Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa
Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns...
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doaj-f5d85ea5a58b47448c44164d6617f6a22020-11-25T00:55:59ZengMDPI AGInternational Journal of Molecular Sciences1422-00672018-07-01197206410.3390/ijms19072064ijms19072064Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapaMingliang Jiang0Xiangshu Dong1Hong Lang2Wenxing Pang3Zongxiang Zhan4Xiaonan Li5Zhongyun Piao6College of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, ChinaSchool of Agriculture, Yunnan University, Kunming 650504, ChinaKey Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, ChinaCollege of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, ChinaCollege of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, ChinaCollege of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, ChinaCollege of Horticulture, Shenyang Agricultural University, #120 Dongling Road, Shenyang 110866, ChinaOrphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.http://www.mdpi.com/1422-0067/19/7/2064Brassica-specific genesidentificationvalidationgene expressionPlasmodiophora brassicae |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mingliang Jiang Xiangshu Dong Hong Lang Wenxing Pang Zongxiang Zhan Xiaonan Li Zhongyun Piao |
spellingShingle |
Mingliang Jiang Xiangshu Dong Hong Lang Wenxing Pang Zongxiang Zhan Xiaonan Li Zhongyun Piao Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa International Journal of Molecular Sciences Brassica-specific genes identification validation gene expression Plasmodiophora brassicae |
author_facet |
Mingliang Jiang Xiangshu Dong Hong Lang Wenxing Pang Zongxiang Zhan Xiaonan Li Zhongyun Piao |
author_sort |
Mingliang Jiang |
title |
Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa |
title_short |
Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa |
title_full |
Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa |
title_fullStr |
Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa |
title_full_unstemmed |
Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa |
title_sort |
mining of brassica-specific genes (bsgs) and their induction in different developmental stages and under plasmodiophora brassicae stress in brassica rapa |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2018-07-01 |
description |
Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa. |
topic |
Brassica-specific genes identification validation gene expression Plasmodiophora brassicae |
url |
http://www.mdpi.com/1422-0067/19/7/2064 |
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