Analyzing the SPL gene family in Salix suchowensis

doi:10.3969/j.issn.1000-2006.2017.02.009

FENG Kai, HOU Jing, DAI Xiaogang, LI Shuxian

Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2017, Vol. 41 ›› Issue (02) : 55-62.

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Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 2017, Vol. 41 ›› Issue (02) : 55-62. DOI: 10.3969/j.issn.1000-2006.2017.02.009

Analyzing the SPL gene family in Salix suchowensis

FENG Kai, HOU Jing, DAI Xiaogang, LI Shuxian^*

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Abstract

【Objective】This study focused mainly on the differential retention and expansion of the SPL gene family in different species and provided a basis for future study of floral development in angiosperms. 【Method】The SPL gene families of Arabidopsis thaliana, Populus trichocarpa, Salix suchowensis, Vitis vinifera, Carica papaya and Oryza sativa were identified using homology comparison against the SPL domain. BLASTN was used to identify different types of homologous gene pairs. We used in-house Perl scripts combined with KaKs_Calculator to calculate the non-synonymous mutation(K_a)and synonymous mutation(K_s)values of each SPL gene pair. Differential retention and expansion of the SPL gene families of these six angiosperms were determined by synteny analysis. 【Result】 We detected 120 SPL genes in the examined plants. By analyzing the paralogous and orthologous SPL genes among the six species, we found that the species of Salicaceae have a total of 24 paralogous SPLs and 50 orthologous SPLs, which are the most abundant among the six species; papaya had no paralogous SPL. Among these six species, woody plants had the most abundant orthologous SPLs compared with herbaceous plants, and dicotyledons were found to have more orthologous SPLs than monocotyledons. It is noteworthy that all the K_a/K_s values for the paralogous and orthologous SPL gene pairs were less than 1.0. In transcriptome analysis, we detected an SPL gene(willow_GLEAN_10025160)that showed significant different expression in flowering tillers compared to vegetative tillers(P≤ 0.01). 【Conclusion】On the basis of bioinformatic analysis, we found that all the K_a/K_s values for the paralogous and orthologous SPL gene pairs were less than 1.0, indicating that the SPL genes in the six examined species have been undergoing purifying selection during the course of evolution, and that their functions should be relatively conserved. We also found that despite whole-genome duplication events, these angiosperms have undergone large-scale gene loss and gene expansion. Based on the results of sequence collinearity, we explored the intraspecific collinearity of SPL genes and tracked their genome duplication events during the evolutionary history of the six plants. This study provides useful information and clues for further studies of the function of SPL genes in the regulation of plant flowering.

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FENG Kai, HOU Jing, DAI Xiaogang, LI Shuxian. Analyzing the SPL gene family in Salix suchowensis[J]. Journal of Nanjing Forestry University (Natural Sciences Edition）. 2017, 41(02): 55-62 https://doi.org/10.3969/j.issn.1000-2006.2017.02.009

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