Organization, Phylogenetic Marker Exploitation, and Gene Evolution in the Plastome of Thalictrum (Ranunculaceae)

Abstract

Thalictrum is a phylogenetically and economically important genus in the family Ranunculaceae, but is also regarded as one of the most challengingly difficult in plants for resolving the taxonomical and phylogenetical relationships of constituent taxa within this genus. Here, we sequenced the complete plastid genomes of two Thalictrum species using Illumina sequencing technology via de novo assembly. The two Thalictrum plastomes exhibited circular and typical quadripartite structure that was rather conserved in overall structure and the synteny of gene order. By updating the previously reported plastome annotation of other nine Thalictrum species, we found that the expansion or contraction of the inverted repeat region affect the boundary of the single-copy regions in Thalictrum plastome. We identified eight highly variable noncoding regions—infA-rps8, ccsA-ndhD, trnSUGA-psbZ, trnHGUG-psbA, rpl16-rps3, ndhG-ndhI, ndhD-psaC, and ndhJ-ndhK—that can be further used for molecular identification, phylogenetic, and phylogeographic in different species. Selective pressure and codon usage bias of all the plastid coding genes were also analyzed for the 11 species. Phylogenetic relationships showed Thalictrum is monophyly and divided into two major clades based on 11 Thalictrum plastomes. The availability of these plastomes offers valuable genetic information for accurate identification of species and taxonomy, phylogenetic resolution, and evolutionary studies of Thalictrum, and should assist with exploration and utilization of Thalictrum plants.

Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

“…In this study, a total of 1968 SSRs were identified in the plastomes of 79 Trichosporeae species, with 89.99% of them being mono-nucleotide repeats ( Figure 4 ; Table S4 ). These results are consistent with previous studies of other angiosperms ( Xiang et al., 2022 ; Yu et al., 2022 ). Plastome SSRs usually consist of short polyA or polyT repeats and mono-nucleotide repeats ( Provan et al., 2001 ).…”

“…Plastome SSRs usually consist of short polyA or polyT repeats and mono-nucleotide repeats ( Provan et al., 2001 ). The variation in the non-coding region was higher than that in the coding region, with the variation in the SC region being higher than that in the IR region, which is like other angiosperms plastomes ( Xiang et al., 2022 ). Five hypervariable CDSs ( rps15 , matK , ndhF , rps16 and rpl32 ) and eight hypervariable non-coding regions ( rpl16/rps3 , rpl14/rpl16 , petB/petD , trnC-GCA/petN , rps15/ycf1 , trnfM-CAU/rps14 , petD/rpoA and trnS-GGA/rps4 ) were identified in Trichosporeae ( Figure 3 ).…”

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

“…Previous studies on other angiosperm groups have shown that chloroplast genomes are conserved or highly polymorphic ( Abdullah et al., 2020 , Abdullah et al., 2021 ). In the present study, the cp genome was highly conserved in terms of gene order, gene content, and intron number, following the findings of many other taxa, including Thalictrum ( Tang et al., 2015 ; Yu et al., 2018 ; Xiang et al., 2022 ). However, in some taxa, such as Amorphophallus of Araceae, some genes were lost ( Liu et al., 2019 ), and in others, such as Pelargonium ( Chumley et al., 2006 ), the structure and gene order diverged from those reported here and in most other angiosperms.…”

“…The plastome of this species varies in terms of genomic structure, nucleotide diversity, structural alterations, and phylogeny with the plastomes of Thalictrum species ( Park et al., 2015 ; He et al., 2019 ; Morales-Briones et al., 2019 ; He et al., 2021 ; Cai et al., 2022 ; Zhe et al., 2023 ). For instance, there is an apparent difference between Thalictrum plastomes in the IR-SC boundary areas, which causes variations in genome size ( Xiang et al., 2022 ). IR-SC contractions or expansions into or out of neighboring single-copy regions are typically observed in angiosperm plastomes, and this process is a primary mechanism and an example of length variation in cp genomes ( Kim and Lee, 2004 ; Yang et al., 2016 ; Zhang et al., 2016 ; Ye et al., 2018 ).…”

“…Previous studies have revealed that Thalictrum species form a highly supported clade, indicating that they are monophyletic ( Cai et al., 2022 ; Michimoto et al., 2022 ). Thalictrum species exhibit small chromosomes compared with those of Rununculus, and this genus is challenging and diverse in terms of taxonomy and phylogeny based on variations in morphological traits ( Langlet, 1927 ; Tamura, 1995 ; Xiang et al., 2022 ). As a critical solution, chloroplast (cp) genomic resources have facilitated the classification of members of the Ranunculaceae family, providing data and insight into evolutionary relationships ( Zhai et al., 2019 ), phylogenetic resolution (bootstrap support and tree certainty) ( Morales-Briones et al., 2019 ), and marker exploration ( Xiang et al., 2022 ).…”