Genome-wide identification and expression analysis of orphan genes in twelve Musa (sub)species.

IF 2.6 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

3 Biotech Pub Date : 2025-02-01 Epub Date: 2025-01-14 DOI:10.1007/s13205-025-04213-9

Qingwen Ren, Yat-Yuen Lim, Chee How Teo

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引用次数: 0

Abstract

Orphan genes (OGs), also known as lineage-specific genes, are species-specific genes that play a crucial role in species-specific adaptations to various stresses. Although OGs have been identified in several plant species, there is no information on OGs in banana genomes. This study aimed to systematically identify OGs in twelve banana (sub)species using comparative genomics. The results showed that OG content varied widely among these (sub)species, from 0.4% in Musa itinerans to 7.3% in Ensete glaucum. Genetic structure analysis showed that banana OGs have significantly shorter protein lengths, smaller molecular weight, fewer exons, and shorter exon lengths than non-orphan genes (NOGs). Subcellular localization predictions showed that banana OGs are mainly found in the chloroplast, nucleus, and cytosol, and are evenly distributed across chromosomes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that OGs may be involved in cellular processes, metabolic processes, and molecular transport. The transcriptome analysis of 9 AAA cultivars against 4 M. acuminata subspecies genomes showed the OGs content. Analysis of gene expression in M. acuminata subsp. malaccensis showed 75 differentially expressed (DE) OGs in response to abiotic stresses and 46 DE OGs related to biotic stresses, indicating that these OGs might play important roles in response to abiotic and biotic stresses. This study provides a foundation for further in-depth research into the functions of OGs in bananas.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04213-9.

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12个Musa（亚）种孤儿基因的全基因组鉴定与表达分析。

孤儿基因（OGs），也被称为谱系特异性基因，是物种特异性基因，在物种特异性适应各种压力中起着至关重要的作用。虽然已经在一些植物物种中发现了OGs，但在香蕉基因组中没有关于OGs的信息。本研究旨在利用比较基因组学技术系统鉴定12个香蕉（亚）种的OGs。结果表明，OG含量在不同亚种间差异较大，从Musa itinerans的0.4%到Ensete glaucum的7.3%不等。遗传结构分析表明，与非孤儿基因（NOGs）相比，香蕉og基因的蛋白长度、分子量、外显子数量和外显子长度显著缩短。亚细胞定位预测表明，香蕉og主要存在于叶绿体、细胞核和细胞质中，并均匀分布在染色体上。基因本体（GO）和京都基因与基因组百科全书（KEGG）富集分析表明，og可能参与细胞过程、代谢过程和分子运输。9个AAA品种对4个尖茅亚种基因组的转录组分析显示了OGs的含量。刺毛螨亚种基因表达分析。malaccensis在非生物胁迫下存在75个差异表达基因（DE），在生物胁迫下存在46个差异表达基因（DE），表明这些差异表达基因可能在非生物胁迫和生物胁迫响应中发挥重要作用。本研究为进一步深入研究香蕉中OGs的功能奠定了基础。补充资料：在线版本提供补充资料，网址为10.1007/s13205-025-04213-9。

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来源期刊

3 Biotech Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

CiteScore

6.00

自引率

0.00%

发文量

314

期刊介绍： 3 Biotech publishes the results of the latest research related to the study and application of biotechnology to: - Medicine and Biomedical Sciences - Agriculture - The Environment The focus on these three technology sectors recognizes that complete Biotechnology applications often require a combination of techniques. 3 Biotech not only presents the latest developments in biotechnology but also addresses the problems and benefits of integrating a variety of techniques for a particular application. 3 Biotech will appeal to scientists and engineers in both academia and industry focused on the safe and efficient application of Biotechnology to Medicine, Agriculture and the Environment.