Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea

Zengxiang Wu,Tingdong Fu,Liping Song,Mengjiao Yan,Jinxiong Shen,Bin Yi,Jing Wen,Chaozhi Ma,Jinxing Tu,Kaining Hu

doi:10.1186/s12864-019-5721-2

Zengxiang Wu, Tingdong Fu + Show 8 more

Open Access

https://doi.org/10.1186/s12864-019-5721-2

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Abstract

BackgroundAlloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea.ResultsThe assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes.ConclusionsOn the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene.

Highlights

Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives
When we blast-searched these chloroplast-derived sequences against published Brassicaceae mitochondrial genomes, we found all of them maintained in Brassica rapa, Brassica oleracea, Brassica nigra, Brassica napus, Brassica juncea, Brassica carinata, Raphanus stivus subspecies, Eruca vesicaria, and Sinapis arvensis
Chimeric open reading frames (ORFs) in mitotype-specific sequences (MSSs) are typically related to CMS; for example, a chimeric orf182 located in an MSSs had been demonstrated to be responsible for non-pollen-type abortion in Dongxiang CMS rice [15], whereas in the present study, we found that orf288 for hau CMS and orf138 for ogura CMS are located in MSSs

Summary

Introduction

Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. Comparative mitochondrial genome sequencing between male sterility and maintainer line in CMS is often performed to elucidate sequence rearrangements by repeats, conduct phylogenetic analysis, and uncover candidate genes for CMS [26, 28, 29, 47]. On the basis of genome sequence, transcriptome analysis of mitochondria facilitates whole-genome expression analysis of protein-coding genes and specific ORFs, and enables profiling of RNA editing, which is commonly observed in mitochondria [9, 48]

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