Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)

Abstract

Urticeae s.l., a tribe of Urticaceae well-known for their stinging trichomes, consists of more than 10 genera and approximately 220 species. Relationships within this tribe remain poorly known due to the limited molecular and taxonomic sampling in previous studies, and chloroplast genome (CP genome/plastome) evolution is still largely unaddressed. To address these concerns, we used genome skimming data—CP genome and nuclear ribosomal DNA (18S-ITS1-5.8S-ITS2-26S); 106 accessions—for the very first time to attempt resolving the recalcitrant relationships and to explore chloroplast structural evolution across the group. Furthermore, we assembled a taxon rich two-locus dataset of trnL-F spacer and ITS sequences across 291 accessions to complement our genome skimming dataset. We found that Urticeae plastomes exhibit the tetrad structure typical of angiosperms, with sizes ranging from 145 to 161 kb and encoding a set of 110–112 unique genes. The studied plastomes have also undergone several structural variations, including inverted repeat (IR) expansions and contractions, inversion of the trnN-GUU gene, losses of the rps19 gene, and the rpl2 intron, and the proliferation of multiple repeat types; 11 hypervariable regions were also identified. Our phylogenomic analyses largely resolved major relationships across tribe Urticeae, supporting the monophyly of the tribe and most of its genera except for Laportea, Urera, and Urtica, which were recovered as polyphyletic with strong support. Our analyses also resolved with strong support several previously contentious branches: (1) Girardinia as a sister to the Dendrocnide-Discocnide-Laportea-Nanocnide-Zhengyia-Urtica-Hesperocnide clade and (2) Poikilospermum as sister to the recently transcribed Urera sensu stricto. Analyses of the taxon-rich, two-locus dataset showed lower support but was largely congruent with results from the CP genome and nuclear ribosomal DNA dataset. Collectively, our study highlights the power of genome skimming data to ameliorate phylogenetic resolution and provides new insights into phylogenetic relationships and chloroplast structural evolution in Urticeae.

Integrated Full-Length Transcriptomics and Metabolomics Reveal Glycosyltransferase Involved in the Biosynthesis of Flavonol Glycosides in Laportea bulbifera

“…L. bulbifera is one of the most important species of Urticaceae, and the phylogenetic analysis of Urticaceae is currently a hot topic for researchers. , However, the genetic resources for Urticaceae are relatively scarce, and previous phylogenetic analyses have been conducted based on the chloroplast genome and gene fragments. The whole genome of Boehmeria nivea, another species of Urticaceae, has been reported; however, generating the whole genome assembly is time-consuming and expensive, whereas full-length transcript sequencing is a more cost-effective and superior strategy.…”

“…Urticaceae species are primarily distributed in tropical and subtropical regions, including eastern and southern Asia . Currently, some studies have been reported on the evolutionary relationship and chemical composition of Urticaceae species, , but their secondary metabolite profiles and biosynthetic mechanisms have received little attention. Laportea bulbifera is one of the most important species of the Urticaceae family and has attracted the attention of researchers because of its monoecious nature .…”

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

“…Despite the typically stable nucleotide content and highly conserved gene structure of chloroplast genomes, mutation hotspots can still occur [ 55 ]. In this research, 10 potential loci were identified that could serve as DNA barcodes for future research in Paeonia .…”

Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)

“…genome assembly, complete cp. genome sequences have been comprehensively accepted as valuable and informative data sources for comprehensive evolutionary investigation and have become a highly useful tool to assess the phylogenetic relationships of puzzling groups of angiosperms [ 15 – 17 ]. More cases also confirmed the advantage of the cp.…”

“…In Urticeae, cp. genome data proved the monophyly of most genera and provided new insights into the phylogenetic relationship and chloroplast structure evolution [ 19 ]. Zhou et al reconstructed the phylogenetic relationship of Bambusoideae based on cp.…”