Phylogenetic insight into ABCE gene subfamily in plants

• Published in: Frontiers in genetics 2024-06, Vol.15, p.1408665
• Main Authors: Jakobson, Liina, Mõttus, Jelena, Suurväli, Jaanus, Sõmera, Merike, Tarassova, Jemilia, Nigul, Lenne, Smolander, Olli-Pekka, Sarmiento, Cecilia
• Format: Article
• Language: English
• Subjects: ABCE; ABCE gene subfamily; gene evolution; Genetics; natural variation; phylogenetics
• ISSN: 1664-8021; 1664-8021
• DOI: 10.3389/fgene.2024.1408665

ATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and most animals possess a single gene encoding the critical translational factor ABCE1. In several plant species, including and , two or more gene copies have been identified, however information related to plant gene family is still missing. In this study we retrieved gene sequences of 76 plant species from public genome databases and comprehensively analyzed them with the reference to gene ( ). Using bioinformatic approach we assessed the conservation and phylogeny of plant ABCEs. In addition, we performed haplotype analysis of and its paralogue using genomic sequences of 1,135 ecotypes. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. We found that over half of the selected species have two to eight genes, suggesting that in plants genes can be classified as a low-copy gene family, rather than a single-copy gene family. The phylogenetic trees of ABCE protein sequences and the corresponding coding sequences demonstrated that and families have independently undergone lineage-specific split of the ancestral gene. Other plant species have gained gene copies through more recent duplication events. We also noticed that ploidy level but not ancient whole genome duplications experienced by a species impacts gene family size. Deeper analysis of and from 1,135 ecotypes revealed four and 35 non-synonymous SNPs, respectively. The lower natural variation in compared to is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor.