Genome-wide Identification, Classification, Molecular Evolution and Expression Analysis of Malate Dehydrogenases in Apple

Abstract

Malate dehydrogenase plays crucial roles in energy homeostasis, plant development and cold and salt tolerance, as it mediates the reversible conversion of malate to oxaloacetate. However, the evolutionary pattern of MDH genes in apple remains elusive. In this study, a total of 20 MDH genes were identified from the “Golden Delicious” apple draft genome. We revealed the physiological and biochemical properties, gene structure, and conserved motifs of MdMDH genes. Chromosomal localization and Ka/Ks ratio analysis of MdMDH genes revealed different selective pressures acted on duplicated MdMDH genes. Exploration of the phylogenetic relationships revealed six clades and similar frequencies between old and recent duplications, and significant differences in the evolutionary rates of the MDH gene family were observed. One MdMDH gene, MDP0000807458, which was highly expressed during apple fruit development and flower bud differentiation, was under positive selection. Thus, we speculated that MDP0000807458 is a likely candidate gene involved in regulation of flower bud differentiation and organic acid metabolism in apple fruits. This study provides a foundation for improved understanding of the molecular evolution of MdMDH genes and further facilitates the functional analysis of MDP0000807458 to unravel its exact role in flower bud differentiation and organic acid metabolism.

Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

“…We performed phylogenetic analyses of these MORF proteins in Populus and A. thaliana . The ratio of nonsynonymous/synonymous substitution rates of PtrMORFs and MORFs in A. thaliana was determined to evaluate the selection pressure on amino acid substitutions (ω = d N /d S ) and the role of Darwinian positive selection in driving gene divergence after duplication [35,36,37]. Generally, ω > 1 indicates positive selection, ω < 1 provides evidence for negative or purifying selection, and ω = 1 supports neutral evolution.…”

Genome-Wide Identification and Characterization of Apple P3A-Type ATPase Genes, with Implications for Alkaline Stress Responses

“…The P 3A -type ATPase (PhPH5) amino acid sequences in petunia [25] and Arabidopsis thaliana [20] were retrieved from the NCBI (https://www.ncbi.nlm.nih.gov/) and The Arabidopsis Information Resource (TAIR) (http://www.arabidopsis.org/) databases, respectively. These sequences were used as queries for identifying homologous genes in basic local alignment search tool (BLAST) searches of the reference genomes of apple [34], pear (Pyrus communis L. "Bartlett") [37], peach (Prunus persica (L.) Batsch) [38], and black raspberry (Rubus occidentalis L.) [39] as described by Tatusov et al [40] and Ma et al [2,3]. Briefly, a local BLAST database was performed for each species with the BLAST 2.2.24 program (http://blast.ncbi.nlm.nih.gov/Blast.cgi), after which the putative orthologous genes were identified using an all-against-all protein BLAST search based on the reciprocal best similarity match.…”

“…The resulting data were performed to estimate the ω value with the ML method of the KaKs Calculator package (version 2.0) [44]. Variations in the ω values were tested with a pairwise comparison as described by Ma et al [2,3].…”

“…Apple (Malus × domestica Borkh.) is one of the most important fruit crops and is primarily cultivated in arid and semiarid regions worldwide [1][2][3]. The stress conditions of salt-alkalinized soil are a major limitation to crop production worldwide.…”

“…Gene duplication and selection are two of the major driving forces of morphogenetic evolution. The duplicated genes are nonfunctional or they evolve novel functions (neofunctionalization) or undergo functional differentiation (subfunctionalization) [2,3,31]. During evolution and domestication, a large proportion of the duplicated genes become nonfunctional because they accumulate deleterious mutations, whereas other duplicated genes undergo neofunctionalization; they are eventually preserved under positive selection pressure [31,32].…”