A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae.

Serena Acha,Lucas C Majure

doi:10.3390/genes13020350

Abstract

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 the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. 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 nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.

Highlights

We found that the loci recovered differed between the main clades in Cactaceae (Table 2 and Table S3): from our Cactoideae samples, 120 loci were retrieved, followed by Opuntioideae (119 loci), outgroups (117 loci), Leuenbergeria + Pereskia (109 loci), and lastly, Maihuenia with 92 loci recovered
We discovered that the highest locus overlap occurred between Opuntioideae and Cactoidae (119 loci) and the least overlap was between Maihuenia and Leuenbergeria + Pereskia (91 loci)
We found differences in the loci recovered in the major clades across Cactaceae (Table 2): 303 loci were recovered for Cactoideae samples, followed by Opuntioideae (295 loci), outgroups (292 loci), Leuenbergeria + Pereskia (273 loci), and lastly Maihuenia with 254 loci

Summary

Introduction

The Cactaceae are a major American radiation consisting of more than 1800 species [1], and they range from Patagonia to Canada [2] in a diversity of habitat types from desert to seasonally dry tropical forests, temperate forests and montane Andean grasslands. Most phylogenetic reconstructions have been based solely or mostly on plastid data derived from Sanger sequencing methods and oftentimes using just a handful of loci (e.g., [3–9]). Arakaki et al [10] employed a combination of plastome and Sanger sequencing data to test the diversification of the family, and more recently transcriptome data (Walker et al 2018), as well as plastome datasets [11–15] have been utilized to more fully resolve species limits and deep phylogenetic history in the family. Nuclear probe sets derived from single-copy loci, which are commonly used in other groups of Angiosperms [16], as well as other vascular and non-vascular plants [17], have not yet been generated for the family. Angiosperms353 has been combined with group specific probe sets, such as in the case of the Malinae (Rosaceae) [21], Asteraceae [22], Gesneriaceae [23] and Ochnaceae [24]. There have been approaches where group-specific probe sets were designed to study different groups of plants at different scales, such as in the genus Burmeistera (Campanulaceae) [25], Annonaceae [26] and Zingiberales [27]

Methods

Results

Conclusion