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Comparative analysis of brain transcriptomics, intestinal metabolomics and intestinal microbial diversity between two body weight-differentiated groups of mandarin fish (Siniperca chuatsi) after artificial feed acclimation. 人工饲料驯化后两个体重分化组鳜鱼脑转录组学、肠道代谢组学和肠道微生物多样性的比较分析
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-025-12446-4
Yin Yuan, Yuezhen Huang, He Li, Ruobing Li, Fubao Wang, Yongsheng Wang
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引用次数: 0
Multiomics transcriptome and metabolome insights into fat metabolism and meat quality in Songliao black pigs and Songlei crossbred pigs. 松辽黑猪和松雷杂交猪脂肪代谢和肉品质的多组学转录组学和代谢组学研究。
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-025-12399-8
Jing Xu, Yunpeng Zhang, Suthar Teerath Kumar, Enlong Liu, Yunlong Zheng, Yalong Zhu, Qi Zhang, Wu-Sheng Sun, Li Pan, Yuan Zhao, Shu-Min Zhang

Background: The rising demand for high-quality pork among consumers has driven interest in genetic improvement strategies. Crossbreeding is well known to influence carcass performance and meat quality; however, the molecular mechanisms underlying these effects are still poorly understood. In this study, the F1 generation of the Songlei Crossbred Pig (SL) was developed through crossing the Songliao Black Pig (male) (SS) and the Leixiang Pig (female) (LL). We integrated the transcriptomes and metabolomes of the longissimus dorsi (LD) muscle of SS and SL under identical conditions to identify key mechanisms regulating the quality of crossbred meat.

Results: Compared with those of SS, the slaughter weight, carcass weight, and dressing percentage of SL were significantly lower, but the backfat thickness was greater; however, meat quality traits, including intramuscular fat (IMF), colour, and pH24h, were significantly greater, and the pressure loss and shear force were lower in SL. Transcriptome and metabolome analyses revealed a total of 616 differentially expressed genes (DEGs) and 681 significantly differentially expressed metabolites (DEMs) in the LD muscles of SS and SL. Protein-protein interaction (PPI) network analysis revealed key FASN, ADIPOQ, IGF1R and SREBF1 genes that regulate fat metabolism. Furthermore, multiomics joint analysis identified 99 common KEGG pathways, among which the first four pathways were related to fat metabolism, including the AMPK signalling pathway, PPAR signalling pathway, and the regulation of lipolysis in adipocytes and insulin resistance. Gene and metabolite association analysis revealed that the expression of alpha-dimorphecolic acid metabolites was strongly correlated with that of the adipose metabolism-related genes IRS1 and ANGPTL4.

Conclusions: The meat quality of SL was better than that of their male parents, but not the carcass traits were not. Additionally, several critical genes and pathways related to lipid metabolism were identified. These findings provide new insights into how meat quality can be improved by hybridization.

背景:消费者对高品质猪肉需求的不断增长,推动了对基因改良策略的兴趣。众所周知,杂交会影响胴体性能和肉品质;然而,这些作用背后的分子机制仍然知之甚少。本研究通过松辽黑猪(公)(SS)与雷香猪(母)(LL)杂交,培育出松雷杂交猪(SL) F1代。在相同条件下,我们整合了SS和SL背最长肌(LD)的转录组和代谢组,以确定调节杂交肉质质的关键机制。结果:与SS相比,SL的屠宰重、胴体重和屠宰率显著低于SS,但背膘厚度较大;然而,肉质性状,包括肌内脂肪(IMF)、颜色和ph 24小时,在SL中显著更高,压力损失和剪切力更低。转录组学和代谢组学分析显示,在SS和SL的LD肌肉中,共有616个差异表达基因(DEGs)和681个显著差异表达代谢物(DEMs)。蛋白质-蛋白质相互作用(PPI)网络分析显示,FASN、ADIPOQ、IGF1R和SREBF1基因调控脂肪代谢。此外,多组学联合分析鉴定出99条常见的KEGG通路,其中前4条通路与脂肪代谢有关,包括AMPK信号通路、PPAR信号通路以及脂肪细胞脂解和胰岛素抵抗的调控。基因与代谢物关联分析显示,α -二态胆酸代谢物的表达与脂肪代谢相关基因IRS1和ANGPTL4的表达密切相关。结论:SL肉质优于父本,但胴体性状优于父本。此外,还鉴定了与脂质代谢相关的几个关键基因和途径。这些发现为如何通过杂交改善肉质提供了新的见解。
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引用次数: 0
Runs of homozygosity in Italian Holstein bulls: a permutation approach and time-based mapping of the genomic regions potentially under selection. 意大利荷斯坦公牛纯合子的运行:一种排列方法和基于时间的基因组区域的潜在选择。
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-026-12564-7
Laura Falchi, Alberto Cesarani, Luiz F Brito, Salvatore Mastrangelo, Alfredo Pauciullo, Nicolò P P Macciotta, Giustino Gaspa

Background: Runs of homozygosity (ROH) occurrence in animal genomes may result from a high level of relatedness within the population or from positive selection. ROH investigation enables the assessment of the degree of individual autozygosity at the genome-wide level, providing insights into genetic background and development history of a population. In this context, the main objectives of this study were to: 1) develop a method based on permutation tests for detecting single nucleotide polymorphisms (SNP) significantly included in ROH genomic regions of Italian Holstein bulls; 2) identify candidate genes close to the SNP frequently positioned within ROH; 3) investigate the effects of genetic selection on ROH distribution and ROH islands; and 4) assess potential associations between ROH and economically important traits in Italian Holstein cattle. We used high-density SNP data of 3,009 Italian Holstein bulls for identifying ROH regions. The threshold for declaring a SNP as significantly included in a ROH region was obtained by randomly shuffling SNP within animals for each chromosome. The chromosome-wide threshold was the 99th percentile of the distribution of the number of times a SNP was included in a ROH segment (SNPROH) for a specific chromosome. To investigate the influence of ROH on relevant traits, a genome-wide association study testing the presence/absence of specific ROH and a mixed model to quantify the effect of ROH-based inbreeding were carried out.

Results: The top 24,905 significant SNP were distributed on ten chromosomes, in genomic regions known to harbor genes involved in milk traits. One region on BTA20 exhibited an interesting pattern of SNPROH occurrence across animals grouped according to the year of birth, underlining an intense selection pressure in this genomic region. The analyses on the relationship between ROH and pseudo-phenotypes for various traits showed a significant influence of inbreeding on milk and protein yields, and a fertility aggregate index, with the presence/absence of 14 ROH regions having a significant effect on different traits (milk, fat, and protein yields; fat percentage; and somatic cell score).

Conclusions: The application of permutation to a high-density (HD) SNP chip data enabled the identification of genomic regions with high levels of homozygosity in Italian Holstein bulls and revealed associations between ROH occurrence and economically important traits in the studied population.

背景:动物基因组中纯合子(ROH)的发生可能是由于种群内的高亲缘关系或正选择所致。ROH调查可以在全基因组水平上评估个体自合子的程度,从而深入了解种群的遗传背景和发展史。在此背景下,本研究的主要目的是:1)建立一种基于排列试验的方法来检测意大利荷斯坦公牛ROH基因组区域中显著包含的单核苷酸多态性(SNP);2)鉴定与ROH中频繁定位的SNP接近的候选基因;3)研究遗传选择对ROH分布和ROH岛的影响;4)评估ROH与意大利荷斯坦牛重要经济性状之间的潜在关联。我们使用了3009头意大利荷斯坦公牛的高密度SNP数据来确定ROH区域。宣布一个SNP显著包含在ROH区域的阈值是通过随机洗牌动物中每条染色体的SNP获得的。染色体宽阈值是特定染色体在ROH片段(SNPROH)中包含SNP的次数分布的第99个百分位数。为了研究ROH对相关性状的影响,研究人员开展了一项全基因组关联研究,测试了特定ROH的存在/不存在,并建立了一个混合模型来量化基于ROH的近交的影响。结果:前24905个显著SNP分布在10条染色体上,在已知的包含与牛奶性状相关的基因的基因组区域。BTA20上的一个区域在根据出生年份分组的动物中显示出一种有趣的SNPROH发生模式,强调了该基因组区域的强烈选择压力。对不同性状的ROH与伪表型的关系分析表明,近交对产奶量和蛋白质产量以及育性综合指数有显著影响,其中14个ROH区域的存在与否对不同性状(产奶量、脂肪量和蛋白质产量、脂肪率和体细胞评分)有显著影响。结论:对高密度(HD) SNP芯片数据的排列应用能够识别意大利荷斯坦公牛高水平纯合的基因组区域,并揭示了所研究人群中ROH发生与经济上重要性状之间的关联。
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引用次数: 0
Enhanced soybean salt tolerance and oil content via marker-assisted pyramiding of GmSALT3 and high-oil QTLs. 通过标记辅助的GmSALT3和高含油量qtl的金字塔化,提高大豆耐盐性和含油量。
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-025-12347-6
Caiting Gao, Ligao Bao, Xinyu Yang, Zhigang Li, Peng Liu
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引用次数: 0
Peptide turnover prediction using transformer architectures on large-scale time-series proteomic data. 基于大规模时间序列蛋白质组学数据的变压器结构的肽周转预测。
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-026-12558-5
Koki Ishino, Akiyasu C Yoshizawa, Yuting Liu, Shujiro Okuda
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引用次数: 0
Genome-wide association study of pre-indicative agronomic traits affecting malt quality in Ethiopian barley (Hordeum vulgare L.) germplasm. 影响埃塞俄比亚大麦(Hordeum vulgare L.)种质品质的指示前农艺性状全基因组关联研究
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-026-12555-8
Birhanu Babiye, Alemayehu Teressa Negawo, Wondimu Fekadu Ejerso, Gizachew Haile Gidamo, Sisay Kidane Alemu, Surafel Shibru Teklemariam, Adugna Abdi Woldesemayat
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引用次数: 0
Identification and characterization of the class III peroxidase gene family in sea buckthorn (Hippophae rhamnoides subsp. sinensis Rousi) and its potential role in lignin biosynthesis. 沙棘III类过氧化物酶基因家族的鉴定与表征。中国木质素(sinensis Rousi)及其在木质素合成中的潜在作用
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-025-12295-1
Jing Zhao, Kai Li, Meng Zhao, Xuan Jiang, Xing Liu, Hongli Wang, Kun Sun

Background: Class Ⅲ peroxidases (PODs) are widely involved in multiple physiological processes, including lignin biosynthesis and stress responses. However, there are no reports on the identification and function of POD family in Hippophae rhamnoides subsp. sinensis Rousi.

Results: In this study, we identified 71 non-redundant HrPODs. Based on phylogenetic analysis, these genes were classified into 7 subgroups. Then, we analyzed the conserved domains of HrPODs proteins and found that they contain highly conserved domain. We also investigated their expression patterns in three developmental stages of sea buckthorn fruit, and the results showed that most of them were highly expressed in early stage. The GO and KEGG functional enrichment analysis showed that they widely involved in oxidative stress response and phenylpropanoid biosynthesis, respectively. According to the Pearson correlation analysis of HrPODs expression with lignin content and peroxidase activity, we further screened five HrPODs that may be involved in fruit texture quality by regulating lignin biosynthesis during fruit development. Sea buckthorn is usually distributed in arid areas with higher salt and alkaline content, and our findings showed that the different degrees of drought, salt, or alkali treatment can also affect the expression of these genes and lignin content during the germination stage. These results will help us better investigate the role of HrPODs in lignin biosynthesis to provide certain theoretical foundation in ideal berry breeding and broad spectrum stress resistance in cultivated sea buckthorn.

Conclusion: In this study, the findings not only provide us with a comprehensive identification and analysis of HrPODs from a bioinformatics perspective, but also preliminary intimation that the POD family may be tightly associated with fruit texture quality and abiotic stress response. These results will help us better investigate the role of HrPODs in lingin biosynthesis, enrich the theoretical research on the formation of sea buckthorn texture quality and understand the roles of HrPODs in abiotic stress resistance in cultivated sea buckthorn.

背景:Ⅲ类过氧化物酶(pod)广泛参与多种生理过程,包括木质素生物合成和应激反应。然而,沙棘亚种POD家族的鉴定和功能尚未见报道。sinensis Rousi。结果:在本研究中,我们鉴定了71个非冗余hrpod。根据系统发育分析,这些基因可分为7个亚群。然后,我们分析了HrPODs蛋白的保守结构域,发现它们含有高度保守结构域。研究了它们在沙棘果实发育的三个阶段的表达规律,结果表明,它们大多在早期高表达。GO和KEGG功能富集分析表明,它们分别广泛参与氧化应激反应和苯丙类生物合成。根据HrPODs表达量与木质素含量和过氧化物酶活性的Pearson相关分析,我们进一步筛选了5个HrPODs,它们可能通过调节果实发育过程中木质素的生物合成参与果实质地质量。沙棘通常分布在盐、碱含量较高的干旱地区,不同程度的干旱、盐、碱处理也会影响萌发阶段这些基因的表达和木质素含量。这些结果将有助于我们更好地研究hrpod在木质素生物合成中的作用,为培养沙棘的理想浆果育种和广谱抗逆性提供一定的理论依据。结论:本研究结果不仅为我们从生物信息学角度对HrPODs进行了全面的鉴定和分析,而且初步提示POD家族可能与果实质地品质和非生物胁迫反应密切相关。这些结果将有助于我们更好地研究HrPODs在lingin生物合成中的作用,丰富沙棘质地品质形成的理论研究,了解HrPODs在人工沙棘非生物抗性中的作用。
{"title":"Identification and characterization of the class III peroxidase gene family in sea buckthorn (Hippophae rhamnoides subsp. sinensis Rousi) and its potential role in lignin biosynthesis.","authors":"Jing Zhao, Kai Li, Meng Zhao, Xuan Jiang, Xing Liu, Hongli Wang, Kun Sun","doi":"10.1186/s12864-025-12295-1","DOIUrl":"10.1186/s12864-025-12295-1","url":null,"abstract":"<p><strong>Background: </strong>Class Ⅲ peroxidases (PODs) are widely involved in multiple physiological processes, including lignin biosynthesis and stress responses. However, there are no reports on the identification and function of POD family in Hippophae rhamnoides subsp. sinensis Rousi.</p><p><strong>Results: </strong>In this study, we identified 71 non-redundant HrPODs. Based on phylogenetic analysis, these genes were classified into 7 subgroups. Then, we analyzed the conserved domains of HrPODs proteins and found that they contain highly conserved domain. We also investigated their expression patterns in three developmental stages of sea buckthorn fruit, and the results showed that most of them were highly expressed in early stage. The GO and KEGG functional enrichment analysis showed that they widely involved in oxidative stress response and phenylpropanoid biosynthesis, respectively. According to the Pearson correlation analysis of HrPODs expression with lignin content and peroxidase activity, we further screened five HrPODs that may be involved in fruit texture quality by regulating lignin biosynthesis during fruit development. Sea buckthorn is usually distributed in arid areas with higher salt and alkaline content, and our findings showed that the different degrees of drought, salt, or alkali treatment can also affect the expression of these genes and lignin content during the germination stage. These results will help us better investigate the role of HrPODs in lignin biosynthesis to provide certain theoretical foundation in ideal berry breeding and broad spectrum stress resistance in cultivated sea buckthorn.</p><p><strong>Conclusion: </strong>In this study, the findings not only provide us with a comprehensive identification and analysis of HrPODs from a bioinformatics perspective, but also preliminary intimation that the POD family may be tightly associated with fruit texture quality and abiotic stress response. These results will help us better investigate the role of HrPODs in lingin biosynthesis, enrich the theoretical research on the formation of sea buckthorn texture quality and understand the roles of HrPODs in abiotic stress resistance in cultivated sea buckthorn.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":"77"},"PeriodicalIF":3.7,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12828949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146028228","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}
引用次数: 0
Building consensus: construction of a juvenile and adult scRNA-seq meta-atlas for dataset comparisons and harmonizing transcriptomic definitions of enteric neuron subtypes. 建立共识:构建青少年和成人scRNA-seq元图谱,用于数据集比较和协调肠道神经元亚型的转录组定义。
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-025-12283-5
Joseph T Benthal, Aaron A May-Zhang, E Michelle Southard-Smith
{"title":"Building consensus: construction of a juvenile and adult scRNA-seq meta-atlas for dataset comparisons and harmonizing transcriptomic definitions of enteric neuron subtypes.","authors":"Joseph T Benthal, Aaron A May-Zhang, E Michelle Southard-Smith","doi":"10.1186/s12864-025-12283-5","DOIUrl":"10.1186/s12864-025-12283-5","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":"50"},"PeriodicalIF":3.7,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12825290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146017462","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}
引用次数: 0
The reduced genome of Candidatus Portiera sp. in Bemisia afer: evolutionary trajectories and functional implications. 贝米西亚候选者Portiera sp.的减少基因组:进化轨迹和功能意义。
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1186/s12864-025-12509-6
Yu-Yi Wang, Yi-Jia Chen, Hua-Ling Wang, Cheng-Cheng Zhu, Teng Lei, Yin-Quan Liu
{"title":"The reduced genome of Candidatus Portiera sp. in Bemisia afer: evolutionary trajectories and functional implications.","authors":"Yu-Yi Wang, Yi-Jia Chen, Hua-Ling Wang, Cheng-Cheng Zhu, Teng Lei, Yin-Quan Liu","doi":"10.1186/s12864-025-12509-6","DOIUrl":"https://doi.org/10.1186/s12864-025-12509-6","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146017384","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
Comparative analysis of complete chloroplast genomes reveals the phylogenetic relationships of Lygodium Sw. (Lygodiaceae) species in China. 通过对枸杞叶绿体全基因组的比较分析,揭示了枸杞的系统发育关系。中国的一种。
IF 3.7 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-21 DOI: 10.1186/s12864-026-12561-w
Wei Liu, Juan Li, Zhichao Fan, Jiayun Tong, Yi Tong, Haibo Huang, Ruoting Zhan
{"title":"Comparative analysis of complete chloroplast genomes reveals the phylogenetic relationships of Lygodium Sw. (Lygodiaceae) species in China.","authors":"Wei Liu, Juan Li, Zhichao Fan, Jiayun Tong, Yi Tong, Haibo Huang, Ruoting Zhan","doi":"10.1186/s12864-026-12561-w","DOIUrl":"https://doi.org/10.1186/s12864-026-12561-w","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146017366","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
期刊
BMC Genomics
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