The Identification of MATE Antisense Transcripts in Soybean Using Strand-Specific RNA-Seq Datasets.

Yee-Shan Ku,Hon-Ming Lam,Gyuhwa Chung,Sau-Shan Cheng,Ting-Fung Chan,Xiao Lin,Kejing Fan

doi:10.3390/genes13020228

Yee-Shan Ku, Hon-Ming Lam + Show 5 more

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https://doi.org/10.3390/genes13020228

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Abstract

Natural antisense transcripts (NATs) have been generally reported as negative regulators of their sense counterparts. Multidrug and toxic compound extrusion (MATE) proteins mediate the transport of various substrates. Although MATEs have been identified genome-wide in various plant species, their transcript regulators remain unclear. Here, using the publicly available strand-specific RNA-seq datasets of Glycine soja (wild soybean) which have the data from various tissues including developing pods, developing seeds, embryos, cotyledons and hypocotyls, roots, apical buds, stems, and flowers, we identified 35 antisense transcripts of MATEs from 28 gene loci after transcriptome assembly. Spearman correlation coefficients suggested the positive expression correlations of eight MATE antisense and sense transcript pairs. By aligning the identified transcripts with the reference genome of Glycine max (cultivated soybean), the MATE antisense and sense transcript pairs were identified. Using soybean C08 (Glycine max), in developing pods and seeds, the positive correlations between MATE antisense and sense transcript pairs were shown by RT-qPCR. These findings suggest that soybean antisense transcripts are not necessarily negative transcription regulators of their sense counterparts. This study enhances the existing knowledge on the transcription regulation of MATE transporters by uncovering the previously unknown MATE antisense transcripts and their potential synergetic effects on sense transcripts.

Highlights

Multidrug and toxic compound extrusion (MATE) transporters typically consist of 12 transmembrane domains (TMDs) [1] and play important roles in cellular transport, metabolism, and physiology [2,3,4]
In a genome-wide survey based on the presence of the conserved MATE domain, 117 MATE genes were identified in the soybean genome [10]
In this study, using strand-specific RNA-seq datasets from the tissues of soybean accession W05 and the reference grade genome of W05 [31], we identified a set of MATE antisense transcripts

Summary

Introduction

Multidrug and toxic compound extrusion (MATE) transporters typically consist of 12 transmembrane domains (TMDs) [1] and play important roles in cellular transport, metabolism, and physiology [2,3,4]. MATE transporters have been reported to be involved in the transportation of various substrates, including ion chelators, phytohormones, alkaloids and flavonoids [4,6,7]. In terms of biological processes, MATE proteins have been reported to regulate various processes such as detoxification, stress tolerance, growth and development, and senescence of plants [8,9]. The diverse substrate specificities of MATE proteins to transport various substrates and regulate diverse biological processes could be the possible reason rendering the big families of MATEs in plant genomes. Some substrates transported by MATE proteins are specific to particular groups of plants. The rich diversity of metabolites in particular plant species hints at the need for a large number of transporters and the big MATE families in plants compared to other eukaryotes. Since MATE genes are differentially expressed in different tissue types and different developmental stages [7,20], it is plausible that there are additional regulatory roles that these genes play besides transcriptional regulation

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