Complete chloroplast genome of seven Fritillaria species, variable DNA markers identification and phylogenetic relationships within the genus

Abstract

Fritillaria spp. constitute important traditional Chinese medicinal plants. Xinjiang is one of two diversity hotspots in China in which eight Fritillaria species occur, two of which are endemic to the region. Furthermore, the phylogenetic relationships of Xinjiang Fritillaria species (including F. yuminensis) within the genus are unclear. In the present study, we sequenced the chloroplast (cp) genomes of seven Fritillaria species in Xinjiang using the Illumina HiSeq platform, with the aim of assessing the global structural patterns of the seven cp genomes and identifying highly variable cp DNA sequences. These were compared to previously sequenced Fritillaria cp genomes. Phylogenetic analysis was then used to evaluate the relationships of the Xinjiang species and assess the evolution of an undivided stigma. The seven cp genomes ranged from 151,764 to 152,112 bp, presenting a traditional quadripartite structure. The gene order and gene content of the seven cp genomes were identical. A comparison of the 13 cp genomes indicated that the structure is highly conserved. Ten highly divergent regions were identified that could be valuable in phylogenetic and population genetic studies. The phylogenetic relationships of the 13 Fritillaria species inferred from the protein-coding genes, large single-copy, small single-copy, and inverted repeat regions were identical and highly resolved. The phylogenetic relationships of the species corresponded with their geographic distribution patterns, in that the north group (consisting of eight species from Xinjiang and Heilongjiang in North China) and the south group (including six species from South China) were basically divided at 40°N. Species with an undivided stigma were not monophyletic, suggesting that this trait might have evolved several times in the genus.

Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution

“…Our results revealed that the whole plastome sequences of 11 newly sequenced Fritillaria species were conserved not only in genome size, but also in gene content, structure, and order (Figure 1), which was consistent with previously published Fritillaria plastomes studies [23][24][25]. Nevertheless, some CDS genes exhibited high variations, mainly in some pseudogenes, for example ψycf15, ψycf68, and ψinfA, which were also reported in other angiosperm plastid genomes [7,9,26,27].…”

“…It is worth noting that there are only F. crassicaulis, F. dajinensis, F. delavayi, F. sichuanica, and F. unibracteata having ψycf15 and ψycf68 in our results, indicating a few common aspects in their evolutionary processes and functions. The absence or presence of ψycf15 and ψycf68 in other Fritillaria species has also been reported by Li et al [25]. The same phenomenon has also been observed in Ipomoea [28].…”

“…So far, a total of fifteen plastid genomes of genus Fritillaria have been sequenced and are available on GenBank. These comparative analyses with different Fritillaria plastid genomes have provided a basic understanding of the plastid genome characteristics of this genus [22][23][24][25].…”

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

“…(Ahmed et al, 2013; Ahmad, 2014; Nguyen et al, 2017). Previously, in several studies, polymorphic loci were identified based on comparisons of chloroplast genome to provide information about suitable loci for the development of molecular markers (Choi, Chung & Park, 2016; Li et al, 2018; Menezes et al, 2018). We found 20 polymorphic regions such as infA, rps12 intron, rps16-trnQ-UUG which have 0.25942, 0.15275, 0.08451 nucleotide diversity respectively that were more polymorphic than frequently used markers such as rbcL , and matK .…”

DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae

“…The whole‐chloroplast genome is termed a “super‐barcode” and provides more abundant informative sites for species identification. These super‐barcodes exhibit higher discrimination power for closely related species and have been applied for the identification of species in various taxa, such as the genera Fritillaria (Li, Zhang, Yang, & Lv, ), Epipremnum (Tian, Han, Chen, & Wang, ), and Papaver (Zhou et al, ). The use of a super‐barcodes is a good option for the identification of closely related Corydalis species and obtaining improved species discrimination power.…”