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

ABSTRACT: 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

SUBMITTER: Tong C 

PROVIDER: S-EPMC11783906 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature