Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution

Abstract

BackgroundThe Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies.ResultsAll plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859–26,451 bp) separated by a large single-copy region (86,089–87,835 bp) and a small single-copy region (18,250–18,856 bp) region. These plastomes encoded the same set of 114 unique genes including 31 transfer RNA, 4 ribosomal RNA and 79 coding genes, with an identical gene order across all examined Cornales species. Two genes (rpl22 and ycf15) contained premature stop codons in seven and five species respectively. The phylogenetic relationships among all sampled species were fully resolved with maximum support. Different filtering strategies (none, light and strict) of sequence alignment did not have an effect on these relationships. The topology recovered from coding and noncoding data sets was the same as for the whole plastome, regardless of filtering strategy. Moreover, mutational hotspots and highly informative regions were identified.ConclusionsPhylogenetic relationships among families and intergeneric relationships within family of Cornales were well resolved. Different filtering strategies and partitioning schemes do not influence the relationships. Plastid genomes have great potential to resolve deep phylogenetic relationships of plants.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4319-9) contains supplementary material, which is available to authorized users.

Comparative Chloroplast Genomics of Fritillaria (Liliaceae), Inferences for Phylogenetic Relationships between Fritillaria and Lilium and Plastome Evolution

“…Plastid genome of angiosperm have a typical quadripartite structure with a pair of inverted repeat (IR) regions separated by a small single-copy (SSC) region and a large single-copy (LSC) region [1,2]. In contrast to mitochondrial and nuclear genomes, plastid genome is highly conserved and generally contains 110-130 distinct genes, ranging in size from 120-160 kb [3]. Although plastid genomes are reported as a highly conserved sequence and structure in most angiosperms, they have been showed considerable variation in many taxa [2].…”

“…Currently, whole chloroplast genomes have been increasingly used for phylogenetic analyses and inferring phylogeographic histories, as the advent and fast development of next-generation sequencing (NGS) technologies. They can provide plenty of variable sites among their entire size for phylogenetic analyses [3]. Thus, whole chloroplast genomes show the potential for resolving evolutionary relationships and have been employed to generate highly resolved phylogenies and genetic diversity, especially in the unresolved relationship of some complex taxa or at low taxonomic levels [2,[11][12][13].…”

“…Thus, whole chloroplast genomes show the potential for resolving evolutionary relationships and have been employed to generate highly resolved phylogenies and genetic diversity, especially in the unresolved relationship of some complex taxa or at low taxonomic levels [2,[11][12][13]. Because different regions of the whole chloroplast genomes differed with their evolutionary rates, partitioning the genome by regions or genes might be preferable for phylogenomic analysis [3]. The concatenated coding genes were most widely used for plastome phylogenomics until now [14,15].…”

Comparative chloroplast genomics of Fritillaria (Liliaceae), inferences for phylogenetic relationships between Fritillaria and Lilium and genome evolution

“…Plastid genome of angiosperm have a typical quadripartite structure with a pair of inverted repeat (IR) regions separated by a small single-copy (SSC) region and a large single-copy (LSC) region [1,2]. In contrast to mitochondrial and nuclear genomes, plastid genome is highly conserved and generally contains 110-130 distinct genes, ranging in size from 120-160 kb [3]. Although plastid genomes are reported as highly conserved sequence and structure in most angiosperms, they have been showed considerable variation in many taxa [2].…”

“…Currently, whole chloroplast genomes have been increasingly used for phylogenetic analyses and inferring phylogeographic histories, as the advent and fast development of next-generation sequencing (NGS) technologies. They can provide plenty of variable sites among their entire size for phylogenetic analyses [3]. Thus, whole chloroplast genomes show the potential for resolving evolutionary relationships and have been employed to generate highly resolved phylogenies and genetic diversity, especially in unresolved relationship of some complex taxon or at low taxonomic levels [2,[11][12][13].…”