Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

Abstract

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.

Brassica rapa orphan genes largely affect soluble sugar metabolism

“…A previous study first investigated the numbers, features, and expression patterns of OG s in B. rapa ( BrOG s), providing valuable biological information for exploring the function of BrOG s 2 . To explore the functions of these OG s, we developed an A. thaliana overexpression library using 43 BrOG s from B. rapa under the control of the CaMV 35S promoter.…”

“…In addition, the floral-dip method is the easiest way to perform highly efficient gene transformation 8 , 10 , 28 . These BrOG s do not contain any homologous sequences in A. thaliana and their ectopic expression would result in phenotypic variations, making it easier to understand the function of OG s 2 . Furthermore, BrOG function could also be analyzed using A. thaliana as a heterologous host, as OG s could play similar roles across species 5 .…”

“…In a previous study, we identified OG s and revealed their possible roles in B. rapa 2 . However, their functional role remains unknown.…”

“…Orphan genes ( OG s), genes that are restricted to a single lineage or species, show either nonsignificant or no sequence similarity with genes in other related species. OG s have been identified in many species or lineages, such as Arabidopsis thaliana 1 , Brassica rapa 2 , and Citrus sinensis 3 , with the continuing sequencing of several genomes. Although there is limited information on the functional significance of OG s in a particular species, they are known to play a role in primary metabolism, respond to biotic and abiotic stresses, and influence species-specific evolution and species-specific traits.…”

Establishment of Agrobacterium-mediated genetic transformation and application of CRISPR/Cas9 gene-editing system to Chinese cabbage (Brassica rapa L. ssp. pekinensis)

“…A Chinese cabbage orphan gene BraA1000785 with unknown function identified from "Chiifu," a material for B. rapa reference genomic sequencing, was used as target gene [32] for vector construction. The sequence of BraA1000785 was isolated from a Chinese cabbage inbred line "C-24" and used as material for genetic transformation using gene-specific primers (Additional file 1 Table S1).…”