Herbarium phylogenomics: Resolving the generic status of the enigmatic Pseudobartsia (Orobanchaceae)

Abstract

The millions of herbarium specimens in collections around the world provide historical resources for phylogenomics and evolutionary studies. Many rare and endangered species exist only as historical specimens. Here, we report a case study of the monotypic Pseudobartsia yunnanensis D. Y. Hong (=Pseudobartsia glandulosa[Bentham] W. B. Yu & D. Z. Li: Orobanchaceae) known from a single Chinese collection taken in 1940. We obtained genomic data of Pseudobartsia glandulosa using high‐throughput short‐read sequencing, and then assembled a complete chloroplast genome and nuclear ribosome DNA region in this study. We found that the newly assembled three plastid DNA regions (atpB‐rbcL, rpl16, and trnS‐G) and nuclear ribosomal internal transcribed spacer (nrITS) of Pseudobartsia glandulosa were more than 99.98% similar to published sequences obtained by target sequencing. Phylogenies of Orobanchaceae using 30 plastomes (including 10 new plastomes), using both supermatrix and multispecies coalescent approaches following a novel plastid phylogenomic workflow, recovered seven recognized tribes and two unranked groups, both of which were proposed as new tribes, that is, Brandisieae and Pterygielleae. Within Pterygielleae, all analyses strongly supported Xizangia D. Y. Hong as the first diverging genus, with Pseudobartsia D. Y. Hong as sister to Pterygiella Oliver + Phtheirospermum Bunge (excluding Phtheirospermum japonicum [Thunberg] Kanitz); this supports reinstatement of Pseudobartsia and Xizangia. Although elements of Buchnereae‐Cymbarieae‐Orobancheae and Brandisieae‐Pterygielleae‐Rhinantheae showed incongruence among gene trees, the topology of the supermatrix tree was congruent with the majority of gene trees and functional‐group trees. Therefore, most plastid genes are evolving as a linkage group, allowing the supermatrix tree approach to yield internally consistent phylogenies for Orobanchaceae.

Complete chloroplast genomes of hemiparasitic genus Cymbaria: Insights into comparative analysis, development of molecular markers, and phylogenetic relationships

“…The unique inversion including rbc L-mat K in the LSC region, which most likely stems from a palindromic repeat-mediated rearrangement. Inversions of the LSC fragments have also been observed in Schwalbea americana (Wicke et al, 2013) andSiphonostegia chinensis (Jiang et al, 2022); this distinct evolutionary mechanism among Orobanchaceae members might explain the unique phylogenetic position of the tribe Cymbarieae. This inversion has also been observed inCodonopsis pilosula subsp.…”

“…Cymbarieae was originally thought to be sister to various parasitic lineages in the family Orobanchaceae (Bennett & Mathews, 2006;McNeal, Bennett, Wolfe, & Mathews, 2013), while analysis of the tribe Orobancheae suggests that this original classification merits reconsideration (Xi Li, Feng, Randle, & Schneeweiss, 2019). Furthermore, although chloroplast genomes of Schwalbea americana (Wicke et al, 2013) and Siphonostegia chinensis (Gao et al, 2019;Jiang et al, 2022) have been previously published, no systematic comparative analysis of chloroplast genomes of various groups within the tribe Cymbarieae has been conducted to date.…”

A comparison of freezer‐stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming

“…R. M. Bateman, Pridgeon & M. W. Chase, herbarium specimens were used to compare historical and present‐day patterns of genetic diversity (Cozzolino et al, 2007 ). Large phylogenomic studies now routinely incorporate DNA obtained from herbarium specimens (e.g., Zeng et al, 2018 ; Nevill et al, 2020 ; Jiang et al, 2022 ). In addition, herbarium specimens themselves can be sources of genetic diversity.…”

The complete chloroplast genomes of three Alismataceae species, including the medicinally importantAlisma orientale

“…Herbarium specimens are an important source for biodiversity science and can be effectively used for extracting chloroplast genome and other genomic data (herbariomics) to address questions on species delimitation and utilization of plant medicinal resources (Jiang et al. 2022 ; Duan et al. 2023 ; Wen et al.…”