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LncRNAs modulate nitrogen metabolism gene expression in rice leaves under elevated CO₂ and/or Cd stress 在CO₂和/或Cd胁迫下,LncRNAs调节水稻叶片氮代谢基因表达。
IF 3 2区 生物学
Genomics Pub Date : 2026-05-01 Epub Date: 2026-04-25 DOI: 10.1016/j.ygeno.2026.111255
Aihua Liu, Liyuan Fu, Caixia Wen, Wenyong Liu, Qi Ma, Xuemei Li, Lianju Ma, Yueying Li, Bin Yang, Wei Fu, Yu Zhou, Yonghui Zhao, Danni Wu, Lanlan Wang
{"title":"LncRNAs modulate nitrogen metabolism gene expression in rice leaves under elevated CO₂ and/or Cd stress","authors":"Aihua Liu,&nbsp;Liyuan Fu,&nbsp;Caixia Wen,&nbsp;Wenyong Liu,&nbsp;Qi Ma,&nbsp;Xuemei Li,&nbsp;Lianju Ma,&nbsp;Yueying Li,&nbsp;Bin Yang,&nbsp;Wei Fu,&nbsp;Yu Zhou,&nbsp;Yonghui Zhao,&nbsp;Danni Wu,&nbsp;Lanlan Wang","doi":"10.1016/j.ygeno.2026.111255","DOIUrl":"10.1016/j.ygeno.2026.111255","url":null,"abstract":"<div><div>With rising atmospheric CO₂ and intensifying cadmium (Cd) pollution negatively affect rice growth and development. Rice seedlings “Liaoxing No. 1” (<em>Oryza sativa</em> L.) were treated under four treatments (AC: CO<sub>2</sub> 400 ± 20 μmol<strong>·</strong>mol<sup>−1</sup> and CdCl<sub>2</sub> 0 μmol<strong>·</strong>L<sup>−1</sup>; EC: CO<sub>2</sub> 800 ± 20 μmol<strong>·</strong>mol<sup>−1</sup> and CdCl<sub>2</sub> 0 μmol<strong>·</strong>L<sup>−1</sup>; Cd: CO<sub>2</sub> 400 ± 20 μmol<strong>·</strong>mol<sup>−1</sup> and CdCl<sub>2</sub>150 μmol<strong>·</strong>L<sup>−1</sup>; EC + Cd: CO<sub>2</sub> 800 ± 20 μmol<strong>·</strong>mol<sup>−1</sup>and CdCl<sub>2</sub> 150 μmol<strong>·</strong>L<sup>−1</sup>) for 7 days. Integrated transcriptome sequencing and quantitative real-time PCR (qPCR) were used to analyze the expression patterns and regulatory networks of long non-coding RNAs (lncRNAs) in rice leaves under elevated CO₂ and/or Cd stress. A total of 841 lncRNAs were identified, and KEGG enrichment analysis showed that differentially expressed lncRNAs (DE-lncRNAs) were primarily associated with nitrogen metabolism. Cd stress significantly inhibited nitrogen assimilation via a lncRNA-mediated network: MSTRG.25360.1 downregulated nitrate reductase (NR) genes, reducing NR activity; MSTRG.19531.1 positively regulated glutamate synthase (GOGAT) activity; and MSTRG.16002.2 was involved in inhibiting carbonic anhydrase (CA) activity. Elevated CO₂ (EC) also suppressed the activities of key enzymes, including NR, nitrite reductase (NIR), GOGAT, and CA, while shifting ammonia assimilation toward the glutamine synthetase (GS) pathway, a process involving MSTRG.1264.1. Under combined stress (EC + Cd), EC partially alleviated Cd toxicity by activating NIR and glutamate dehydrogenase (GDH), leading to a higher nitrogen metabolism efficiency than under Cd stress alone. However, the activities of NR and GOGAT failed to recover, and CA activity was further suppressed synergistically via MSTRG.25184.5. In conclusion, elevated CO₂ only partially mitigates Cd-induced inhibition of nitrogen assimilation in an enzyme-specific manner, which is mediated by distinct lncRNA regulatory networks targeting key nitrogen metabolism enzymes.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 3","pages":"Article 111255"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147768289","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}
引用次数: 0
Dynamics of deleterious mutation and selection at seven nuclear genes during barley domestication and de-domestication 大麦驯化和去驯化过程中7个核基因的有害突变和选择动态。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-01-11 DOI: 10.1016/j.ygeno.2026.111203
Yu Zhou , Yuxi Tong , Yonggang Wang , Xiaoqin Fu , Chen Zhang , Genlou Sun , Qifei Wang , Sisi Huang , Xifeng Ren
{"title":"Dynamics of deleterious mutation and selection at seven nuclear genes during barley domestication and de-domestication","authors":"Yu Zhou ,&nbsp;Yuxi Tong ,&nbsp;Yonggang Wang ,&nbsp;Xiaoqin Fu ,&nbsp;Chen Zhang ,&nbsp;Genlou Sun ,&nbsp;Qifei Wang ,&nbsp;Sisi Huang ,&nbsp;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> &lt; 0.05), suggesting that domestication bottlenecks may purge these mutations. In wild barley, Nonsynonymous-to-synonymous substitution rate (dN/dS) ratios were ∼ 1 or &gt; 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}
引用次数: 0
Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis 时间过程与多组学显示高脂血症失调的昼夜节律在肠-肝轴。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-01-08 DOI: 10.1016/j.ygeno.2026.111198
Jinxing Su , Shangquan Jiang , Min Chu , Xiang Dong , Caiyun Zhang , Xiaoxing Li , Kan He
{"title":"Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis","authors":"Jinxing Su ,&nbsp;Shangquan Jiang ,&nbsp;Min Chu ,&nbsp;Xiang Dong ,&nbsp;Caiyun Zhang ,&nbsp;Xiaoxing Li ,&nbsp;Kan He","doi":"10.1016/j.ygeno.2026.111198","DOIUrl":"10.1016/j.ygeno.2026.111198","url":null,"abstract":"<div><h3>Background</h3><div>Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.</div></div><div><h3>Results</h3><div>Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes—including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1—that are regulated by the hepatic circadian clock and modulate metabolites via the gut–liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.</div></div><div><h3>Discussion</h3><div>Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut–liver axis—a key mechanism in hyperlipidemia pathogenesis.</div></div><div><h3>Conclusions</h3><div>This study identifies critical temporal windows and core microbial taxa involved in microbiota–metabolite–gene crosstalk via the gut–liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111198"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145948720","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}
引用次数: 0
Genomics Special Issue on 10 Years of FAANG 基因组学10年特刊 FAANG十年。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-02-12 DOI: 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}
引用次数: 0
Identification and functional analysis of miR-34c-5p target genes during chicken myogenesis 鸡肌肉形成过程中miR-34c-5p靶基因的鉴定和功能分析。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-02-20 DOI: 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
{"title":"Identification and functional analysis of miR-34c-5p target genes during chicken myogenesis","authors":"Shuohan Li ,&nbsp;Ke Zhang ,&nbsp;Yixiang Tian ,&nbsp;Miaomiao Guo ,&nbsp;Xu Wang ,&nbsp;Peng Ding ,&nbsp;Yulong Guo ,&nbsp;Hong Li ,&nbsp;Zhuanjian Li ,&nbsp;Yadong Tian ,&nbsp;Xiangtao Kang ,&nbsp;Xiaojun Liu ,&nbsp;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}
引用次数: 0
Genetic analysis of blood traits and stress resistance in Kirghiz sheep 柯尔克孜羊血液性状及抗逆性遗传分析。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2025-12-30 DOI: 10.1016/j.ygeno.2025.111189
Yanhao Li , Yuwei Peng , Ruizhi Yang , Lingfeng Kong , Lijun Zhu , Fumin Kou , Jialei He , Shudong Liu
{"title":"Genetic analysis of blood traits and stress resistance in Kirghiz sheep","authors":"Yanhao Li ,&nbsp;Yuwei Peng ,&nbsp;Ruizhi Yang ,&nbsp;Lingfeng Kong ,&nbsp;Lijun Zhu ,&nbsp;Fumin Kou ,&nbsp;Jialei He ,&nbsp;Shudong Liu","doi":"10.1016/j.ygeno.2025.111189","DOIUrl":"10.1016/j.ygeno.2025.111189","url":null,"abstract":"<div><div>The Kirghiz (KIR) sheep is a native sheep breed adapted to the extreme ecological environment of the Pamir Plateau. To explore the genetic mechanisms underlying its environmental adaptability, we collected whole-genome resequencing data from 100 KIR sheep and high-density genomic chip data from 509 individuals across 12 breeds. The genetic diversity of the population was evaluated through the inbreeding coefficient (F), nucleotide diversity (π), and linkage disequilibrium (LD). Subsequently, we performed genome-wide association studies (GWAS) on 13 blood traits in KIR populations and identified key environmentally adaptive genes through selective sweeps. The results indicate that while the KIR population exhibits high genetic diversity, its inbreeding coefficient is increasing, reflecting a lack of systematic breeding and improvement. GWAS identified 21 key genes (e.g., <em>IL11</em>, <em>TRPC6</em>, <em>CASP9</em>) significantly associated with blood traits for the first time. Selective sweep analysis identified multiple candidate genes (e.g., <em>THSR</em>, <em>NF1</em>, and <em>MITF</em>) involved in regulating environmental adaptability. Enrichment analysis and functional annotation further elucidated the potential mechanisms of these candidate genes in environmental adaptation. Our study provides a crucial scientific foundation for conserving genetic resources and implementing adaptive breeding strategies for this valuable local breed.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111189"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145889026","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}
引用次数: 0
Alternative splicing signatures correlate with disease severity and clinical subtypes in primary Sjögren's syndrome 选择性剪接特征与原发性Sjögren综合征的疾病严重程度和临床亚型相关。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-02-04 DOI: 10.1016/j.ygeno.2026.111215
Jiaxu Chen , Zhenghao Shi , Jingyuan Cao , Xiangxiang Wu , Guoling Li , Ben Li , Jiaqi Hou , Luan Xue
{"title":"Alternative splicing signatures correlate with disease severity and clinical subtypes in primary Sjögren's syndrome","authors":"Jiaxu Chen ,&nbsp;Zhenghao Shi ,&nbsp;Jingyuan Cao ,&nbsp;Xiangxiang Wu ,&nbsp;Guoling Li ,&nbsp;Ben Li ,&nbsp;Jiaqi Hou ,&nbsp;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}
引用次数: 0
P-GRe: An efficient pipeline for pseudogenes annotation P-GRe:伪基因注释的高效管道。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-02-09 DOI: 10.1016/j.ygeno.2026.111216
Sébastien Cabanac, Christophe Dunand, Catherine Mathé
{"title":"P-GRe: An efficient pipeline for pseudogenes annotation","authors":"Sébastien Cabanac,&nbsp;Christophe Dunand,&nbsp;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}
引用次数: 0
Human-mediated dispersal and breeding reshape global genomic patterns in black soldier flies 人类介导的扩散和繁殖重塑了黑兵蝇的全球基因组模式。
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-01-25 DOI: 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
{"title":"Human-mediated dispersal and breeding reshape global genomic patterns in black soldier flies","authors":"Peter Muchina ,&nbsp;Johnson Kinyua ,&nbsp;Fathiya Khamis ,&nbsp;Chrysantus M. Tanga ,&nbsp;Rawlynce Bett ,&nbsp;Geoffrey Ssepuuya ,&nbsp;Dorothy Nakimbugwe ,&nbsp;Mikkel-Holger S. Sinding ,&nbsp;Grum Gebreyesus ,&nbsp;Goutam Sahana ,&nbsp;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}
引用次数: 0
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 高糖果蔬残渣微氧发酵过程中微生物群落演替和功能代谢物积累特征:对指导家庭生产环保型生物活性肥料的潜在意义
IF 3 2区 生物学
Genomics Pub Date : 2026-03-01 Epub Date: 2026-01-13 DOI: 10.1016/j.ygeno.2026.111204
Piao Liu , Guandi He , Zicheng Guo , Yu Tang , Zhengqian Tan , Yulin Song , Tengbing He , Siew Ling Lee
{"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 ,&nbsp;Guandi He ,&nbsp;Zicheng Guo ,&nbsp;Yu Tang ,&nbsp;Zhengqian Tan ,&nbsp;Yulin Song ,&nbsp;Tengbing He ,&nbsp;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> &lt; 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (<em>p</em> &lt; 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}
引用次数: 0
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