Complete Plastid Genome Sequencing of Eight Species from Hansenia, Haplosphaera and Sinodielsia (Apiaceae): Comparative Analyses and Phylogenetic Implications

Abstract

Hansenia Turcz., Haplosphaera Hand.-Mazz. and Sinodielsia H.Wolff are three Apiaceae genera endemic to the Hengduan Mountains and the Himalayas, which usually inhabit elevations greater than 2000 m. The phylogenetic relationships between and within the genera were uncertain, especially the placement of Hap. himalayensis and S. microloba. Therefore, we aimed to conduct comparative (simple sequence repeat (SSR) structure, codon usage bias, nucleotide diversity (Pi) and inverted repeat (IR) boundaries) and phylogenetic analyses of Hansenia, Haplosphaera and Sinodielsia (also compared with Chamaesium and Bupleurum) to reduce uncertainties in intergeneric and interspecific relationships. We newly assembled eight plastid genomes from Hansenia, Haplosphaera and Sinodielsia species, and analyzed them with two plastid genomes from GenBank of Hap. phaea,S. yunnanensis. Phylogenetic analyses used these ten genomes and another 22 plastid genome sequences of Apiaceae. We found that the newly assembled eight genomes ranged from 155,435 bp to 157,797 bp in length and all had a typical quadripartite structure. Fifty-five to 75 SSRs were found in Hansenia, Haplosphaera and Sinodielsia species, and the most abundant SSR was mononucleotide, which accounted for 58.47% of Hansenia, 60.21% of Haplosphaera and 48.01% of Sinodielsia. There was no evident divergence of codon usage frequency between the three genera, where codons ranged from 21,134 to 21,254. The Pi analysis showed that trnE(UUC)-trnT(GGU), trnH(GUG)-psbA and trnE(UUC)-trnT(GGU) spacer regions had the highest Pi values in the plastid genomes of Hansenia (0.01889), Haplosphaera (0.04333) and Sinodielsia (0.01222), respectively. The ndhG-ndhI spacer regions were found in all three genera to have higher diversity values (Pi values: 0.01028–0.2), and thus may provide potential DNA barcodes in phylogenetic analysis. IR boundary analysis showed that the length of rps19 and ycf1 genes entering IRs were usually stable in the same genus. Our phylogenetic tree demonstrated that Hap. himalayensis is sister to Han. weberbaueriana; meanwhile, Haplosphaera and Hansenia are nested together in the East Asia clade, and S. microloba is nested within individuals of S. yunnanensis in the Acronema clade. This study will enrich the complete plastid genome dataset of the Apiaceae genera and has provided a new insight into phylogeny reconstruction using complete plastid genomes of Hansenia, Haplosphaera and Sinodielsia.

Complete plastid genome of Angelica, Ostericum and related species (Apiaceae): genomic evolution and phylogenetic implications

“…chinense and O. sieboldii) had hexanucleotide SSRs (Figure 4). This is consistent with other Apiaceae species [34,37,40,41] and Allium [35,36,42], but dinucleotide repeats are most numerous in Forthysia [43], and trinucleotide repeats are most abundant in Nitotiana [44].…”

“…The most abundant SSRs were mononucleotide in our studied species, followed by (in decreasing abundance) dinucleotide, tetranucleotide, trinucleotide, pentanucleotide, and hexanucleotide repeats. This phenomenon is common in Allium [35,36,42] and Apiaceae [34,37,40,41]. In our species, mononucleotide and dinucleotide compositions were similar, but trinucleotide, tetranucleotide and pentanucleotide were different across clades.…”

“…Repeat sequences are important in the identi cation of mutational hotspots and play an important role in genome rearrangement [62,63]. Hence, these repeats are used extensively for population genetics and biogeography studies [37,40,41]. Overall, we found that forward and palindromic repeats were more common in our studied species and reverse and complementary repeats were rare, indicating these species tend to generate the forward and palindromic repeats rather than the reverse and complement repeats (Figure 4b).…”

Phylogenetic position of Ligusticopsis (Apiaceae, Apioideae): evidence from molecular data and carpological characters

“…Plastomes (i.e. plastid genomes) are one of the good choices, as there have been many reports on the use of plastomes and comparative analyses to construct and resolve the phylogenetic relationships of genera under Apiaceae subfamily Apioideae ( Gou et al 2020 ; Guo et al 2020 ), while latest study has used plastomes to indicate backbone phylogeny and evolution of subfamily Apioideae with good contributions ( Wen et al 2021 ). What is more, it is reasonable to use the mapping of carpological to phylogenetic results in finding diagnostic characters ( Yu et al 2011 ).…”

Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae)

“…In Apiaceae plastomes, gene order and genome structure are significantly conserved [ 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. However, while for land plant’s plastomes (from early non-vascular plants to angiosperms), a general trend of IR enlarging can be seen [ 1 , 29 ], in the Apioideae subfamily of Apiaceae, a contrary tendency of IR shrinking is observed [ 26 , 30 ].…”