Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

Abstract

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

“…The majority of the preferred codons (RSCU >1) ended with A or U, with the exception of UUG (RSCU = 1.25). This phenomenon is congruent with the results from other plant studies (Table S4) (Lu et al, 2018;Yi & Kim, 2012).…”

“…IR regions are the most conserved regions in the cp genomes. Frequent expansions and contractions at the junctions of SSR and LSC with IRs illustrate the relationships among taxa and have been recognized as evolutionary signals (Khakhlova & Bock, 2006;Inkyu et al, 2018;Lu et al, 2018;Raubeson et al, 2007;Wang et al, 2008). In this study, only a few variations were found among the five Dicliptera species.…”

“…The interspecies relationships among the five species were resolved. However, further phylogenetic analysis using additional genes from the nucleus will have to be conducted in order to understand how gene introgression and hybridization affects the phylogeny of Dicliptera (Birky, 1995;Meng et al, 2018;Lu et al, 2018). A single gene, ycf15, was found to be positively selected among all of the protein coding genes that were identified.…”

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…These results also prove that the IR regions were more conserved than the LSC and SSC regions, and the average value of Pi in the non-coding regions was more than three times as much as in the coding regions. Among these regions, ycf1, rps15, rpl22, infA, psbT-psbN, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, and rpl32-ccsA have also been reported as highly variable regions in other plant species, such as Kaempferia species [23], Aristolochis species [26], orchid species [42], Lythraceae species [43], Quercus species [44], Lilium species [45], Croomia species [46], Stemona species [46], and Eucommia species [47]. The ndhF-rpl32 and ccsA-ndhD regions had been used as molecular markers for phylogenetic analyses [18,19].…”

Characterization and phylogenetic relationship of the complete chloroplast genome of Stemona japonica as an herb to treat bone tuberculosis at China

“…Stemona japonica is important one of herb plant in China, which belongs to the genus Stemona the family Stemonaceae (Lu et al 2018). It is native to China, the Indian Subcontinent, Southeast Asia and northern Australia (Yang et al 2006).…”