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

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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References

[1]	Ma N, Wang Y, Qiu S, et al. Overexpression of OsEXPA8, a root-specific gene, improves rice growth and root system architecture by facilitating cell extension[J/OL]. PLoS One, 2013, 8(10): e75997 (2013−10−04) [2019−03−13]. https://doi.org/10.1371/journal.pone.0075997.eCollection 2013.
[2]	Kuluev B, Safiullina M, Knyazev A, et al. Effect of ectopic expression of NtEXPA5 gene on cell size and growth of organs of transgenic tobacco plants[J]. Russian Journal of Developmental Biology, 2013, 44: 28−34. doi: 10.1134/S1062360413010049.
[3]	Yan A, Wu M, Yan L, et al. AtEXP2 is involved in seed germination and abiotic stress response in Arabidopsis[J/OL]. PLoS One, 2014, 9(1): e85208 (2014−01−03) [2019−04−07]. https://doi.org/10.1371/journal.pone.0085208.
[4]	Ouyang K X, Liu M Q, Pian R Q, et al. Methodology Isolation and analysis of α-expansin genes in the tree Anthocephalus chinensis (Rubiaceae)[J]. Genetics and Molecular Research, 2013, 12(2): 1061−1073. doi: 10.4238/2013.April.10.2.
[5]	Zenoni S, Fasoli M, Tornielli G B, et al. Overexpression of PhEXPA1 increases cell size, modifies cell wall polymer composition and affects the timing of axillary meristem development in Petunia hybrida[J]. New Phytologist, 2011, 191(3): 662−677. doi: 10.1111/j.1469-8137.2011.03726.x.
[6]	Perini M A, Sin I N, Villarreal N M, et al. Overexpression of the carbohydrate binding module from, Solanum lycopersicum, expansin 1 (Sl-EXP1) modifies tomato fruit firmness and Botrytis cinereal susceptibility[J]. Plant Physiology and Biochemistry, 2017, 113: 122−132. doi: 10.1016/j.plaphy.2017.01.029.
[7]	Castillo F M, Canales J, Claude A, et al. Expansin genes expression in growing ovaries and grains of sunflower are tissue-specific and associate with final grain weight[J/OL]. BMC Plant Biology, 2018, 18(1): 327 (2018−12−10) [2019−01−14]. https://doi.org/10.1186/s12870-018-1535-7.
[8]	Feng X, Xu Y, Peng L, et al. TaEXPB7-B, a β-expansin gene involved in low-temperature stress and abscisic acid responses, promotes growth and cold resistance in Arabidopsis thaliana [J/OL]. Journal of Plant Physiology, 2019, 240: 153004 (2019−06−25) [2019−09−07]. https://doi.org/10.1016/j.jplph.2019.153004.
[9]	Ren Y Q, Chen Y H, An J, et al. Wheat expansin gene, TaEXPA2, is involved in conferring plant tolerance to Cd toxicity[J]. Plant Science, 2018, 270: 245−256. doi: 10.1016/j.plantsci.2018.02.022.
[10]	Chen L J, Zou W S, Wu G, et al. Tobacco alpha-expansin EXPA4 plays a role in Nicotiana benthamiana defence against tobacco mosaic virus[J]. Planta, 2018, 247(2): 355−368. doi: 10.1007/s00425-017-2785-6
[11]	Ding A, Marowa P, Kong Y. Genome-wide identification of the expansin gene family in tobacco (Nicotiana tabacum)[J]. Molecular Genetics & Genomics, 2016, 291(5): 1891−1907.
[12]	Han Z S, Liu Y L, Deng X, et al. Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)[J/OL]. BMC Genomics, 2019, 20(1): 101 (2019−02−01) [2019−11−25]. https://doi.org/10.1186/s12864-019-5455-1.
[13]	李昊阳, 施杨, 丁亚娜. 杨树扩展蛋白基因家族的生物信息学分析[J]. 北京林业大学学报, 2014, 36(2):59−67. Li H Y, Shi Y, Ding Y N. Bioinformatics analysis of expansin gene family in poplar genome[J]. Journal of Beijing Forestry University, 2014, 36(2): 59−67.
[14]	Hou L, Zhang Z Y, Dou S H, et al. Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.)[J]. Planta, 2019, 249(3): 815−829.
[15]	Santiago T R, Pereira V M, de Souza W R, et al. Genome-wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.)[J/OL]. PLoS One, 2018, 13(4): e0196140 (2018−04−17)[2019−05−17]. https://doi.org/10.1371/journal.pone.0196140.eCollection2018.
[16]	Li N, Pu Y, Gong Y, et al. Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in Triticum aestivum[J]. Genes & Genomics, 2016, 38(5): 1021−1030.
[17]	Zhang H, Li J, Wang R X, et al. Comparative analysis of expansin gene codon usage patterns among eight plant species[J]. Journal of Biomolecular Structure and Dynamics, 2019, 37(4): 910−917. doi: 10.1080/07391102.2018.1442746.
[18]	Quiñones Martorello A S, Fernández M E, Monterubbianesi M G, et al. Effect of combined stress (salinity + hypoxia) and auxin rooting hormone addition on morphology and growth traits in six Salix spp. clones[J]. New Forests, 2020, 51: 61−80. doi: 10.1007/s11056-019-09719-8.
[19]	耿云红. 干旱胁迫对绿化木本植物抗逆性研究[J]. 山东农业大学学报(自然科学版), 2019, 50(1):12−18. Geng Y H. Study on resistance of woody plants under drought stress[J]. Journal of Shandong Agricultural University (Natural Science), 2019, 50(1): 12−18.
[20]	刘春风. 淹水对15个树种苗木生长和形态特征的影响[D]. 南京: 南京林业大学, 2009. Liu C F. Effects of artificial flooding on the growth and morphological characteristics of 15 trees species seedlings[D]. Nanjing: Nanjing Forestry University, 2009.
[21]	Shu Y, Li K L, Song J F, et al. Single and competitive adsorption of Cd (Ⅱ) and Pb (Ⅱ) from aqueous solution by activated carbon prepared with Salix matsudana Kiodz[J]. Water Science and Technology, 2016, 74 (12): 2751−2761. doi: 10.2166/wst.2016.428.
[22]	Gullberg U. Towards making willows pilot species for coppicing production[J]. The Forestry Chronicle, 1993, 69(6): 721−726. doi: 10.5558/tfc69721-6.
[23]	Argus G W. Infrageneric classification of Salix (Salicaceae) in the new world[J]. Systematic Botany Monographs, 1997, 52: 1−121. doi: 10.2307/25096638.
[24]	Zhang J, Yuan H, Li M, et al. A high-density genetic map of tetraploid Salix matsudana using specific length amplified fragment sequencing (SLAF-seq)[J/OL]. PLoS ONE, 2016, 11(6): e0157777 (2016−06−21) [2019−02−12]. https://doi.org/10.1371/journal.pone.0157777.eCollection2016.
[25]	Zhang J, Yuan H, Yang Q, et al. The genetic architecture of growth traits in Salix matsudana under salt stress[J/OL]. Horticulture Research, 2017, 4: 17024 (2017−06−14) [2019−01−21]. https://doi.org/10.1038/hortres.2017.24. eCollection2017.
[26]	Prabha R, Singh D P, Sinha S, et al. Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes[J]. Marine Genomics, 2017, 32: 31−39. doi: 10.1016/j.margen.2016.10.001.
[27]	Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhab-ditis, Drosophila, and Arabidopsis[J]. Proceedings of the National Academy of Sciences, 1999, 96: 4482−4487. doi: 10.1073/pnas.96.8.4482.
[28]	王兰伟. 异源多倍体物种的形成和演化:来自菊科蓍草属的证据[D]. 开封: 河南大学, 2011. Wang L W. Allotetraploid speciation and evolution: evidence from the eastern asia Achillea species[D]. Kaifeng: Henan University, 2011.
[29]	Tayale A, Parisod C. Natural pathways to polyploidy in plants and consequences for genome reorganization[J]. Cytogenetic & Genome Research, 2013, 140: 2−4.
[30]	Liu B, Wendel J F. Non-Mendelian phenomena in allopolyploid genome evolution[J]. Current Genomics, 2002, 3(6): 489−505. doi: 10.2174/1389202023350255.
[31]	Wei S, Yang Y, Yin T. The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution [J/OL]. Horticulture Research, 2020, 7: 45 (2020−04−01) [2020−04−25]. https://www.nature.com/articles.
[32]	Grantham R, Gautier C, Gouy M, et al. Codon catalog usage and the genome hypothesis[J]. Nucleic Acids Research, 1980, 8(1): 49−62.
[33]	Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type[J]. Nucleic Acids Research, 1980, 8(9): 1893−1912.
[34]	Lloyd A T, Sharp P M. Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae[J]. Nucleic Acids Research, 1992, 20(20): 5289−5295. doi: 10.1093/nar/20.20.5289.
[35]	Grocock R J, Sharp P M. Synonymous codon usage in Cryptosporidium parvum: identification of two distinct trends among genes[J]. International Journal for Parasitology, 2001, 31(4): 402−412. doi: 10.1016/S0020-7519(01)00129-1.
[36]	Povolotskaya I S, Kondrashov F A, Ledda A, et al. Stop codons in bacteria are not selectively equivalent[J/OL]. Biology Direct, 2012, 7: 30 (2012−09−13)[2019−06−19]. https://link.springer.com/article/10.1186/1745-6150-7-30.
[37]	Korkmaz G, Holm M, Wiens T, et al. Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance[J]. Journal of Biological Chemistry, 2014, 289(44): 30334−30342. doi: 10.1074/jbc.M114.606632.
[38]	Krisko A, Copic T, Gabaldón T, et al. Inferring gene function from evolutionary change in signatures of translation efficiency [J/OL]. Genome Biology, 2014, 15: 44 (2014−03−03) [2019−06−08]. https://link.springer.com/article/10.1186/gb-2014-15-3-r44.
[39]	Presnyak V, Alhusaini N, Chen Y H, et al. Codon optimality is a major determinant of mRNA stability[J]. Cell, 2015, 160(6): 1111−1124. doi: 10.1016/j.cell.2015.02.029.
[40]	Navarro A, Barton N H. Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes[J]. Science, 2003, 300: 321−324. doi: 10.1126/science.1080600.

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

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