Pub Date : 2026-01-22DOI: 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.
{"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}
Pub Date : 2026-01-22DOI: 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}
Pub Date : 2026-01-21DOI: 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}
Pub Date : 2026-01-21DOI: 10.1186/s12864-026-12557-6
Xiaojing Liu, Lei Wang, Panpan Qiu, Baomei Wu, Weizhong Liu
{"title":"Transcriptome and metabolome analyses reveal the roles of APX2 in regulating tiller growth and metabolism in rice (Oryza sativa L.).","authors":"Xiaojing Liu, Lei Wang, Panpan Qiu, Baomei Wu, Weizhong Liu","doi":"10.1186/s12864-026-12557-6","DOIUrl":"https://doi.org/10.1186/s12864-026-12557-6","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":"146008967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic survey and expression analysis of the CDPK genes in Liriodendron Chinense to explore their potential functions under multiple abiotic stresses.","authors":"Yuanlin Guan, Siqin Liu, Delight Hwarari, Yunpeng Wang, Liming Yang, Jiabao Yao","doi":"10.1186/s12864-025-12393-0","DOIUrl":"https://doi.org/10.1186/s12864-025-12393-0","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":"146008989","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 : 2026-01-21DOI: 10.1186/s12864-026-12554-9
Neil D Young, Tao Wang, Ching-Seng Ang, Dilara Lale, Hans-Peter Fuehrer, Sunita B Sumanam, Pasi K Korhonen, Bill C H Chang, Robin B Gasser
{"title":"Chromosome-scale nuclear genome and proteome of Anoplocephala perfoliata elucidate lineage-specific features of a 'neglected' equine tapeworm.","authors":"Neil D Young, Tao Wang, Ching-Seng Ang, Dilara Lale, Hans-Peter Fuehrer, Sunita B Sumanam, Pasi K Korhonen, Bill C H Chang, Robin B Gasser","doi":"10.1186/s12864-026-12554-9","DOIUrl":"https://doi.org/10.1186/s12864-026-12554-9","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":"146017324","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}
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