis and NETotic cell death were appraised as independent risk factors for DN (Odds Ratio &gt; 1, <em>p</em> &lt; 0.05). Next, we further refined 588 apoptosis- and NETotic cell death-associated genes through WGCNA and Mfuzz analysis, resulting in the identification of 17 DN-PCDs. Integrating protein-protein interaction (PPI) network analyses, network topology, and machine learning, we pinpointed hub genes (e.g., IL33, RPL11, and CX3CR1) as significant DN risk factors with expression corroborating in subsequent meta-analyses and experimental validations. Our GSEA enrichment analysis discerned differential enrichments between DN and control samples within pathways such as IL2/STAT5, IL6/JAK/STAT3, TNF-α via NF-κB, apoptosis, and oxidative phosphorylation, with related proteins such as IL2, IL6, and TNFα, which we subsequently submitted to experimental verification.</p></div><div><h3>Conclusion</h3><p>Innovatively stemming from from PCD interactions, in this study, we discerned PCDs with an independent impact on DN: apoptosis and NETotic cell death. We further screened DN evolution- and progression-related biomarkers, i.e. IL33, RPL11, and CX3CR1, all of which we empirically validated. This study not only poroposes a PCD-centric perspective for DN studies but also provides evidence for PCD-mediated immune cell infiltration exploration in DN regulation. Our results could motivate further exploration of DN pathogenesis, such as how the inflammatory microenvironment mediates NETotic cell death in DN regulation, representing a promising direction for fu","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001009/pdfft?md5=648ec43a7700b1605e2b94b729fcb8d7&pid=1-s2.0-S0888754324001009-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293314","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":"Identifying MiR-140-3p as a stable internal reference to normalize MicroRNA qRT-PCR levels of plasma small extracellular vesicles in lung cancer patients","authors":"Yuan Jiang ,&nbsp;Weiwei Wang ,&nbsp;Faqing Tang ,&nbsp;Wei Zhang ,&nbsp;Sheng Chen ,&nbsp;Xiumei Gu ,&nbsp;Ping Chen ,&nbsp;Xiaoya Xu ,&nbsp;Baoning Nian ,&nbsp;Zhikuan Li ,&nbsp;Chunzhu Chen ,&nbsp;Hanbing Yin ,&nbsp;Linlin Su ,&nbsp;Honghou Sun ,&nbsp;Wei Chen ,&nbsp;Dadong Zhang ,&nbsp;Yuejin Li","doi":"10.1016/j.ygeno.2024.110875","DOIUrl":"10.1016/j.ygeno.2024.110875","url":null,"abstract":"<div><p>Exploration of a stably expressed gene as a reference is critical for the accurate evaluation of miRNAs isolated from small extracellular vesicles (sEVs). In this study, we analyzed small RNA sequencing on plasma sEV miRNAs in the training dataset (<em>n</em> = 104) and found that miR-140-3p was the most stably expressed candidate reference for sEV miRNAs. We further demonstrated that miR-140-3p expressed most stably in the validation cohort (<em>n</em> = 46) when compared to two other reference miRNAs, miR-451a and miR-1228-3p, and the commonly-used miRNA reference U6. Finally, we compared the capability of miR-140-3p and U6 as the internal reference for sEV miRNA expression by evaluating key miRNAs expression in lung cancer patients and found that miR-140-3p was more suitable as a sEV miRNA reference gene. Taken together, our data indicated miR-140-3p as a stable internal reference miRNA of plasma sEVs to evaluate miRNA expression profiles in lung cancer patients.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400096X/pdfft?md5=74e2661aed946c9deaaf4a5b18727d0e&pid=1-s2.0-S088875432400096X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288004","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":"Early detection and stratification of colorectal cancer using plasma cell-free DNA fragmentomic profiling","authors":"Jiyuan Zhou ,&nbsp;Yuanke Pan ,&nbsp;Shubing Wang ,&nbsp;Guoqiang Wang ,&nbsp;Chengxin Gu ,&nbsp;Jinxin Zhu ,&nbsp;Zhenlin Tan ,&nbsp;Qixian Wu ,&nbsp;Weihuang He ,&nbsp;Xiaohui Lin ,&nbsp;Shu Xu ,&nbsp;Kehua Yuan ,&nbsp;Ziwen Zheng ,&nbsp;Xiaoqing Gong ,&nbsp;Chenhao JiangHe ,&nbsp;Zhoujian Han ,&nbsp;Bingding Huang ,&nbsp;Ruyun Ruan ,&nbsp;Mingji Feng ,&nbsp;Pin Cui ,&nbsp;Hui Yang","doi":"10.1016/j.ygeno.2024.110876","DOIUrl":"10.1016/j.ygeno.2024.110876","url":null,"abstract":"<div><p>Timely accurate and cost-efficient detection of colorectal cancer (CRC) is of great clinical importance. This study aims to establish prediction models for detecting CRC using plasma cell-free DNA (cfDNA) fragmentomic features. Whole-genome sequencing (WGS) was performed on cfDNA from 620 participants, including healthy individuals, patients with benign colorectal diseases and CRC patients. Using WGS data, three machine learning methods were compared to build prediction models for the stratification of CRC patients. The optimal model to discriminate CRC patients of all stages from healthy individuals achieved a sensitivity of 92.31% and a specificity of 91.14%, while the model to separate early-stage CRC patients (stage 0-II) from healthy individuals achieved a sensitivity of 88.8% and a specificity of 96.2%. Additionally, the cfDNA fragmentation profiles reflected disease-specific genomic alterations in CRC. Overall, this study suggests that cfDNA fragmentation profiles may potentially become a noninvasive approach for the detection and stratification of CRC.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000971/pdfft?md5=9215668aa701ceca2567affa9cc981f2&pid=1-s2.0-S0888754324000971-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288003","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":"Cost-effective genomic prediction of critical economic traits in sturgeons through low-coverage sequencing","authors":"Hailiang Song ,&nbsp;Tian Dong ,&nbsp;Wei Wang ,&nbsp;Boyun Jiang ,&nbsp;Xiaoyu Yan ,&nbsp;Chenfan Geng ,&nbsp;Song Bai ,&nbsp;Shijian Xu ,&nbsp;Hongxia Hu","doi":"10.1016/j.ygeno.2024.110874","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110874","url":null,"abstract":"<div><p>Low-coverage whole-genome sequencing (LCS) offers a cost-effective alternative for sturgeon breeding, especially given the lack of SNP chips and the high costs associated with whole-genome sequencing. In this study, the efficiency of LCS for genotype imputation and genomic prediction was assessed in 643 sequenced Russian sturgeons (∼13.68×). The results showed that using BaseVar+STITCH at a sequencing depth of 2× with a sample size larger than 300 resulted in the highest genotyping accuracy. In addition, when the sequencing depth reached 0.5× and SNP density was reduced to 50 K through linkage disequilibrium pruning, the prediction accuracy was comparable to that of whole sequencing depth. Furthermore, an incremental feature selection method has the potential to improve prediction accuracy. This study suggests that the combination of LCS and imputation can be a cost-effective strategy, contributing to the genetic improvement of economic traits and promoting genetic gains in aquaculture species.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000958/pdfft?md5=01ca2ae401b39215d97aee9cf1df9f3a&pid=1-s2.0-S0888754324000958-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141249667","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}