Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500, TruSeq mRNA-seq
ORGANISM(S): Flatbergium sericeum
SUBMITTER: Nicolas Devos
PROVIDER: E-MTAB-4112 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Purpose: We conducted an evolutionary-based genome-wide analysis of the MYB-CC gene family in Brassica species. Methods: B. napus (accession Zhongshuang11) was kindly provided by the Oilcrops Research Institute, Chinese Academy of Agricultural Sciences. The seeds were disinfected in 70% ethanol for 1 min, washed with ddH2O three to four times, placed on a petri dish lined with two layers of filter paper, and then germinated at 24oC in growth chamber. After three days, the germinated seedlings were transferred to MS medium containing 0.3% agar and 3% sucrose at pH 5.7. The seedlings grew at 24oC under a long-day light cycle (16 h light/8 h dark) and a relative humidity of 65%. Then the two-week-old plants were cultured in 1 mM and 1 μM Pi liquid medium for 24 h, respectively. Rapeseed seedlings’ shoots and roots were collected and frozen in liquid nitrogen. The RNA-seq analysis was carried out by Biomarker (Beijing). A total of 16 RNA samples were sequenced using the Illumina HiSeq 2,000 platform (Illumina, USA). Results: The position of the MYB-CC genes was investigated according to the B. napus database (http://www.genoscope.cns.fr), the B. oleracea genome database (http://www.ocri-genomics.org), and the Brassica database (BRAD, http://brassicadb.org), respectively. MapInspect software was used to locate the MYB-CC genes. The gene duplication was defined as: a coverage region between two sequences of more than 70% with more than 85% similarity in the coverage region (Zhou et al., 2004; Yang et al., 2008). Additionally, the ka (non-synonymous mutation rate) and ks (synonymous mutation rate) values of the repeating gene pairs were calculated using DnaSp software. Conclusions:This study comprehensively evaluated the identification, classification, expression and evolution analyses of MYB-CC gene family of Brassica species. A total of 30, 34, and 55 MYB-CC genes were identified in B. rapa, B. oleracea, and B. napus, respectively. All of the MYB-CC genes were divided into nine groups in the phylogenetic tree. Members of the same group have similar gene structures and conserved motifs, indicating that they could be conserved during evolution. In Brassica, WGT and allotetraploidy were vital for the expansion of MYB-CC genes.
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