A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

Applications in Plant Sciences

Brian J. Sanderson¹  Matthew S. Olson¹  Stephen P. DiFazio²  Quentin C. B. Cronk³  Tao Ma⁴ 

[1] Department of Biological Sciences Texas Tech University Lubbock Texas79409‐3131USA;Department of Biology West Virginia University Morgantown West Virginia26506USA;Department of Botany University of British Columbia Vancouver British ColumbiaV6T 1Z4Canada;Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu610065People’s Republic of China;

关键词: phylogenetics;    Populus;    Salicaceae;    Salix;    targeted sequence capture;   

DOI  :  10.1002/aps3.11394

来源: DOAJ

【 摘 要 】

Premise The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus. Methods We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300–1200 bp of exonic regions of 972 genes. Results We recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci. Conclusions Our sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.

【 授权许可】

Unknown