PJB-2023-70
Genetic evolution analysis and SNP development of Taxus spp. by SLAF-SEQ
Bihua Chen, Yong Li, Jianmin Li, Huihua Fan, Xinghao Tang, Guibin Zhou and Shengliang Huang
Abstract
The molecular markers within whole genome were obtained, evolutionary tree was constructed, and the genetic structure, PCA (principal co-ordinates analysis) and genetic diversity analysis were carried out to understand the genetic evolutionary relationship and specific SNP markers of Taxus species or provenances, The protocol was predicted by using the genome of Taxus chinensis var. mairei and digested with the Hpy166II restriction enzyme, the SLAF (specific-locus amplified fragment) tags of length 314-364 bp read length 126 bp×2 used for subsequent data assessment and analysis, a total of 148.78 Mb reads data were obtained from 62 Taxus spp. Samples including 7 species, with 94.46% of an average Q30 and 37.99% of an average GC content. 140,405 SLAF tags were developed with an average sequencing depth of 7.54×. SNPs were developed by genome analysis toolkits GATK and Sam Tools, and the intersection of SNPs acquired using the two methods was applied as the reliable SNP marker dataset, and a total of 7,795,093 population SNPs were obtained. The phylogenetic tree showed that the 62 Taxus spp. could be divided into two clades, T. yunnanensis was the first clade, and the others clustered as the second clade. The data amount obtained could be used for the verification and development of specific SNP markers and reveal the genetic relationship for the 7 Taxus species
To Cite this article:
Chen, B., Y. Li, J. Li, H. Fan, X. Tang, G. Zhou and S. Huang. 2024. Genetic evolution analysis and SNP development of Taxus spp. by SLAF-SEQ. Pak. J. Bot., 56(1): DOI: http://dx.doi.org/10.30848/PJB2024-1(24)
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