Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

Abstract

Eucommia ulmoides (E. ulmoides), the sole species of Eucommiaceae with high importance of medicinal and industrial values, is a Tertiary relic plant that is endemic to China. However, the population genetics study of E. ulmoides lags far behind largely due to the scarcity of genomic data. In this study, one complete chloroplast (cp) genome of E. ulmoides was generated via the genome skimming approach and compared to another available E. ulmoides cp genome comprehensively at the genome scale. We found that the structure of the cp genome in E. ulmoides was highly consistent with genome size variation which might result from DNA repeat variations in the two E. ulmoides cp genomes. Heterogeneous sequence divergence patterns were revealed in different regions of the E. ulmoides cp genomes, with most (59 out of 75) of the detected SNPs (single nucleotide polymorphisms) located in the gene regions, whereas most (50 out of 80) of the indels (insertions/deletions) were distributed in the intergenic spacers. In addition, we also found that all the 40 putative coding-region-located SNPs were synonymous mutations. A total of 71 polymorphic cpDNA fragments were further identified, among which 20 loci were selected as potential molecular markers for subsequent population genetics studies of E. ulmoides. Moreover, eight polymorphic cpSSR loci were also developed. The sister relationship between E. ulmoides and Aucuba japonica in Garryales was also confirmed based on the cp phylogenomic analyses. Overall, this study will shed new light on the conservation genomics of this endangered plant in the future.

Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

“…Numerous divergence hotspot regions (e.g., trnH-psbA, trnT-trnL, atpF-atpH, ccsA-ndhD, petD-rpoA, and trnL-trnF) were identified through calculating and comparing the nucleotide diversity (Pi) values (Figure 3). ose highly variable loci can be used as potential molecular markers for the phylogenetic studies in the future [85,86]. Among those, trnL-trnF has been proved to be a useful marker for the phylogenetic studies of Toxicodendron.…”

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

“…By contrast, there were more mutational events (SNPs and indels) in Eucommia ulmoides [47] and Scutellaria baicalensis [48]. There were 75 SNPs and 80 indels in two different individuals of E. ulmoides [47], 25 SNPs and 29 indels between the two S. baicalensis genotypes [48]. These 23 indels and 20 SNPs could be used for identification of different sources of A. oxyphylla.…”

“…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 of the complete chloroplast genome of sugar maple (Acer saccharum)

“…Despite its great value, to date the genetic and genomic data for this species are rather limited (Khodwekar et al 2015). In the present study we generated the complete chloroplast (cp) genome of A. saccharum via genome-skimming method (Wang et al 2018a), which will facilitate genetic studies and molecular breeding of sugar maple.…”