Genome-Wide Identification and Characterization of Short-Chain Dehydrogenase/Reductase (SDR) Gene Family in Medicago truncatula

Abstract

Short-chain dehydrogenase/reductase (SDR) belongs to the NAD(P)(H)-dependent oxidoreductase superfamily. Limited investigations reveal that SDRs participate in diverse metabolisms. A genome-wide identification of the SDR gene family in M. truncatula was conducted. A total of 213 MtSDR genes were identified, and they were distributed on all chromosomes unevenly. MtSDR proteins were categorized into seven subgroups based on phylogenetic analysis and three types including 'classic', 'extended', and 'atypical', depending on the cofactor-binding site and active site. Analysis of the data from M. truncatula Gene Expression Atlas (MtGEA) showed that above half of MtSDRs were expressed in at least one organ, and lots of MtSDRs had a preference in a tissue-specific expression. The cis-acting element responsive to plant hormones (salicylic acid, ABA, auxin, MeJA, and gibberellin) and stresses were found in the promoter of some MtSDRs. Many genes of MtSDR7C,MtSDR65C, MtSDR110C, MtSDR114C, and MtSDR108E families were responsive to drought, salt, and cold. The study provides useful information for further investigation on biological functions of MtSDRs, especially in abiotic stress adaptation, in the future.

Keywords: Medicago truncatula; abiotic stress; cis-acting elements; expression profiles; short-chain dehydrogenase/reductase.

Figure 1

Phylogenetic tree of the domain relationship of MtSDRs. The different colors perform the different groups (or subgroups) of MtSDR.

Figure 2

Details of Ten Motifs of MtSDRs.

Figure 3

Synteny analysis of interchromosomal relationships of MtSDR genes. Red lines indicate duplicated gene pairs.

Figure 4

Synteny analysis of MtSDR genes in the genomes between M. truncatula and A. thaliana or G.max. (A) M. truncatula and A. thaliana; (B) M. truncatula and G.max. The gray lines show collinear blocks. The red and blue lines indicate the syntenic gene pairs between M. truncatula and A. thaliana or G. max, respectively.

Figure 5

Heat map of MtSDRs in different organs. The expression data of MtSDRs in flowers, leaves, petioles, flowers, roots, stems, and seeds were collected from M. truncatula Gene Expression Atlas (MtGEA, https://mtgea.noble.org/v3/, accessed on 5 April 2021). The relative expression of heat map was characterized by log₂ transformed.

Figure 6

The number of cis-acting elements was tested in the promoter region of MtSDRs. The name of cis-acting elements was listed on the left side of the image, and the corresponding function annotation was listed on the right side.

Figure 7

Heat map of MtSDRs expression in response to salt and drought stress. The expression data were collected from M. truncatula Gene Expression Atlas (MtGEA, https://mtgea.noble.org/v3/, accessed on 5 April 2021). (A) Two-week-old seedlings were treated with 180 mM NaCl for 0, 6, 24, and 48 h, respectively. (B) Twenty-four-day-old seedlings were withholding irrigation for soil drying for 14 d, followed by 1 d of rewatering.

Figure 8

Relative expression of MtSDR7C6 (A), SDR65C8 (B), SDR108E3 (C), SDR108E18 (D), SDR110C15 (E), and SDR132C6 (F) in response to cold treatment. Four-week-old seedlings were placed in a growth chamber at 4 °C for 0, 2, 6, 12, and 24 h. Mean values and standard errors were calculated from three biological replicates. * indicates significant difference between cold treatment and control using one-way ANOVA at p ≤ 0.05.

Figure 9

Subcellular localization of MtSDRs. The injected tobacco was used for observation. PM-marker: plasma membrane localization protein AtAKT1. Bars = 20 µm.