Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

Abstract

Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genome of Santalum (Santalaceae)

“…We identified three variable regions (ccsA-trnL, ΨndhE-ΨndhG-rps15, and ycf1) by comparing the Santalum chloroplast genomes. The ycf1 gene has been identified to be highly variable in several lineages, such as Dalbergia [78], Diospyros [62], and Quercus [79]. Studies have shown that ycf1 is phylogenetically useful [80] and is associated with a high success rate for DNA barcoding [81].…”

Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

“…In previous studies, several unique characteristics of the plastome have been widely reported, such as its monophyletic inheritance [12], conserved coding region sequences [13] and genome structure [14,15]. These reliable resources provide rich information for the study of evolution, DNA barcoding, taxonomy and phylogeny [16][17][18]. Although the plastid genome is highly conserved, some interesting structural variations have been observed in some taxa, such as the rare expansion of IR regions in Strobilanthes [15], the insertion of mitochondrial DNA in the plastome of Anacardium [19], and the complete or partial loss of IR regions in some legumes [16,20,21].…”

Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

“…We identi ed three variable regions (ccsA-trnL, ΨndhE-ΨndhG-rps15, and ycf1) compared with the Santalum chloroplast genome. The ycf1 gene has been identi ed in several lineages, such as Dalbergia [39], Diospyros [22], and Quercus [40]. Studies have shown that ycf1 is phylogenetically useful [41] and is associated with a high success rate for DNA barcoding [42].…”