Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses

Abstract

Lilium is a large genus that includes approximately 110 species distributed throughout cold and temperate regions of the Northern Hemisphere. The species-level phylogeny of Lilium remains unclear; previous studies have found universal markers but insufficient phylogenetic signals. In this study, we present the use of complete chloroplast genomes to explore the phylogeny of this genus. We sequenced nine Lilium chloroplast genomes and retrieved seven published chloroplast genomes for comparative and phylogenetic analyses. The genomes ranged from 151,655 bp to 153,235 bp in length and had a typical quadripartite structure with a conserved genome arrangement and moderate divergence. A comparison of sixteen Lilium chloroplast genomes revealed ten mutation hotspots. Single nucleotide polymorphisms (SNPs) for any two Lilium chloroplast genomes ranged from 8 to 1,178 and provided robust data for phylogeny. Except for some of the shortest internodes, phylogenetic relationships of the Lilium species inferred from the chloroplast genome obtained high support, indicating that chloroplast genome data will be useful to help resolve the deeper branches of phylogeny.

Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

“…Another phenomenon observed in all six orders, is that SSC regions and LSC have higher divergence than IR regions, indicating the IR is more conserved than single copy sequences (Figure 3). This pattern is also been reported in other plants [24–26].…”

The Complete Chloroplast Genome of Tamarix Ramosissima and Comparative Analysis of Tamaricaceae Species 

“…The high abundance of A and T in chloroplast SSRs were also observed in plastomes of the other four Tamaricaceae species. The ndings in our study are consistent with those described previously in other species, including Xanthium sibiricum (Somaratne et al 2019), Populus species (Gao et al 2019), and Lilium plants (Du et al 2017). The SSRs identi ed in T. ramosissima plastome, as well as those in other four Tamaricaceae species, could be developed as potential molecular markers facilitating future phylogenetic research.…”

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].…”