Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family

Applications in Plant Sciences

Carolina M. Siniscalchi¹  Jennifer R. Mandel²  Luis Palazzesi³  Ilia J. Leitch⁴  Lisa Pokorny⁴  Felix Forest⁴  Olivier Maurin⁴  Oriane Hidalgo⁴  William J. Baker⁴  Jaume Pellicer⁴ 

[1] Department of Biological Sciences Mississippi State University Mississippi State Mississippi 39762 USA;Department of Biological Sciences University of Memphis Memphis Tennessee 38152 USA;División Paleobotánica Museo Argentino de Ciencias Naturales CONICET Buenos Aires C1405DJR Argentina;Royal Botanic Gardens, Kew Richmond Surrey TW9 3AE United Kingdom;

关键词: angiosperms;    Asteraceae;    paralogy;    phylogenomics;    target capture;   

DOI  :  10.1002/aps3.11422

来源: DOAJ

【 摘 要 】

Premise Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family‐specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family‐specific kit and those obtained with the universal kit can be merged for downstream analyses. Methods We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. Results Our results show that the Compositae1061 kit provides an average of 721 loci, with 9–46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. Discussion Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.

【 授权许可】

Unknown