Bioinformatics Analysis of BnMYB80 Genes in Brassica napus

doi:10.11983/CBB16006

Abstract

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.

Key words: bioinformatics, Brassica napus, MYB80, pollen development, tapetum

Jia Ledong, Li Shimeng, Xu Daixiang, Qu Cunmin, Li Jiana, Wang Rui. Bioinformatics Analysis of BnMYB80 Genes in Brassica napus [J]. Chinese Bulletin of Botany, 2016, 51(5): 620-630.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB16006

https://www.chinbullbotany.com/EN/Y2016/V51/I5/620

Figures/Tables 7

References 39

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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

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

Gene name	CDS (bp)	Exon	MYB80 conserved domain (aa)
Gene name	CDS (bp)	Exon	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

Gene name	CDS (bp)	Exon	MYB80 conserved domain (aa)
Gene name	CDS (bp)	Exon	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

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