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

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.

Net diversification rates of the woody plant genus Petalidium (Acanthaceae) are highest in the ancient and arid Namib Desert

“…Given the young age (1.63 Ma) and the high species richness of the diverse arid clade, incomplete lineage sorting could be a plausible explanation for the lack of support, but new genetic data, from full genomes or numerous unlinked nuclear loci (c.f. Morais et al, 2019), will be necessary to fully address this issue in Petalidium.…”

Diversity, Phylogeny and 3-D Protein Modeling of Family Acanthaceae Based on Rps14 Gene Sequence in Pakistan

“…However, a lot of plant species are still unidentified and new approaches are required to more clarify the evolutionary positions of species in a family (Hameed et al 2022. Likewise, family Acanthaceae is one of the important family that exhibit 250 genera and 4,000 species (Morais et al 2019). It belongs to order Lamiales and distributed throughout the tropical and subtropical regions including Australia and extending to Mediterranean regions, Indonesia, Malaysia, Brazil and Africa, and Pakistan (Perveen and Qaiser 2010).…”

“…To limit these complexities and shortcomings of morphological identifications, molecular characterizations which is cost effective and sustainable can be used by molecular biologists to identify and classify such complex families (Channa et al 2018, Ayaz et al 2020, Khan et al 2020. Recent research on the morphological variation and evolution of Acanthaceae provides a phylogenetic framework for understanding and identifying the taxonomic characters (including micro-morphological structures) contained by the family (McDade et al 2008, Morais et al 2019, Khan et al 2020.…”

Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq

“…The alignments are useful for targeted enrichment probe design and other downstream applications (Chamala et al, 2015). This approach has been successful in aiding development of targeted sequencing probes in multiple plant lineages (Villaverde et al, 2018; Morais et al, 2019; Jantzen et al, 2020).…”