Pub Date : 2026-03-01Epub Date: 2026-02-12DOI: 10.1016/j.ygeno.2026.111220
Emily L. Clark
{"title":"Genomics Special Issue on 10 Years of FAANG","authors":"Emily L. Clark","doi":"10.1016/j.ygeno.2026.111220","DOIUrl":"10.1016/j.ygeno.2026.111220","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111220"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146197478","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}
Pub Date : 2026-03-01Epub Date: 2026-02-20DOI: 10.1016/j.ygeno.2026.111221
Shuohan Li , Ke Zhang , Yixiang Tian , Miaomiao Guo , Xu Wang , Peng Ding , Yulong Guo , Hong Li , Zhuanjian Li , Yadong Tian , Xiangtao Kang , Xiaojun Liu , Weihua Tian
Accumulating evidence has indicated that microRNAs (miRNAs) participate in chicken skeletal muscle development by post-transcriptionally regulating myogenesis-related gene expression. Our previous study showed that miR-34c-5p inhibited proliferation and myogenic differentiation of chicken primary myoblasts (CPMs), but its molecular mechanisms remain unclear. Here, miR-34c-5p was overexpressed in CPMs for transcriptome sequencing. The 159 differentially expressed genes (DEGs) were identified and were mainly involved in myogenesis-related processes and signaling pathways, including cytoskeleton regulation, PPAR, and cardiac muscle contraction. Intersection of DEGs and predicted targets of miR-34c-5p yielded 15 candidate genes. Of these, miR-34c-5p could inhibit the mRNA expression of MYH7B and TGM4 genes by directly interact with their 3′ untranslated regions as determined by dual-luciferase reporter systems Gain- and loss-of-function assays demonstrated that TGM4 gene could promote CPMs proliferation. These findings elucidate the regulatory network of miR-34c-5p underlying myogenesis and provide potential molecular marker for genetic improvement of meat production in chicken.
{"title":"Identification and functional analysis of miR-34c-5p target genes during chicken myogenesis","authors":"Shuohan Li , Ke Zhang , Yixiang Tian , Miaomiao Guo , Xu Wang , Peng Ding , Yulong Guo , Hong Li , Zhuanjian Li , Yadong Tian , Xiangtao Kang , Xiaojun Liu , Weihua Tian","doi":"10.1016/j.ygeno.2026.111221","DOIUrl":"10.1016/j.ygeno.2026.111221","url":null,"abstract":"<div><div>Accumulating evidence has indicated that microRNAs (miRNAs) participate in chicken skeletal muscle development by post-transcriptionally regulating myogenesis-related gene expression. Our previous study showed that miR-34c-5p inhibited proliferation and myogenic differentiation of chicken primary myoblasts (CPMs), but its molecular mechanisms remain unclear. Here, miR-34c-5p was overexpressed in CPMs for transcriptome sequencing. The 159 differentially expressed genes (DEGs) were identified and were mainly involved in myogenesis-related processes and signaling pathways, including cytoskeleton regulation, PPAR, and cardiac muscle contraction. Intersection of DEGs and predicted targets of miR-34c-5p yielded 15 candidate genes. Of these, miR-34c-5p could inhibit the mRNA expression of <em>MYH7B</em> and <em>TGM4</em> genes by directly interact with their 3′ untranslated regions as determined by dual-luciferase reporter systems Gain- and loss-of-function assays demonstrated that <em>TGM4</em> gene could promote CPMs proliferation. These findings elucidate the regulatory network of miR-34c-5p underlying myogenesis and provide potential molecular marker for genetic improvement of meat production in chicken.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111221"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147270401","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}
Pub Date : 2026-03-01Epub Date: 2026-01-11DOI: 10.1016/j.ygeno.2026.111203
Yu Zhou , Yuxi Tong , Yonggang Wang , Xiaoqin Fu , Chen Zhang , Genlou Sun , Qifei Wang , Sisi Huang , Xifeng Ren
Understanding how barley domestication affects deleterious mutations is crucial for breeding and germplasm conservation. This study analyzed seven single-copy nuclear genes (Alcohol dehydrogenase 2 (ADH2), Alcohol dehydrogenase 3 (ADH3), Dehydrin9 (DHN9), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Phosphoenolpyruvate carboxylase (PEPC), Photoperiod response gene (PPD-H1), and Granule-bound starch synthase (WAXY)) in 179 wild, 185 domesticated, and 21 de-domesticated barley accessions. Results showed that wild barley has the highest genetic diversity and the most private haplotypes. Deleterious SNPs were identified, with fewer in domesticated and de-domesticated groups compared to wild. Deleterious mutation load decreased from wild to domesticated barley as nucleotide diversity decreased (R = 0.78; p < 0.05), suggesting that domestication bottlenecks may purge these mutations. In wild barley, Nonsynonymous-to-synonymous substitution rate (dN/dS) ratios were ∼ 1 or > 1, indicating neutral or weak positive selection. These findings highlight how domestication shapes deleterious mutation patterns and provide insights for breeding and germplasm management.
{"title":"Dynamics of deleterious mutation and selection at seven nuclear genes during barley domestication and de-domestication","authors":"Yu Zhou , Yuxi Tong , Yonggang Wang , Xiaoqin Fu , Chen Zhang , Genlou Sun , Qifei Wang , Sisi Huang , Xifeng Ren","doi":"10.1016/j.ygeno.2026.111203","DOIUrl":"10.1016/j.ygeno.2026.111203","url":null,"abstract":"<div><div>Understanding how barley domestication affects deleterious mutations is crucial for breeding and germplasm conservation. This study analyzed seven single-copy nuclear genes (<em>Alcohol dehydrogenase 2</em> (<em>ADH2</em>), <em>Alcohol dehydrogenase 3</em> (<em>ADH3</em>), <em>Dehydrin9</em> (<em>DHN9</em>), <em>Glyceraldehyde-3-phosphate dehydrogenase</em> (<em>GAPDH</em>), <em>Phosphoenolpyruvate carboxylase</em> (<em>PEPC</em>), <em>Photoperiod response gene</em> (<em>PPD-H1</em>), and <em>Granule-bound starch synthase</em> (<em>WAXY</em>)) in 179 wild, 185 domesticated, and 21 de-domesticated barley accessions. Results showed that wild barley has the highest genetic diversity and the most private haplotypes. Deleterious SNPs were identified, with fewer in domesticated and de-domesticated groups compared to wild. Deleterious mutation load decreased from wild to domesticated barley as nucleotide diversity decreased (<em>R</em> = 0.78; <em>p</em> < 0.05), suggesting that domestication bottlenecks may purge these mutations. In wild barley, Nonsynonymous-to-synonymous substitution rate (dN/dS) ratios were ∼ 1 or > 1, indicating neutral or weak positive selection. These findings highlight how domestication shapes deleterious mutation patterns and provide insights for breeding and germplasm management.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111203"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145965882","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}
Pub Date : 2026-03-01Epub Date: 2026-02-04DOI: 10.1016/j.ygeno.2026.111215
Jiaxu Chen , Zhenghao Shi , Jingyuan Cao , Xiangxiang Wu , Guoling Li , Ben Li , Jiaqi Hou , Luan Xue
Primary Sjögren's Syndrome (pSS) is a chronic, systemic autoimmune disease characterized by sicca symptoms due to exocrine gland involvement, but also presenting with a wide range of extraglandular manifestations and diverse subjective burdens, leading to significant clinical heterogeneity that complicates accurate diagnosis and objective assessment of disease activity. While transcriptome sequencing technologies have revolutionized the global analysis of alternative splicing (AS) events and aberrant AS has been implicated in the pathogenesis of various autoimmune diseases, research into AS in pSS remains limited to individual genes. Therefore, this study analyzed peripheral blood transcriptomes from pSS patients and healthy controls, utilizing key co-expression module eigengene values to stratify patients into homogeneous subgroups. Clear differential AS analysis was further obtained. Ten genes with significant AS events were identified, with AS in WARS1, OASL, DDX60, C2, RMI2, PALM2AKAP2, and MYO7B significantly associated with various laboratory indicators. Furthermore, by combining expression and usage rate changes with protein sequence structure predictions, their detailed functional implications in pSS were fully discussed. In conclusion, novel AS signatures significantly associated with pSS severity were revealed, which may serve as potential biomarkers for disease stratification and therapeutic targets in pSS, further providing opportunities for mechanistic research.
{"title":"Alternative splicing signatures correlate with disease severity and clinical subtypes in primary Sjögren's syndrome","authors":"Jiaxu Chen , Zhenghao Shi , Jingyuan Cao , Xiangxiang Wu , Guoling Li , Ben Li , Jiaqi Hou , Luan Xue","doi":"10.1016/j.ygeno.2026.111215","DOIUrl":"10.1016/j.ygeno.2026.111215","url":null,"abstract":"<div><div>Primary Sjögren's Syndrome (pSS) is a chronic, systemic autoimmune disease characterized by sicca symptoms due to exocrine gland involvement, but also presenting with a wide range of extraglandular manifestations and diverse subjective burdens, leading to significant clinical heterogeneity that complicates accurate diagnosis and objective assessment of disease activity. While transcriptome sequencing technologies have revolutionized the global analysis of alternative splicing (AS) events and aberrant AS has been implicated in the pathogenesis of various autoimmune diseases, research into AS in pSS remains limited to individual genes. Therefore, this study analyzed peripheral blood transcriptomes from pSS patients and healthy controls, utilizing key co-expression module eigengene values to stratify patients into homogeneous subgroups. Clear differential AS analysis was further obtained. Ten genes with significant AS events were identified, with AS in WARS1, OASL, DDX60, C2, RMI2, PALM2AKAP2, and MYO7B significantly associated with various laboratory indicators. Furthermore, by combining expression and usage rate changes with protein sequence structure predictions, their detailed functional implications in pSS were fully discussed. In conclusion, novel AS signatures significantly associated with pSS severity were revealed, which may serve as potential biomarkers for disease stratification and therapeutic targets in pSS, further providing opportunities for mechanistic research.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111215"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146131509","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}
Formerly considered as part of “junk DNA”, pseudogenes are nowadays known for their role in the post-transcriptional regulation of functional genes. Their identification also contributes to a better understanding of gene evolution, particularly in relation to adaptive responses and the evolution of multigene families. Despite this, there is, to our knowledge, no fully automatic pipeline allowing annotation of the pseudogenes on a whole genome. Here, we propose a new software named Pseudo-Gene Retriever (P-GRe). This is a completely automated pseudogene prediction tool requiring only a genome sequence, its corresponding GFF annotation file, and a protein sequences file. The aligner miniprot has been integrated in our pipeline, because of its high speed and sensitivity. With several filtering and post-analysis steps P-GRe outperforms existing software, while being more sensitive and bringing the new capacity of annotating unitary pseudogenes.
{"title":"P-GRe: An efficient pipeline for pseudogenes annotation","authors":"Sébastien Cabanac, Christophe Dunand, Catherine Mathé","doi":"10.1016/j.ygeno.2026.111216","DOIUrl":"10.1016/j.ygeno.2026.111216","url":null,"abstract":"<div><div>Formerly considered as part of “junk DNA”, pseudogenes are nowadays known for their role in the post-transcriptional regulation of functional genes. Their identification also contributes to a better understanding of gene evolution, particularly in relation to adaptive responses and the evolution of multigene families. Despite this, there is, to our knowledge, no fully automatic pipeline allowing annotation of the pseudogenes on a whole genome. Here, we propose a new software named Pseudo-Gene Retriever (P-GRe). This is a completely automated pseudogene prediction tool requiring only a genome sequence, its corresponding GFF annotation file, and a protein sequences file. The aligner miniprot has been integrated in our pipeline, because of its high speed and sensitivity. With several filtering and post-analysis steps P-GRe outperforms existing software, while being more sensitive and bringing the new capacity of annotating unitary pseudogenes.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111216"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146165034","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}
Pub Date : 2026-03-01Epub Date: 2026-01-25DOI: 10.1016/j.ygeno.2026.111208
Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Rawlynce Bett , Geoffrey Ssepuuya , Dorothy Nakimbugwe , Mikkel-Holger S. Sinding , Grum Gebreyesus , Goutam Sahana , Zexi Cai
Human activities, either intentional or unintentional, have significantly influenced the global distribution and genetic composition of many species. The black soldier fly (Hermetia illucens; BSF) is a species native to North America that has rapidly gained commercial importance due to its bioconversion efficiency, upcycling organic waste into higher-value products. Through human-mediated dispersal associated with trade and insect farming, BSF has been introduced widely across the Old World, including Africa, where both wild and captive populations are now established. Despite its expanding global distribution, the demographic history and genomic consequences of these introductions remain poorly understood, particularly in Africa. This work integrates whole-genome sequencing of newly sampled East African wild and captive populations with publicly available global datasets to characterize patterns of genetic diversity, population structure, and historical spread. Wild populations displayed high genetic diversity and clear geographic structuring, whereas many captive populations showed markedly reduced diversity, elevated inbreeding, and extensive runs of homozygosity. Our results reveal that a substantial fraction of global captive lines can be traced to a narrow lineage of North American origin, while additional captive colonies reflect more recent, independent derivations from local wild populations. These genomic patterns are consistent with demographic processes such as founder effects, genetic drift, and small effective population sizes, rather than coordinated or directional domestication. By resolving the origins and demographic trajectories of African and global BSF populations, this work clarifies the genetic consequences of unstructured breeding and provides a foundation for managing genetic resources in this rapidly expanding insect-farming industry.
{"title":"Human-mediated dispersal and breeding reshape global genomic patterns in black soldier flies","authors":"Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Rawlynce Bett , Geoffrey Ssepuuya , Dorothy Nakimbugwe , Mikkel-Holger S. Sinding , Grum Gebreyesus , Goutam Sahana , Zexi Cai","doi":"10.1016/j.ygeno.2026.111208","DOIUrl":"10.1016/j.ygeno.2026.111208","url":null,"abstract":"<div><div>Human activities, either intentional or unintentional, have significantly influenced the global distribution and genetic composition of many species. The black soldier fly (<em>Hermetia illucens</em>; BSF) is a species native to North America that has rapidly gained commercial importance due to its bioconversion efficiency, upcycling organic waste into higher-value products. Through human-mediated dispersal associated with trade and insect farming, BSF has been introduced widely across the Old World, including Africa, where both wild and captive populations are now established. Despite its expanding global distribution, the demographic history and genomic consequences of these introductions remain poorly understood, particularly in Africa. This work integrates whole-genome sequencing of newly sampled East African wild and captive populations with publicly available global datasets to characterize patterns of genetic diversity, population structure, and historical spread. Wild populations displayed high genetic diversity and clear geographic structuring, whereas many captive populations showed markedly reduced diversity, elevated inbreeding, and extensive runs of homozygosity. Our results reveal that a substantial fraction of global captive lines can be traced to a narrow lineage of North American origin, while additional captive colonies reflect more recent, independent derivations from local wild populations. These genomic patterns are consistent with demographic processes such as founder effects, genetic drift, and small effective population sizes, rather than coordinated or directional domestication. By resolving the origins and demographic trajectories of African and global BSF populations, this work clarifies the genetic consequences of unstructured breeding and provides a foundation for managing genetic resources in this rapidly expanding insect-farming industry.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111208"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146061792","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}
Pub Date : 2026-03-01Epub Date: 2026-01-13DOI: 10.1016/j.ygeno.2026.111204
Piao Liu , Guandi He , Zicheng Guo , Yu Tang , Zhengqian Tan , Yulin Song , Tengbing He , Siew Ling Lee
Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.
家用发酵罐为果蔬废弃物的利用提供了简单、低成本的解决方案，但糖介导的发酵过程中代谢物的分期形成仍有待研究。利用宏基因组学和代谢组学方法，我们对28天内的微生物演替和代谢物动态进行了表征。出现了三个阶段：底物激活（1-7d），肠杆菌/埃希氏菌优势产生有机酸；代谢转变（8-21d）与乳酸杆菌增殖（增加312.5%）积累植物激素3-羟基肉桂酸（2.84倍）和腺嘌呤（1.38倍）；功能稳定（21-28d）建立乳酸杆菌-醋酸杆菌协同作用，丰富抗氧化剂和抗菌肽。多组学分析显示，氨基酸代谢与功能代谢物之间存在很强的相关性（r = 0.78, p < 0.01）。发酵液（1:500稀释）使生菜发芽率提高到92.22% （p < 0.05）。虽然家庭农业的潜力是通过分阶段的微生物群落发展和生物活性产品的形成来证明的，但除了种子发芽试验之外，还需要在土壤-植物系统中验证功能特征。
{"title":"Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer","authors":"Piao Liu , Guandi He , Zicheng Guo , Yu Tang , Zhengqian Tan , Yulin Song , Tengbing He , Siew Ling Lee","doi":"10.1016/j.ygeno.2026.111204","DOIUrl":"10.1016/j.ygeno.2026.111204","url":null,"abstract":"<div><div>Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with <em>Enterobacter</em>/<em>Escherichia</em> dominance producing organic acids; metabolic transition (8-21d) with <em>Lactiplantibacillus</em> proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing <em>Lactiplantibacillus-Acetobacter</em> synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (<em>r</em> = 0.78, <em>p</em> < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (<em>p</em> < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111204"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145975340","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}
Pub Date : 2026-03-01Epub Date: 2026-01-27DOI: 10.1016/j.ygeno.2026.111210
Qing Liu , Dongli Cui , Yaqi Tian , Yehan Wang , Mathieu Rouard , John Seymour Heslop-Harrison , Trude Schwarzacher , Ziwei Wang
Musella lasiocarpa (MLA, 2n = 18, Musaceae) is an endangered species native to south-western China. We assembled its haplotype-resolved, telomere-to-telomere genomes with a genome size of 503.6 Mb consisting of 52.8% repetitive DNA. A 134 bp tandem repeat, Mlcen, was identified at all centromeres, and telomere sequences were present at 30 of 36 assembled pseudo-chromosome ends. The distal gene-rich regions display high synteny, whereas retrotransposon polymorphisms between haplotypes occurred throughout chromosomes, contributing to diversity. Phylogenetic analysis shows MLA diverged from Ensete 42 million years ago, and together they share a common ancestor with Musa. Among 35,312 protein-coding genes, 14 up-regulated and 34 down-regulated transcription factors were identified under cold treatment. This high-quality genomic resource advances our understanding of MLA chromosomal evolution characterized by structural variations, repetitive DNA dynamics, and cold-responsive genes at both haplotype and species levels; and enables genome-assisted improvement of more resilient crops such as bananas and Ensete.
{"title":"Haplotype-resolved genome assembly of Musella lasiocarpa reveals the critical role of structural variations in chromosomal and genome evolution","authors":"Qing Liu , Dongli Cui , Yaqi Tian , Yehan Wang , Mathieu Rouard , John Seymour Heslop-Harrison , Trude Schwarzacher , Ziwei Wang","doi":"10.1016/j.ygeno.2026.111210","DOIUrl":"10.1016/j.ygeno.2026.111210","url":null,"abstract":"<div><div><em>Musella lasiocarpa</em> (MLA, 2<em>n</em> = 18, Musaceae) is an endangered species native to south-western China. We assembled its haplotype-resolved, telomere-to-telomere genomes with a genome size of 503.6 Mb consisting of 52.8% repetitive DNA. A 134 bp tandem repeat, Mlcen, was identified at all centromeres, and telomere sequences were present at 30 of 36 assembled pseudo-chromosome ends. The distal gene-rich regions display high synteny, whereas retrotransposon polymorphisms between haplotypes occurred throughout chromosomes, contributing to diversity. Phylogenetic analysis shows MLA diverged from <em>Ensete</em> 42 million years ago, and together they share a common ancestor with <em>Musa</em>. Among 35,312 protein-coding genes, 14 up-regulated and 34 down-regulated transcription factors were identified under cold treatment. This high-quality genomic resource advances our understanding of MLA chromosomal evolution characterized by structural variations, repetitive DNA dynamics, and cold-responsive genes at both haplotype and species levels; and enables genome-assisted improvement of more resilient crops such as bananas and <em>Ensete</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111210"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146085369","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}
Pub Date : 2026-03-01Epub Date: 2026-01-05DOI: 10.1016/j.ygeno.2026.111194
Qianqian Pan , Mengyu Lou , Jing Jing , Tianwei Liu , Yan Huang , Shuang Li , Lu Zhu , Yong Liu , Sihuan Zhang , Yinghui Ling
Skeletal muscle development is crucial for goat meat production. While most research focuses on transcriptional regulation, translational control is often overlooked. This study integrated transcriptomic data to analyze the translational landscape during myogenic differentiation of goat skeletal muscle satellite cells (SMSCs). We found that differentiation pathways were activated at both levels, with enhancement at translation. Furthermore, we identified 25 novel lncORFs and 36 circORFs with coding potential. Among these, LncORF32653 and LncORF98488 encoded micropeptides promoting SMSCs proliferation and differentiation. We also identified circUSP25, encoding circUSP25-177aa, which inhibited proliferation but promoted differentiation. Thus, lncORF32653-53aa, lncORF98488-98aa, and circUSP25-177aa are key regulators of myogenesis, revealing the potential of RNAs annotated as non-coding to encode functional micropeptides.
{"title":"The translation landscape revealed the novel micropeptides involved in myogenic differentiation of goat skeletal muscle satellite cells","authors":"Qianqian Pan , Mengyu Lou , Jing Jing , Tianwei Liu , Yan Huang , Shuang Li , Lu Zhu , Yong Liu , Sihuan Zhang , Yinghui Ling","doi":"10.1016/j.ygeno.2026.111194","DOIUrl":"10.1016/j.ygeno.2026.111194","url":null,"abstract":"<div><div>Skeletal muscle development is crucial for goat meat production. While most research focuses on transcriptional regulation, translational control is often overlooked. This study integrated transcriptomic data to analyze the translational landscape during myogenic differentiation of goat skeletal muscle satellite cells (SMSCs). We found that differentiation pathways were activated at both levels, with enhancement at translation. Furthermore, we identified 25 novel lncORFs and 36 circORFs with coding potential. Among these, LncORF32653 and LncORF98488 encoded micropeptides promoting SMSCs proliferation and differentiation. We also identified circUSP25, encoding circUSP25-177aa, which inhibited proliferation but promoted differentiation. Thus, lncORF32653-53aa, lncORF98488-98aa, and circUSP25-177aa are key regulators of myogenesis, revealing the potential of RNAs annotated as non-coding to encode functional micropeptides.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111194"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916794","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}
Pub Date : 2026-03-01Epub Date: 2026-01-05DOI: 10.1016/j.ygeno.2025.111191
Chengqi Gao , Wei Xiao , Chao Zhu , Mengwei Liu , Zhenguo Zeng , Kun Xiao , Kuai Yu
The inflammatory responses of severe patients before and after Convalescent COVID-19 plasma (CCP) transfusion are poorly understood. To clarify the immune response and potential pro-inflammatory factors in severe patients after CCP transfusion, we performed single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) from severe COVID-19 patients before and 24 h after CCP transfusion. At 24 h after CCP transfusion, T and B cell proportions increased modestly without significant changes in TCR/BCR diversity. Importantly, concurrent upregulation of S100A8 in both CD4 memory T cells and B cells suggests that CCP transfusion may promote an inflammatory response in these cell subsets. Cell communication analysis revealed that CCP transfusion induced selective disruption of NK cell communication with TCR-negative T cells and BCR-positive B cells. Our data suggest CCP transfusion promoted the inflammatory response and interrupt the communication between adaptive immune cells and innate immune cells in severe COVID-19.
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