Pangenome and pantranscriptome as the new reference for gene-family characterization: A case study of basic helix-loop-helix (bHLH) genes in barley

作者：Cen Tong, Yong Jia, Haifei Hu, Zhanghui Zeng, B.E. Chapman, Chengdao Li · 发表于：Plant Communications · 年份：2024 · DOI：10.1016/j.xplc.2024.101190 · 被引用次数：62 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Plant Genetic and Mutation Studies、Plant tissue culture and regeneration

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 ups...