Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers

Abstract

Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (G. dahurica, G. siphonantha and G. officinalis). We further compared them with the previously published plastomes from sect. Cruciata and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (accD, clpP, matK and ycf1) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. Cruciata and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication.

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

“…Most of the amino acids had codon preferences except Met and Trp. The total number of codons in the five Bupleurum species ranged from 21,188 to 21,195 (Table S1 in Supplementary Material). Leucine (Leu) and cysteine (Cys) were the most and least abundant amino acids, respectively.…”

“…The gene content, order and structure are highly conserved at low taxonomic levels [20], but there are still variations especially in the intergenic regions and IR boundaries. Some hotspot regions with much nucleotide information have been applied to species identification [21,22]. The evolutionary rates of conserved coding regions are low, which are high in non-coding regions.…”

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

“…These structural variations are always involved in the contraction or extension of the IR region [1], appearance of large inversions or deletions [4,5], and genes gain or loss [2,6]. Some hotspot regions with single nucleotide polymorphisms could be identified, which may be used for species identification in terms of enough information [7]. Due to low rates of nucleotide substitutions, lack of recombination, and uniparental inheritance, many plastid DNA sequences have been used for inferring plant phylogenies and population genetic analyses [8,9], such as matK, rbcL, and trnH-psbA [10].…”

Complete plastid genome of an alpine plant Gentiana filistyla (Gentianaceae) and phylogenetic analysis

“…The plastome was de novo assembled in NOVOPlasty 2.6.1 (Dierckxsens et al 2017) and then annotated in GeSeq (Tillich et al 2017) using the default parameters. Comparative analysis was conducted in mVISTA (Frazer et al 2004) with species from four plastome-available Gentiana sections, Kudoa (Sun et al 2018), Cruciata (Zhou et al 2018), Microsperma (Sun et al 2019b) and Frigidae (Sun et al 2019a). Shared protein coding genes in plastomes of available Gentiana species were extracted and aligned using MAFFT (Katoh et al 2002).…”

“…A total of 123 genes were annotated, containing 81 proteincoding genes, 34 tRNA genes and 8 rRNA genes. Comparison analysis indicated that gene composition of G. filistyla platome is similar with section Kudoa (Sun et al 2018), but different with species in section Cruciata (Zhou et al 2018) due to absence of seven ndh genes. The hotspots among sections Isomeria, Kudoa, Cruciata, Microsperma and Frigidae located at intergenic regions such as trnH-GUG -psbA, trnK-UUU -rps16, atpH-atpI, petN-trnD and trnL-UAG -ccsA.…”