Chin Bull Bot ›› 2016, Vol. 51 ›› Issue (5): 620-630.doi: 10.11983/CBB16006

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Bioinformatics Analysis of BnMYB80 Genes in Brassica napus

Jia Ledong, Li Shimeng, Xu Daixiang, Qu Cunmin, Li Jiana, Wang Rui*()   

  1. College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
  • Received:2016-01-11 Accepted:2016-04-26 Online:2018-08-10 Published:2016-09-01
  • Contact: Wang Rui E-mail:ruiwang71@163.com
  • About author:# Co-first authors

Abstract:

MYB transcription factors play a key role in anther development and pollen formation in higher plants, and MYB80 is an important transcription factor involved in the development of tapetum and initiation of male sterility. In this study, we performed BLASTN and TBLASTX searches of the Arabidopsis thaliana MYB80 (AtMYB80) amino acid sequences against the published database and identified 2, 2 and 6 homologous sequences of MYB80 gene in Brassica rapa, B. oleracea and B. napus, respectively. The composition of nucleic acid sequence and amino acid sequences, subcellular localization, phosphorylation sites, hydrophilicity and hydrophobicity, secondary and tertiary structure of protein, conserved domains of the MYB80 were predicted and analyzed by bioinformatics tools and resources from the Internet. The results showed that the MYB80 transcription factors are located in the nucleus by analyzing subcellular localization, with a number of different phosphorylation sites, and the peptide chains are hydrophilia. The predicted secondary structure and tertiary structure showed that the main structural elements of the MYB80 protein were α helix and random coil. Conserved domain analysis indicated that the MYB80 transcription factor belongs to the MYB-R2R3 type transcription factor, with 2 tandem SANT domains in the N-terminal sequence. The multiple sequence ratio and phylogenetic tree were constructed with MYB80 proteins from different plants; similarity among B. napus and B. rapa, and B. oleracea was more than 92%, and the conserved functional domains had high homology and strong sequence conservation. These results are helpful for resolving the biological functions of MYB80 and the molecular mechanism of sterility regulation and lay a foundation for the heterosis utilization in B. napus.

Table 1

Physicochemical parameters of MYB80 transcription factors"

Gene name Gene ID Chromosome Length (aa) MW (kDa) pI Instability Aliphatic index Gravy
BrMYB80A02 103851848 A02 320 36.1054 6.95 35.89 65.88 -0.808
BrMYB80A10 103845046 A10 320 35.8452 7.24 33.15 69.81 -0.721
BolMYB80C02 106327859 C02 324 36.5430 7.75 37.04 66.57 -0.790
BolMYB80C09 106317148 C09 320 35.9113 7.22 31.94 68.56 -0.740
BnMYB80A02 106389601 A02 322 36.3678 6.95 35.55 65.47 -0.792
BnMYB80A10 674915774 A10 320 35.8232 7.24 34.62 68.59 -0.712
BnMYB80C02 106379735 C02 320 35.9113 7.22 31.94 68.56 -0.740
BnMYB80C03 106385056 C03 320 35.9113 7.22 31.94 68.56 -0.740
BnMYB80C05 106400365 C05 319 35.7842 6.90 33.76 68.50 -0.738
BnMYB80Cnn 106389601 Cnn 324 36.5490 6.93 35.65 66.57 -0.771

Table 2

Analysis of conserved domains of MYB80 transcription factors"

Gene name CDS (bp) Exon MYB80 conserved domain (aa)
SANT SANT IRO KNOX1 Cir_N
BrMYB80A02 1772 3 13-63 66-114 - - -
BrMYB80A10 1631 3 13-63 66-114 - - -
BolMYB80C02 1891 4 13-63 66-114 123-140 130-173 246-282
BolMYB80C09 1573 3 13-63 66-114 123-140 130-173 -
BnMYB80A02 1653 3 13-63 66-114 123-140 130-173 244-280
BnMYB80A10 1471 3 13-63 66-114 123-140 130-173 -
BnMYB80C02 1471 3 13-63 66-114 123-140 130-173 -
BnMYB80C03 1471 3 13-63 66-144 123-140 130-173 -
BnMYB80C05 1461 3 13-63 66-144 123-140 130-173 -
BnMYB80Cnn 1668 3 13-63 66-144 123-140 130-173 246-282

Figure 1

Phosphorylation sites of MYB80 transcription factors"

Table 3

Predicted secondary structure of MYB80 protein"

Gene name α helix (%) Extend strand (%) β turn (%) Random coil (%)
BrMYB80A02 41.25 11.56 10.00 37.19
BrMYB80A10 37.81 14.06 10.00 38.12
BolMYB80C02 44.14 10.19 8.64 37.04
BolMYB80C09 35.94 15.31 10.94 37.81
BnMYB80A02 42.55 11.18 9.63 36.65
BnMYB80A10 37.19 15.00 10.31 37.50
BnMYB80C02 35.94 15.31 10.94 37.81
BnMYB80C03 35.94 15.31 10.94 37.81
BnMYB80C05 36.68 14.73 10.03 38.56
BnMYB80Cnn 44.14 10.49 9.57 35.80

Figure 2

Predicted tertiary structure of BnMYB80 proteins (A) BnMYB80A02; (B) BnMYB80A10; (C) BnMYB80C02; (D) BnMYB80C03; (E) BnMYB80C05; (F) BnMYB80Cnn"

Figure 3

Homologous comparison of the MYB80 proteins"

Figure 4

Phylogenetic tree of MYB80 proteins from different Cruciferous species"

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