Abstract Detail

Phylogenomics

Acha, Serena [1], Majure, Lucas [2].

A new approach using targeted sequence capture for phylogenomic studies across Cactaceae.

Cactaceae are one of the most fascinating plant families in Angiosperms. This family encompasses roughly 1755 species including highly diverse clades in both North and South America, and exhibiting a wide range of morphological variation across the clade. Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species level relationships remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with a subset of the Angiosperm353 probe set. We then tested both probes sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and discarded less informative loci. Finally, we tested each probe set through sequencing 96 species across Cactaceae and reconstructed a preliminary phylogeny using RAxML-ng. Our MarkerMiner probe set consisted of 122 single copy loci with a size range of 123-3460 bp and a mean of 1118 bp. The Angiosperm353 probe set comprised 294 loci with 120-2322 bp size range and a mean of 720 bp. Overall, our MarkerMiner set mapped more successfully (99%) to our sequenced data, with 35-96 (mean 93) loci recovered per sample. The Angiosperm353 set mapped less (87%) sequences with 4-95 (mean 74) loci recovered per sample. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our probe set results to plastome datasets, especially at the generic level. Our MarkerMiner probe set phylogeny showed higher support at shallower levels, while the Angiosperm353 phylogeny displayed higher support at deeper nodes. Our results revealed great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application in improving phylogenetic resolution for Cactaceae and for other studies.

1 - University of Florida, Florida Museum of Natural History, University of Florida,1659 Museum RD, Po Box 117800, Gainesville, Florida, 32611-7800, United States
2 - University of Florida, 1659 Museum RD, PO Box 117800, Gainesville, Florida, 32611-7800, United States

Keywords:
Cacti
Opuntia
Hyb-Seq
Neotropics
Target enrichment.

Presentation Type: Oral Paper
Session: PHYLOIV, Phylogenomics IV
Location: Virtual/Virtual
Date: Friday, July 23rd, 2021
Time: 12:45 PM(EDT)
Number: PHYLOIV002
Abstract ID:756
Candidate for Awards:None