Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications

Abstract

Chamaerhodos is a small genus with ca 7-8 species with a disjunct distribution in Asia and western North America. Due to limited sampling of species and genes in previous studies, little is known about the phylogenetic relationships among the species. Moreover, chloroplast genomic resources for Chamaerhodos have been limited. Herein, we conducted a comparative analysis of the complete chloroplast (cp) genomes of five Chamaerhodos species. The five cp genomes had a typical quadripartite structure with high conservation of gene content and gene order. These five cp genomes encoded an identical set of 129 genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes. Comparison of the boundaries between the IRs and single copy regions revealed only very slight boundary differences and the five cp genomes showed only little sequence divergence. Seven regions (trnR-UCU-atpA, trnS-GCU-trnG-UCC, TrnG-GCC-trnfM-CAU, trnL-UAA intron, trnH-GUG-psbA, trnF-GAA-ndhJ, matK-5′-trnK-UUU) were identified as excellent candidate markers. A total of 117, 108, 116, 117 and 118 perfect SSRs were detected in the cp genomes of Ch. altaica, Ch. canescens, Ch. erecta, Ch. sabulosa and Ch. trifida, respectively. A phylogenetic analysis support the monophyly of Chamaerhodos and place it as part of the Fragariinae clade sister to the clade of Dasiphora, Drymocallis and Potaninia. Within Chamaerhodos, Ch. canescens was inferred sister to a clade containing the other four species. The detailed characterization of the Chamaerhodos chloroplast genomes sets the foundation for further studies on the genus and its close relatives in the economically important Rosaceae.

Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating

“…The pseudogene ( ψycf1 ) is located in the IRb/SSC junction and is the result of an incomplete duplication of the normal functional copy of ycf1 in the symmetrical region (Fig. 2, Gao et al 2018, Li et al 2021). In general, the nine cp genomes of Sanguisorba were similar in structure and content.…”

“…We screened out 16 variation hotspots with higher Pi values (Pi >1.5%), including 11 in LSC region ( rpl22‐rps19 , ndhC‐trnV‐UAC , ycf3‐trnS‐GGA , trnH‐GUG‐psbA , rps14‐psaB , trnR‐UCU‐atpA , psbC‐trnS‐UGA , trnG‐UCC‐trnR‐UCU , 5'‐trnK‐UUU‐rps16 , rps2‐rpoC2 , rps3‐rpl22 ), four in SSC region ( ψycf1‐ndhF , ccsA‐ndhD , trnL‐UAG‐ccsA , rps15‐ycf1 ) and one in IRb/SSC boundary ( rps19‐rpl2 ). Among them, eight sequences ( ndhC‐trnV‐UAC , ccsA‐ndhD , ycf3‐trnS‐GGA , trnH‐GUG‐psbA , trnR‐UCU‐atpA , psbC‐trnS‐UGA , rps15‐ycf1 , 5'‐trnK‐UUU‐rps16 ) with lengths more than 200 bp were chosen as excellent candidate markers following Li et al (2021) and were suitable for developing specific barcodes of Sanguisorba . In agreement with Park et al (2021), trnH‐GUG‐psbA , trnR‐UCU‐atpA and ccsA‐ndhD were selected as areas with high divergence; however, in disagreement with Park et al (2021), petB‐petD was not selected as candidate markers of Sanguisorba in our study considering that the Pi value of petB‐petD was only 0.2116%.…”

“…Subsequently, the software NOVOPlasty (Dierckxsens et al 2017) was used to assemble the cp genomes of the four taxa, with the cp genome sequence of S. filiformis (NC_044693) as reference. Following Li et al (2021), chloroplast genome annotation of S. officinalis was performed by GeSeq (Tillich et al 2017; <https://chlorobox.mpimp-golm.mpg.de/geseq.html>) and CPGAVAS2 (Shi et al 2019; <https://www.herbalgenomics.org/cpgavas2>) with the cp genome of S. filiformis (NC_044693) and Geum macrophyllum Willd. (MT774132) as custom reference.…”

“…3.2.2, respectively (Ronquist et al 2012). The ML analysis was conducted following Li et al (2021). In the Bayesian analysis, the GTR + I + G model was selected as the best‐fit model using PartitionFinder2 (Lanfear et al 2017).…”

Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution

“…The genome of cp is generally maternal inheritance; there is no problem of gene recombination ( Li et al., 2014 ; Zhao et al., 2015 ). In recent years, the cp genome has been mainly used in phylogenetic, population genetics, and phylogeography studies ( Wang et al., 2022b ), in which plant phylogenetic analysis is the most basic cp genome analysis, which has been widely used in the phylogenetic study of the plant kingdom or one of the groups and to identify the relationships of angiosperm order, family, genus, interspecies, and intraspecies ( Sun et al., 2020 ; Guo et al., 2021 ; Li et al., 2021 ; Xie et al., 2021 ; Liu et al., 2022 ; Raman et al., 2022 ; Wang et al., 2022a ). The cp genome has unique advantages in plant phylogenetic studies.…”