Genome-Wide Identification and Characterization of the Vacuolar H⁺-ATPase Subunit H Gene Family in Crop Plants

• Main Authors: Chen Kang, Fengjie Sun, Lei Yan, Rui Li, Jianrong Bai, Gustavo Caetano-Anollés
• Format: Article
• Language: English
• Published: MDPI AG 2019-10-01
• Series: International Journal of Molecular Sciences
• Subjects: v-atpase subunit h; exon-intron structure; alternative splicing; structural domains; vacuole
• Online Access: https://www.mdpi.com/1422-0067/20/20/5125

The vacuolar H⁺-ATPase (V-ATPase) plays many important roles in cell growth and in response to stresses in plants. The V-ATPase subunit H (VHA-H) is required to form a stable and active V-ATPase. Genome-wide analyses of <i>VHA-H</i> genes in crops contribute significantly to a systematic understanding of their functions. A total of 22 <i>VHA-H</i> genes were identified from 11 plants representing major crops including cotton, rice, millet, sorghum, rapeseed, maize, wheat, soybean, barley, potato, and beet. All of these <i>VHA-H</i> genes shared exon-intron structures similar to those of <i>Arabidopsis thaliana</i>. The C-terminal domain of VHA-H was shorter and more conserved than the N-terminal domain. The <i>VHA-H</i> gene was effectively used as a genetic marker to infer the phylogenetic relationships among plants, which were congruent with currently accepted taxonomic groupings. The <i>VHA-H</i> genes from six species of crops (<i>Gossypium raimondii</i>, <i>Brassica napus</i>, <i>Glycine max</i>, <i>Solanum tuberosum</i>, <i>Triticum aestivum</i>, and <i>Zea mays</i>) showed high gene structural diversity. This resulted from the gains and losses of introns. Seven <i>VHA-H</i> genes in six species of crops (<i>Gossypium raimondii</i>, <i>Hordeum vulgare</i>, <i>Solanum tuberosum</i>, <i>Setaria italica</i>, <i>Triticum aestivum</i>, and <i>Zea mays</i>) contained multiple transcript isoforms arising from alternative splicing. The study of cis-acting elements of gene promoters and RNA-seq gene expression patterns confirms the role of <i>VHA-H</i> genes as eco-enzymes. The gene structural diversity and proteomic diversity of <i>VHA-H</i> genes in our crop sampling facilitate understanding of their functional diversity, including stress responses and traits important for crop improvement.