Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria

Abstract

The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People’s Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.

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].…”

“…Therefore, the relationships between the New World and the Old World clades of Fritillaria and Lilium still remain unsolved. In comparison with previous studies [24,25], our results detected further phylogenetic relationships between Fritillaria and Lilium with more plastomes data, and the subgenus Fritillaria was confirmed polyphyletic, which has a high resolution than previous studies ( Figure 5) [16,17]. Our results also proved that the plastome data are of great advantages in phylogenetic analyses, although more extensive plastid genomic sampling was needed for further resolution of Fritillaria and Lilium.…”

“…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].…”

Comparative chloroplast genomics of Fritillaria (Liliaceae), inferences for phylogenetic relationships between Fritillaria and Lilium and genome evolution

“…Our results revealed that the whole plastome sequences newly obtained herein for 11 Fritillaria species only slightly vary in size (151,652bp-152,434bp) (Table1), and also largely similar in overall gene content, structure and order (Fig.1). The genome size in our study is accord with previously sequenced plastid genomes of Fritillaria [23][24][25]. Nonetheless, we have been able to document that the CDS genes vary in the plastomes of these eleven species, mainly there are particular (pseudo) genes: ψycf15, ψycf68 and ψinfA in some species.…”

“…Thus, the relationship between the New World and the Old world clades of Fritillaria and Lilium still remains unsolved. But our results provide further evidence for relationships between the two clades of Fritillaria and Lilium from phylogenomic analyses based on the most complete plastid genomes sampling by far compared with those of the earlier study by Bi et al [24] and Li et al [25]. More extensive plastid genomic sampling should be needed for further resolution.…”