Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

Abstract

Comparative chloroplast genome analysis presents new opportunities for performing molecular phylogeny studies and revealing the significant evolutionary features in higher plants, which has been widely documented from conifers to grass family. However, a systematic analysis of chloroplast genomes in Asteraceae family has not been conducted up to now. In this study, we compared and analyzed the gene content, genomic organization, and RNA editing sites of eight representative Asteraceae chloroplast genomes. Results showed that Asteraceae chloroplast had relatively conservative gene content. No gain or loss events occurred in the proteincoding genes, while some differences were found to be present in the gene structure and transfer RNA (tRNA) abundance. Genome structure analysis found some Asteraceae-specific or species-specific structure variations, and sequence rearrangement events were present in these genomes, suggesting specific evolutionary processes have occurred in this family. Some DNA regions containing parsimony-informative characters higher than 5 % were also identified, which could be used as the new molecular markers for phylogenetic analysis and plant identification of Asteraceae species. Furthermore, RNA editing in these genomes was investigated through computational analysis, and some species-specific sites were identified. Finally, phylogenetic analysis of 81 genes from 70 species supported the monophyly of the Asteraceae. Our study for the first time compared the organization, structure, and sequence divergence of eight Asteraceae chloroplast genomes, which will provide the valuable resource for molecular phylogeny of Asteraceae species and also facilitate the genetic and evolutionary studies in this family.

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

“…The ψycf1 gene was located at the junction between SSC and IRb. This pattern of IR expansion and contraction of partial copies of non-coding genes is a common occurrence in most terrestrial species [66]. These outcomes can provide insight into the evolutionary processes of chloroplast genomes, as well as being a source of DNA barcodes.…”

Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

“…Since Palmer (1983) originally documented this phenomenon in Phaseolus vulgaris , it has been confi rmed in a wide variety of plant species ( Palmer, 1985 ), including algae ( Aldrich et al, 1985 ;Bourne et al, 1992 ;Linne von Berg and Kowallik, 1992 ;Cattolico et al, 2008 ) and ferns ( Stein et al, 1986 ), and is now a well-accepted feature of chloroplast genomes (e.g., Heinhorst and Cannon, 1993 ;Doyle and Doyle, 1999 ). Nonetheless, this phenomenon has been overlooked in several recent analyses that have evaluated the orientation of the SSC region a phylogenetic context (e.g., Ibrahim et al, 2006 ;Yang et al, 2010 ;Liu et al, 2013 ;Walker et al, 2014 ;Zhang et al, 2014 ;Wang et al, 2015 ). Th ese analyses compare the SSC orientation among lineages using a single plastome to represent each lineage and thus have missed the withinindividual variation that exists in this region.…”

“…For example, two sequences of Lactuca sativa that have been independently published (NC_007578 and DQ_383816) were entered with diff erent orientations of the SSC region, which could be interpreted as a major inversion existing within the species if the investigators are not aware that two isomers naturally exist (e.g., Walker et al, 2014 ). Th is misinterpretation has now occurred in several studies (e.g., Ibrahim et al, 2006 ;Yang et al, 2010 ;Liu et al, 2013 ;Walker et al, 2014 ;Zhang et al, 2014 ;Wang et al, 2015 ), leading to the hypothesis that the SSC region is an inversion "hotspot" ( Liu et al, 2013 ). Experiments that attempted to use PCR to allegedly confi rm a single orientation of the SSC region within samples have likely perpetuated this misconception (e.g., Nie et al, 2012 ;Liu et al, 2013 ).…”

Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method

“…The most parsimonious interpretation of our results suggests that structural heteroplamsy should be extremely common across all angiosperms. In light of this, it may be necessary to re-examine many previous suggestions of structural differences in the chloroplast genomes of angiosperms between species (9-13), as Emery et al (14) suggested. For example, Ibrahim et al (9) implied that the SSC of Gossypium barbadense was inverted when compared to Gossypium hirsutum .…”

“…A better understanding of chloroplast genome structural heteroplasmy is important for a number of reasons. First, some recent papers have suggested that the orientation of the single copy regions differ between species (9-13), but Emery et al (14) pointed out that these studies seem to have overlooked the possibility that both orientations may coexist in a single individual. Second, the relationship between the structure of the chloroplast genome and the existence or otherwise of structural heteroplasmy remains poorly understood.…”