Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants

Abstract

The chloroplast genome originated from photosynthetic organisms and has retained the core genes that mainly encode components of photosynthesis. However, the causes of variations in chloroplast genome size in seed plants have only been thoroughly analyzed within small subsets of spermatophytes. In this study, we conducted the first comparative analysis on a large scale to examine the relationship between sequence characteristics and genome size in 272 seed plants based on cross-species and phylogenetic signal analysis. Our results showed that inverted repeat regions, large or small single copies, intergenic regions, and gene number can be attributed to the variations in chloroplast genome size among closely related species. However, chloroplast gene length underwent evolution affecting chloroplast genome size in seed plants irrespective of whether phylogenetic information was incorporated. Among chloroplast genes, atpA, accD and ycf1 account for 13% of the variation in genome size, and the average Ka/Ks values of homologous pairs of the three genes are larger than 1. The relationship between chloroplast genome size and gene length might be affected by selection during the evolution of spermatophytes. The variation in chloroplast genome size may influence energy generation and ecological strategy in seed plants.

A systematic comparison of chloroplast genome assembly tools

“…Chloroplast genome content and structure are reviewed for example in [4,5]. Chloroplast genomes are widely used for evolutionary analyses [6,7], barcoding [8,9,10], and meta-barcoding [11,12]. Interesting aspects of chloroplast genomes are their small size (120 kbp to 160 kbp, [1]), caused through endosymbiotic gene transfer [13,14] and the low number of 100 to 120 genes that are still encoded on the chloroplast genome [4].…”

Resolution of Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

“…The prospective of chloroplast phylogenomics to resolve contentious phylogenetic relationships, at nearly all taxonomic levels, have been proven over the recent past, e.g., in providing strong support for the evolutionary clades of the basal Angiosperms [4,7], the earlydiverging eudicots [8,23], and the early-diverging monocots [6]. Furthermore, through comparative phylogenomics, the availability of complete chloroplast genome sequences have significantly contributed to our understanding of genome evolutionary patterns driven by events such as gene transfers, duplications, and rearrangements [24,25].…”

In silico analysis of Pinus L. chloroplast DNA to microsatellites regions

“…In terrestrial plants, the cpDNA varies between ≈120,000 and ≈160,000 bp (PALMER, 1995). For Gymnosperm, the size of cpDNA the chloroplast genome is significantly lower than for Angiosperm (XIAO-MING et al, 2017) and, for Eucalyptus spp. and another superior genus, cpDNAs with around 160,000 bp are commonly observed (EGUILUZ et al, 2017;LI et al, 2017;PAIVA et al, 2011;SAINA et al, 2018;STEANE et al, 2005 Regarding the cpSSR regions identified, the majority were classified as mononucleotides.…”

“…The size range observed in cpDNAs of closer species can be attributed to variations in intergenic regions length, that can be associated to species evolution process (XIAO-MING et al, 2017). In terrestrial plants, the cpDNA varies between ≈120,000 and ≈160,000 bp (PALMER, 1995).…”