Abstract
BackgroundThe cabbage, Brassica oleracea var. capitata L., has a distinguishable phenotype within the genus Brassica. Despite the economic and genetic importance of cabbage, there is little genomic data for cabbage, and most studies of Brassica are focused on other species or other B. oleracea subspecies. The lack of genomic data for cabbage, a non-model organism, hinders research on its molecular biology. Hence, the construction of reliable transcriptomic data based on high-throughput sequencing technologies is needed to enhance our understanding of cabbage and provide genomic information for future work.Methodology/Principal FindingsWe constructed cDNAs from total RNA isolated from the roots, leaves, flowers, seedlings, and calcium-limited seedling tissues of two cabbage genotypes: 102043 and 107140. We sequenced a total of six different samples using the Illumina HiSeq platform, producing 40.5 Gbp of sequence data comprising 401,454,986 short reads. We assembled 205,046 transcripts (≥ 200 bp) using the Velvet and Oases assembler and predicted 53,562 loci from the transcripts. We annotated 35,274 of the loci with 55,916 plant peptides in the Phytozome database. The average length of the annotated loci was 1,419 bp. We confirmed the reliability of the sequencing assembly using reverse-transcriptase PCR to identify tissue-specific gene candidates among the annotated loci.ConclusionOur study provides valuable transcriptome sequence data for B. oleracea var. capitata L., offering a new resource for studying B. oleracea and closely related species. Our transcriptomic sequences will enhance the quality of gene annotation and functional analysis of the cabbage genome and serve as a material basis for future genomic research on cabbage. The sequencing data from this study can be used to develop molecular markers and to identify the extreme differences among the phenotypes of different species in the genus Brassica.
Highlights
Crops of the genus Brassica are commonly used in many foods
High-throughput mRNA sequencing is useful for gene expression profiling in non-model organisms that lack genomic sequence data
There are some sequencing and functional genomics studies of B. oleracea [8,56,57,58,59,60], most genomic or transcriptomic sequencing data from the genus Brassica are focused on B. napus and B. rapa
Summary
Crops of the genus Brassica (tribe Brassiceae) are commonly used in many foods. The model organism Arabidopsis thaliana is a member of the Brassicaceae family. One of the most important crops in the genus Brassica, is a cruciferous vegetable that is native to coastal southern and western Europe. B. oleracea is a diploid species with a CC-type genome containing nine chromosomes: x = 9 (2x = 2n = 18) [2]. Capitata L., has a distinguishable phenotype within the genus Brassica. Despite the economic and genetic importance of cabbage, there is little genomic data for cabbage, and most studies of Brassica are focused on other species or other B. oleracea subspecies. The lack of genomic data for cabbage, a non-model organism, hinders research on its molecular biology. The construction of reliable transcriptomic data based on highthroughput sequencing technologies is needed to enhance our understanding of cabbage and provide genomic information for future work
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