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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.


Phylogenetic relationships and hypothetical evolutionary progress of the clustering of BnLEA genes in B. napus chromosome C5.(A) Phylogenetic relationships of selected BnLEA genes in the cluster. (B) Hypothetical mechanism of BnLEA gene cluster formation. The letters T, S, and W in the schematic diagram of the hypothetical origins of BnLEA genes indicate putative tandem duplication, segmental duplication and whole-genome duplication, respectively.
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f6: Phylogenetic relationships and hypothetical evolutionary progress of the clustering of BnLEA genes in B. napus chromosome C5.(A) Phylogenetic relationships of selected BnLEA genes in the cluster. (B) Hypothetical mechanism of BnLEA gene cluster formation. The letters T, S, and W in the schematic diagram of the hypothetical origins of BnLEA genes indicate putative tandem duplication, segmental duplication and whole-genome duplication, respectively.

Mentions: Furthermore, the synteny maps of the genes in the clusters located in chromosomes A9 and C4 revealed the process of gene expansion and clustering (Fig. 5). In chromosome C4, the genes in two A. thaliana chromosomes (chromosomes 2 and 3) were linked to B. oleracea genes and were accompanied by gene expansion in B. napus (Fig. 5A). Among the analyzed genes, nearly half of them contained crossovers. In chromosome A9, the homologous A. thaliana LEA genes are distributed in all five Arabidopsis chromosomes. The clustering progress from A. thaliana to B. rapa is more obvious (Fig. 5B), and all groups of genes linked to B. napus contain crossovers, suggesting that the crossover events occurred during the allopolyploidy progress. The BnLEA gene clusters likely formed via the duplication of an ancestral gene during the WGD event, followed by tandem duplication and segmental duplication in the clusters. In the cluster of chromosome C5, BnLEA66/BnLEA65 and BnLEA12/BnLEA13 are tandem duplication genes, although phylogenetic analysis regrouped BnLEA63 and BnLEA11 together with these genes, respectively, indicating that these genes might have descended from a common ancestor (Fig. 6A). Moreover, in the gene cluster, BnLEA4 and BnLEA6 are associated with segmental duplication because they exhibitsynteny relationships with BnLEA3 and BnLEA5, respectively. Phylogenetic analysis also demonstrated that BnLEA3/BnLEA4 and BnLEA5/BnLEA6 are pairs of homologous genes, suggesting that the four genes might have descended from two ancestors. Interestingly, BnLEA3 and BnLEA5 are located in close proximity on chromosome A10, which implies that segmental duplication also played a role in LEA gene cluster formation (Fig. 6B).


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)

Phylogenetic relationships and hypothetical evolutionary progress of the clustering of BnLEA genes in B. napus chromosome C5.(A) Phylogenetic relationships of selected BnLEA genes in the cluster. (B) Hypothetical mechanism of BnLEA gene cluster formation. The letters T, S, and W in the schematic diagram of the hypothetical origins of BnLEA genes indicate putative tandem duplication, segmental duplication and whole-genome duplication, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Phylogenetic relationships and hypothetical evolutionary progress of the clustering of BnLEA genes in B. napus chromosome C5.(A) Phylogenetic relationships of selected BnLEA genes in the cluster. (B) Hypothetical mechanism of BnLEA gene cluster formation. The letters T, S, and W in the schematic diagram of the hypothetical origins of BnLEA genes indicate putative tandem duplication, segmental duplication and whole-genome duplication, respectively.
Mentions: Furthermore, the synteny maps of the genes in the clusters located in chromosomes A9 and C4 revealed the process of gene expansion and clustering (Fig. 5). In chromosome C4, the genes in two A. thaliana chromosomes (chromosomes 2 and 3) were linked to B. oleracea genes and were accompanied by gene expansion in B. napus (Fig. 5A). Among the analyzed genes, nearly half of them contained crossovers. In chromosome A9, the homologous A. thaliana LEA genes are distributed in all five Arabidopsis chromosomes. The clustering progress from A. thaliana to B. rapa is more obvious (Fig. 5B), and all groups of genes linked to B. napus contain crossovers, suggesting that the crossover events occurred during the allopolyploidy progress. The BnLEA gene clusters likely formed via the duplication of an ancestral gene during the WGD event, followed by tandem duplication and segmental duplication in the clusters. In the cluster of chromosome C5, BnLEA66/BnLEA65 and BnLEA12/BnLEA13 are tandem duplication genes, although phylogenetic analysis regrouped BnLEA63 and BnLEA11 together with these genes, respectively, indicating that these genes might have descended from a common ancestor (Fig. 6A). Moreover, in the gene cluster, BnLEA4 and BnLEA6 are associated with segmental duplication because they exhibitsynteny relationships with BnLEA3 and BnLEA5, respectively. Phylogenetic analysis also demonstrated that BnLEA3/BnLEA4 and BnLEA5/BnLEA6 are pairs of homologous genes, suggesting that the four genes might have descended from two ancestors. Interestingly, BnLEA3 and BnLEA5 are located in close proximity on chromosome A10, which implies that segmental duplication also played a role in LEA gene cluster formation (Fig. 6B).

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.