Tong Cen, Jia Yong, Hu Haifei, Zeng Zhanghui, Chapman Brett, Li Chengdao
Western Crop Genetic Alliance, Murdoch University, Murdoch, WA 6150, Australia; State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
Western Crop Genetic Alliance, Murdoch University, Murdoch, WA 6150, Australia; State Agricultural Biotechnology Centre (SABC), College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
Plant Commun. 2025 Jan 13;6(1):101190. doi: 10.1016/j.xplc.2024.101190. Epub 2024 Nov 9.
Genome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161-176 bHLHs in 20 barley genomes, which can be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 softcore, 29 shell, and 20 line-specific/cloud bHLHs, revealing the complete profile of bHLH genes in barley. Using a genome-scanning approach, we overcame the genome annotation bias and identified an average of 1.5 un-annotated core bHLHs per barley genome. We found that whole-genome/segmental duplicates are predominant mechanisms contributing to the expansion of most core/softcore bHLHs, whereas dispensable bHLHs are more likely to result from small-scale duplication events. Interestingly, we noticed that the dispensable bHLHs tend to be enriched in the specific subfamilies SF13, SF27, and SF28, implying the potentially biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least 1 intact transposon element (TE) within the 2-kb upstream-to-downstream region. bHLHs with copy-number variations (CNVs) have 1.48 TEs on average, significantly more than core bHLHs without CNVs (1.36), supporting a potential role of TEs in bHLH expansion. Analyses of selection pressure showed that dispensable bHLHs have experienced clear relaxation of selection compared with core bHLHs, consistent with their conservation patterns. We also integrated the pangenome data with recently available barley pantranscriptome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene-family analyses can better describe the previously untapped, genuine evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley. We expect that this study will inspire similar analyses in many other gene families and species.
全基因组鉴定和比较基因家族分析通常用于研究与各种性状和分子途径相关的物种特异性进化。然而，大多数先前的研究仅限于在单个参考基因组中进行基因筛选，未能考虑物种中的基因存在/缺失变异（gPAVs）。在这里，我们提出了一种基于泛基因组的创新方法，用于基于直系同源基因组（OGGs）进行基因家族分析。以大麦中的基本螺旋-环-螺旋（bHLH）转录因子家族为例，我们在20个大麦基因组中鉴定出161-176个bHLH，可分为201个OGG。这201个OGG进一步分为140个核心、12个软核心、29个外壳和20个谱系特异性/云bHLH，揭示了大麦中bHLH基因的完整概况。使用基因组扫描方法，我们克服了基因组注释偏差，每个大麦基因组平均鉴定出1.5个未注释的核心bHLH。我们发现全基因组/片段重复是导致大多数核心/软核心bHLH扩增的主要机制，而可有可无的bHLH更可能是小规模重复事件的结果。有趣的是，我们注意到可有可无的bHLH往往在特定亚家族SF13、SF27和SF28中富集，这意味着大麦中特定bHLH可能存在偏向性扩增。我们发现50%的bHLH在2 kb上下游区域内至少含有1个完整的转座子元件（TE）。具有拷贝数变异（CNV）的bHLH平均有1.48个TE，明显多于没有CNV的核心bHLH（1.36个），这支持了TE在bHLH扩增中的潜在作用。选择压力分析表明，与核心bHLH相比，可有可无的bHLH经历了明显的选择放松，这与它们的保守模式一致。我们还将泛基因组数据与最近来自5个组织的大麦泛转录组数据相结合，发现bHLH亚家族内部和之间存在明显的转录差异。我们得出结论，基于泛基因组的基因家族分析可以更好地描述bHLH以前未被挖掘的真实进化状态，并为大麦中bHLH的进化提供新的见解。我们期望这项研究将激发许多其他基因家族和物种的类似分析。
