Comparative chloroplast genome analysis of Ardisia (Myrsinoideae, Primulaceae) in China and implications for phylogenetic relationships and adaptive evolution.

Numerous species of Ardisia are widely used for their medicinal and ornamental values in China. However, accurately identifying Ardisia species at the molecular level remains a challenge due to the morphological similarities among different species, the complexity of interspecific variation, and the limited availability of genetic markers. In this study, we reported 20 chloroplast genomes of Ardisia species from China and combined them with 8 previously published chloroplast genomes to conduct a comprehensive analysis for phylogenetic relationships and adaptive evolution. For the 28 Ardisia species analyzed in this study, the size of the chloroplast genomes ranged from 155,088 bp to 156,999 bp, and all exhibited a typical tetrad structure with conserved gene content and number. Each genome contained 85-88 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analysis showed that the genomic structures and gene order were relatively conserved with slight variations in the inverted repeat regions (IRs). Simple sequence repeats (SSRs) were predominantly single nucleotide repeats, while repeat sequences were mainly composed of palindromic and forward repeats. Twelve highly variable regions were identified as potential DNA barcodes for species identification and phylogenetic analysis of Ardisia. The phylogenetic tree supported the division of the subgenus Bladhia s.l. into two subgenera: Bladhia s.str. and Odontophylla (Yang) Huang. Further investigation revealed that two protein-coding genes (rbcL and rpoC2) were under positive selection and might be associated with the adaptation of Ardisia species to shaded environments. Our study analyzed the chloroplast genomes of 20 Ardisia species from China to explore their phylogenetic relationships and adaptive evolution. By combining these results with data from eight previously published chloroplast genomes, the essential characteristics of Ardisia chloroplast genomes were clarified. The research establishes a theoretical basis for the classification, identification, and comprehension of the adaptive evolution of Ardisia species.

Zhang J ，Ning Y ，Li J ，Deng Y ，Wang L ，Mao S ，Zhao B ... -  《BMC PLANT BIOLOGY》

Comparative analysis of the complete chloroplast genome of Pueraria provides insights for species identification, phylogenetic relationships, and taxonomy.

Pueraria is an edible and medicinal raw material, which is of great value to the pharmaceutical and food industries. Nonetheless, due to morphological diversity and complex domestication history, the classification of Pueraria plants is ambiguous. As the varieties on the market are mixed, the species are difficult to distinguish, and their morphological characteristics are similar to the physical and chemical properties. It is difficult to accurately identify them by traditional identification methods. Chloroplast (cp) genomes are widely used in species identification and phylogenetic studies to achieve accurate identification of medicinal plants, and can also provide more reference information for phylogenetic studies. Based on interspecific and intraspecific sampling, the cp genomes of eight species or varieties of Pueraria plants were examined in this study. The study unveiled that the cp genome size varied from 151,555 to 153,668 base pairs (bp), with the total GC content ranging from 35.4 to 37.0%. Moreover, it was discerned that the cp genome contained between 128 and 135 genes. Comparative analysis indicated that the highest number of Simple Sequence Repeats (SSRs) was identified in P. montana and P. alopecuroides, with a preponderance of these SSRs being rich in Adenine (A) and Thymine (T) nucleotides. Complete comparison and sliding window analysis of the cp genome established that the non-coding region exhibited greater sequence differences than the coding region, and that the large single copy (LSC) region demonstrated higher nucleotide polymorphism levels. Fourteen highly variable loci such as rpoB,ycf1,rbcL,trnF-GAA-trnL,psbC-psbD, and ycf4-cemA were detected as potential molecular markers for Pueraria species identification. Moreover, the phylogenetic tree demonstrated that other Pueraria species had the most distant relationship with Haymondia wallichii and Toxicopueraria peduncularis, thereby offering fresh perspectives into the species classification of Pueraria. The molecular clock analysis results indicate that the divergence time of Pueraria may occur at ∼6.46 Ma. It is speculated that the cold climate may be the cause of Pueraria species diversity and promote the radiation of the genus. This research provides theoretical backing and serves as a reference point for the identification and taxonomical classification of Pueraria species. The findings will prove beneficial in future studies on the preservation of medicinal resources, phylogenetic relationships, and genetic engineering of Pueraria plants.

Hai Y ，Huang X ，Sun H ，Sun J ，Li J ，Zhang Y ，Qian Y ，Wu J ，Yang Y ，Xia C ... -  《BMC PLANT BIOLOGY》

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Zhang Y ，Song M ，Tang D ，Li X ，Xu N ，Li H ，Qu L ，Wang Y ，Yin C ，Zhang L ，Zhang Z ... -  《BMC PLANT BIOLOGY》

Exploring the phylogenetic framework and trait evolution of Impatiens through chloroplast genome analysis.

The genus Impatiens, which includes both annual and perennial herbs, holds considerable ornamental, economic, and medicinal value. However, it posed significant challenges for taxonomic and systematic reconstruction. This was largely attributed to its high intraspecific diversity and low interspecific variation in morphological characteristics. In this study, we sequenced samples from 12 Impatiens species native to China and assessed their phylogenetic resolution using the complete chloroplast genome, in conjunction with published samples of Impatiens. In addition, a comparative analysis of chloroplast genomes were conducted to explore the evolution of the chloroplast genome in Impatiens. The chloroplast genomes of 12 Impatiens species exhibited high similarity to previously published samples in terms of genome size, gene content, and sequence. The chloroplast genome of Impatiens exhibited a typical four-part structure, with lengths ranging from 146,987 bp(I. morsei)- 152,872 bp(I. jinpingensis). Our results identified 10 mutant hotspot regions (rps16, rps16-trnG, trnS-trnR, and rpoB-trnC) that could serve as effective molecular markers for phylogenetic analyses and species identification within the Impatiens. Phylogenetic analyses supported the classification of Impatiens as a monophyletic taxon. The identified affinities supported the taxonomic classification of the subgenus Clavicarpa within the Impatiens, with subgenus Clavicarpa being the first taxon to diverge. In phylogenetic tree,the Impatiens was divided into eight distinct clades. The results of ancestral trait reconstruction suggested that the ancestral traits of Impatiens included a perennial life cycle, four sepals and three pollen grooves. However, the ancestral morphology regarding fruit shape, flower colour, and spacing length remained ambiguous. Our study largely supported the family-level taxonomic treatment of Impatiens species in China and demonstrated the utility of whole chloroplast genome sequences for phylogenetic resolution. Comparative analysis of the chloroplast genomes of Impatiens facilitated the development of molecular markers.The results of ancestral trait reconstruction showed that the ancestor type of habit was perennial, the number of sepals was 4, and morphology and number of aperture was 3 colpus. The traits of capsule shape, flower colour, and spur length underwent a complex evolutionary process. Our results provided data support for further studies and some important new insights into the evolution of the Impatiens.

Lan WX ，Mo Q ，Jin MM ，Wen YH ，Yang MQ ，Ma H ，Huang HQ ，Huang MJ ... -  《BMC PLANT BIOLOGY》

Comparative plastomic analysis of cultivated Dioscorea polystachya and its close relatives provides insights on the inter- and intraspecific phylogenies and potential wild origins of domestication.

Dioscorea polystachya and its closely related species are original plants of the tuber crop "yam", which had been intensively use for medicinal and food purposes and widely cultivated in northern China and its surrounding areas with a long history. Many cultivars of these species are often confused with one another because of similar tuber morphology, however, conventional DNA barcoding faces practical limitations restricting the method to effectively identify closely related species. In addition, phylogenetic relationships among various cultivar groups of Chinese yam (D. polystachya) remains unclear. To solve these problems, genomic DNAs of 15 Dioscorea samples were sequenced to assemble and annotate chloroplast genomes, which were used for analyzing their structural characteristics and identifying phylogenetic relationships at the inter- and intraspecific levels. The size of chloroplast genomes of the tested samples is about 153 kb, and 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes are annotated. Phylogenetic analysis showed that D. polystachya were sister to Dioscorea japonica, and for Huaishan yams, Dioscorea persimilis did not cluster with Dioscorea alata and Dioscorea fordii. Four cultivar groups of Chinese yam were determined, namely Tiegun group, Anping group, Foshou group and Taihang complex group. Among these cultivar groups, Foshou and Taihang complex are clustered with different wild yams, respectively. Amino acid preferences are similar at the inter- and intraspecific levels, while synonymous codon usage reflects distinct patterns in the majority of cultivars of D. polystachya. There are distinct SSR variations among species, as well as four cultivar groups. Collinearity and SNP analyses show that nucleotide hypervariable regions among Dioscorea species are mainly concentrated in trnK-atpA, rps16-trnQ, atpA-atpH, rpoB-psbD, atpH-atpI, trnV-ndhC in the LSC region, and ccsA-ndhF in the SSC region, while intraspecific variation of Chinese yam is enriched in the intergenic spacers of rpoB-psbC, ndhD-ndhF, and trnQ-trnS, as well as the gene ycf1. Phylogenetic analysis supports that Huaishan yams are not of monophyletic origin and the cultivated Chinese yam has at least two wild origins of domestication, which is consistent with the historical records of these wild yams from Mt. Dabie and Mt. Taihang. The identification efficiency of the newly developed barcodes for cultivar groups based on chloroplast genome SNP screening is significantly better than those of conventional barcodes. This approach to generate viable candidate markers based on the comparison from interspecific and intraspecific hypervariable regions of chloroplast genomes can be applied to conduct phylogenetic relationships of more important crop species and their close relatives, which are difficult to identify, as well as their wild origins of domestication.

Feng W ，Zhang Z ，Zhang J ，Nan P ，Song Z ，Zhang W ，Yang J ，Wang Y ... -  《BMC PLANT BIOLOGY》