Expansin gene family in association with the genome differentiation of <i>Salix matsudana</i>

Yang Ruixia; Yin Peng; Liu Xiao; Wang Yan; Liu Jiafu; Xu Jichen

doi:10.12171/j.1000-1522.20200216

Journal of Beijing Forestry University > 2021 > 43(1): 37-48. > DOI: 10.12171/j.1000-1522.20200216

Yang Ruixia, Yin Peng, Liu Xiao, Wang Yan, Liu Jiafu, Xu Jichen. Expansin gene family in association with the genome differentiation of Salix matsudana[J]. Journal of Beijing Forestry University, 2021, 43(1): 37-48. DOI: 10.12171/j.1000-1522.20200216

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Expansin gene family in association with the genome differentiation of Salix matsudana

National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China

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Received Date: July 12, 2020
Revised Date: August 27, 2020
Available Online: December 28, 2020
Published Date: February 04, 2021

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Abstract

Abstract

Objective Expansin, an important gene family in plants, plays a critical role in plant growth and development and resistance to various biotic and abiotic stresses. The purpose of this study was to investigate the variation of expansin genes in Salix matsudana so as to provide theoretical basis for understanding the AA and BB genome differentiation in Salix matsudana, and to contribute greatly for molecular design and breeding of Salix.
Method According to the expansin gene sequences of Populus trichocarpa, the expansin family genes in Salix matsudana were individually identified. The characteristics and variations of the expansin genes in AA and BB genome were analyzed and evaluated by the bioinformatics softwares.
Result A total of 65 expansin genes were identified in allotetraploid Salix matsudana based on the conservation of sequence and structure of the expansin genes. Both genomes shared 28 genes with 3 genes duplicated. Moreover, 3 expansin genes were missed and 2 genes were with a domain deficient in AA genome, while 3 expansin genes were missed and 1 gene was with a domain deficient in BB genome, respectively. Gene structure analysis showed the considerable changes in the number and cutting sites of intron between the relative gene pairs of both genomes. Besides, AA and BB expansin genes both had 5 high-frequency codons, and separately had 5 and 10 optimal codons. Some codons had significant usage bias such as AGG and UAG. Evaluation of the protein physicochemical properties showed that the AA and BB expansins changed a lot, especially in terms of hydrophilicity and structural stability. Ka/Ks calculation displayed that EXPA23 gene had experienced positive selection during AA and BB genome differentiation, while the other genes underwent purification selection with Ka/Ks value changed widely.
Conclusion The report here characterized the composition, structure and expression of the expansin genes in AA and BB genomes, which probably advanced the genome differentiation and further confirmed the important status of expansins in species classification.
- Salix matsudana,
- expansin,
- gene family,
- codon usage bias,
- differentiation analysis

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Expansin gene family in association with the genome differentiation of Salix matsudana