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Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus.

Liang Y, Xiong Z, Zheng J, Xu D, Zhu Z, Xiang J, Gan J, Raboanatahiry N, Yin Y, Li M - Sci Rep (2016)

Bottom Line: More than two-thirds of the BnLEA genes are associated with segmental duplication.These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family.This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China.

ABSTRACT
Late embryogenesis abundant (LEA) proteins are a diverse and large group of polypeptides that play important roles in desiccation and freezing tolerance in plants. The LEA family has been systematically characterized in some plants but not Brassica napus. In this study, 108 BnLEA genes were identified in the B. napus genome and classified into eight families based on their conserved domains. Protein sequence alignments revealed an abundance of alanine, lysine and glutamic acid residues in BnLEA proteins. The BnLEA gene structure has few introns (<3), and they are distributed unevenly across all 19 chromosomes in B. napus, occurring as gene clusters in chromosomes A9, C2, C4 and C5. More than two-thirds of the BnLEA genes are associated with segmental duplication. Synteny analysis revealed that most LEA genes are conserved, although gene losses or gains were also identified. These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family. Expression profiles analysis indicated that expression of most BnLEAs was increased in leaves and late stage seeds. This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family.

No MeSH data available.


Distribution of BnLEA gene family members on B. napus chromosomes.The 96 BnLEA genes for which exact chromosomal information was available in the database were mapped to the 19 B. napus chromosomes. The color of each gene indicates the corresponding family.
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f4: Distribution of BnLEA gene family members on B. napus chromosomes.The 96 BnLEA genes for which exact chromosomal information was available in the database were mapped to the 19 B. napus chromosomes. The color of each gene indicates the corresponding family.

Mentions: The chromosomal location of the LEA genes was analyzed, and the positions and chromosome locations of 96 BnLEA genes were clearly identified on the 19 chromosomes of B. napus (Table 1, Fig. 4). The number of BnLEA genes varies considerably among the different chromosomes, and chromosomes C3 and A6 contain the greatest (n = 12) and lowest (n = 1) numbers, respectively (Fig. 4). In general, genes belonging to the same family are distributed in different chromosomes to realize full functionality. Interestingly, genes of the dehydrin and LEA_4 families are only located on chromosomes A7, C6 and A8, suggesting that these genes have a tendency to duplicate and evolve more conservatively within one chromosome. High-density LEA gene clusters were identified in certain chromosomal regions, e.g., at the top of chromosomes A9, C2, C4, and C5 and in the middle of chromosome C3 (Fig. 4). Thus, the final chromosomal locations of the LEA genes may be the result of LEA gene duplication patterns.


Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus.

Liang Y, Xiong Z, Zheng J, Xu D, Zhu Z, Xiang J, Gan J, Raboanatahiry N, Yin Y, Li M - Sci Rep (2016)

Distribution of BnLEA gene family members on B. napus chromosomes.The 96 BnLEA genes for which exact chromosomal information was available in the database were mapped to the 19 B. napus chromosomes. The color of each gene indicates the corresponding family.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829847&req=5

f4: Distribution of BnLEA gene family members on B. napus chromosomes.The 96 BnLEA genes for which exact chromosomal information was available in the database were mapped to the 19 B. napus chromosomes. The color of each gene indicates the corresponding family.
Mentions: The chromosomal location of the LEA genes was analyzed, and the positions and chromosome locations of 96 BnLEA genes were clearly identified on the 19 chromosomes of B. napus (Table 1, Fig. 4). The number of BnLEA genes varies considerably among the different chromosomes, and chromosomes C3 and A6 contain the greatest (n = 12) and lowest (n = 1) numbers, respectively (Fig. 4). In general, genes belonging to the same family are distributed in different chromosomes to realize full functionality. Interestingly, genes of the dehydrin and LEA_4 families are only located on chromosomes A7, C6 and A8, suggesting that these genes have a tendency to duplicate and evolve more conservatively within one chromosome. High-density LEA gene clusters were identified in certain chromosomal regions, e.g., at the top of chromosomes A9, C2, C4, and C5 and in the middle of chromosome C3 (Fig. 4). Thus, the final chromosomal locations of the LEA genes may be the result of LEA gene duplication patterns.

Bottom Line: More than two-thirds of the BnLEA genes are associated with segmental duplication.These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family.This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China.

ABSTRACT
Late embryogenesis abundant (LEA) proteins are a diverse and large group of polypeptides that play important roles in desiccation and freezing tolerance in plants. The LEA family has been systematically characterized in some plants but not Brassica napus. In this study, 108 BnLEA genes were identified in the B. napus genome and classified into eight families based on their conserved domains. Protein sequence alignments revealed an abundance of alanine, lysine and glutamic acid residues in BnLEA proteins. The BnLEA gene structure has few introns (<3), and they are distributed unevenly across all 19 chromosomes in B. napus, occurring as gene clusters in chromosomes A9, C2, C4 and C5. More than two-thirds of the BnLEA genes are associated with segmental duplication. Synteny analysis revealed that most LEA genes are conserved, although gene losses or gains were also identified. These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family. Expression profiles analysis indicated that expression of most BnLEAs was increased in leaves and late stage seeds. This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family.

No MeSH data available.