Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae

Author(s)
Erica B. Morais, Jürg Schönenberger, Elena Conti, Alexandre Antonelli, Peter Szoevenyi
Abstract

Premise Information on orthologous groups of genes, their sequence variability, and annotation is required for project design in phylogenetic reconstruction. This resource is unavailable for the flowering plant family Acanthaceae (>4000 species). Methods We compared transcriptome sequences spanning the extant diversity of Acanthaceae in order to provide a set of orthologous low-copy nuclear genes and assess their utility for reconstructing phylogenetic relationships within this group of plants. Results We present new transcriptome assemblies for eight species representing all major clades of Acanthaceae. The assemblies of five of these species are entirely based on new sequence data. Of these five species, three are from subfamilies for which no genomic resources were previously available (Nelsonioideae and Thunbergioideae). These five new transcriptomes are more complete than all others from public databases. Furthermore, we provide alignments with sequence information, annotation, and statistics for potential phylogenetic utility of 1619 orthologous low-copy nuclear markers. Discussion Our method of inferring assemblies from multiple pooled tissue samples delivers more complete transcriptomes than any available ones from Acanthaceae. We make available to the community new resources (e.g., sequence information, variability, and annotation of orthologous low-copy nuclear genes) that will help phylogenetic reconstruction in Acanthaceae.

Organisation(s)
Department of Botany and Biodiversity Research
External organisation(s)
Universität Zürich (UZH), Royal Botanic Gardens Kew, Gothenburg Global Biodiversity Centre
Journal
Applications in Plant Sciences
Volume
7
No. of pages
6
ISSN
2168-0450
DOI
https://doi.org/10.1002/aps3.11290
Publication date
09-2019
Peer reviewed
Yes
Austrian Fields of Science 2012
106042 Systematic botany, 106008 Botany, 106012 Evolutionary research
Keywords
Portal url
https://ucris.univie.ac.at/portal/en/publications/orthologous-nuclear-markers-and-new-transcriptomes-that-broadly-cover-the-phylogenetic-diversity-of-acanthaceae(de6db4bb-2661-4fee-a49a-ebe95c0d78dc).html