DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes

Abstract

The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely “F. omeiensis” and “F. hupehensis” in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.

Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

“…First, the direct reason for failing in species identification was the lack of genetic variation within the DNA barcode regions we applied in Schima . The sequence divergence of Schima was much lower than that observed in Fritillaria and Olea , on which DNA barcodes worked effectively (Chen et al, 2022; Dong et al, 2021). Shallow sequence divergence indicates a recent evolutionary history in Schima .…”

“…Since complete plastome and nrDNA arrays were proposed to be the next generation DNA barcodes for plant species identification (Coissac et al, 2016; Hollingsworth et al, 2016; Kane et al, 2012; Kane & Cronk, 2008; Li et al, 2015; Nock et al, 2011), much advancement has gone into molecular species identification of taxonomically difficult taxa, such as Panax (Araliaceae) with 70% of species discriminated (Ji et al, 2019), and Taxus (Taxaceae) with all species (100%) discriminated (Fu et al, 2019). Despite a steep increase in super‐barcode‐related studies (Chen et al, 2022; Dong et al, 2021; Ślipiko et al, 2020; Wang et al, 2018), the discriminatory power of super‐barcodes remains controversial. Some studies argue that the power of super‐barcodes as a species identification tool is quite limited (Krawczyk et al, 2018; Liu et al, 2021).…”

Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

“…D. leptopodum contained the highest number (50) of long repeat sequences, and Me. horridula had the lowest number (16) among the compared species. The numbers of forward and palindromic sequence repeats detected in D. leptopodum were 46 and 4, respectively.…”

“…The chloroplast genome, which is characterized primarily by maternal inheritance, has been widely used in the reconstruction of phylogenetic relationships at different taxonomic levels [11][12][13][14][15] and species identification [16] due to its highly conserved nature in terms of stable structure, gene arrangement, GC (guanine and cytosine) content, and lack of recombination during genetic processes. To date, most of the studies on Dicranostigma have focused mainly on the medicinal properties of its extracts [1,2], ecophysiological index, and seed germination characteristics [5]; in contrast, almost no research has been conducted on its phylogeny.…”

Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.)

“…Chloroplast genome sequences are commonly used in various areas of biology, i.e., phylogenetics [37,38], DNA barcoding [39,40], taxonomy, evolution, and population genetics [41] of both angiosperms and gymnosperms. In the last five years, many genomic studies of various representatives of the genus Dracaena [25,26] and the family Asparagaceae [22,23,42,43] have also been published, but so far, none have included D. cinnabari.…”