Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Abstract

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

Whole genome based insights into the phylogeny and evolution of the Juglandaceae

“…The identification of these regions of variability in protein-coding genes (CDS) and intergenic spacer (IGS) regions will be useful for the study of the evolution, phylogeny, biogeography of the walnut family (Juglandaceae) and Fagales [ 4 , 27 – 29 , 34 , 35 ] and, potentially, for DNA barcoding. Three potential pseudogenes ( infA , rpl22 , and ycf15 ) will also be valuable genetic resource for study of plastid transfer to the nucleus and for studies of the evolution of the walnut family and Fagales [ 10 , 20 ].…”

“…Whole genome scale studies can be useful—and in some cases necessary—supplements to previous research. Whole genomes are particularly suited to resolution of evolutionary relationships where sequence variation is limited by taxonomic level, early divergence, large difference in morphology, rapid speciation or slow genome evolution [ 7 , 17 – 20 ].…”

Chloroplast Genome of Lithocarpus Dealbatus: Identification of Hotspots for Sequence Variability and Phylogeny Analysis in Quercoideae, a Sub-family of Fagaceae

“…Extremely low resolution of universal DNA barcode was also reported in the 12 Italian oak species [19]. As a result, several reports have been published highlighting the need to develop additional barcodes in Quercoidaeae species [17,20]. Researchers have demonstrated that chloroplast genome mutations are clustered into hotspots, and these hotspot regions can be considered as real DNA barcodes [21].…”

“…Following the approach of mutational hotspots from the entire chloroplast genome, the species-speci c barcodes in oak and Castanea species have been designed [17,20]. Despite the fact that some speci c barcodes with the highest discriminatory power have previously been reported in Quercus, additional markers are still required for the rest of the Quercoidaeae species considering their complex evolutionary background.…”

Chloroplast Genome of Lithocarpus dealbatus (Hook.f. & Thomson ex Miq.) Rehder Establishes Monophyletic Origin of the Species and Reveals Mutational Hotspots with Taxon Delimitation Potential

“…An extremely low-resolution power of DNA barcode was reported in the 12 Italian oak species [ 20 ]. Therefore, several workers have highlighted the need to develop novel barcodes in Quercoideae species [ 17 , 21 ]. Researchers have demonstrated that chloroplast-genome mutations are clustered into hotspots, and these hotspot regions can be potential candidates for new DNA barcodes [ 22 ].…”