Abstract
Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species that is endemic to, but widely distributed across, the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we compared the fully assembled chloroplast (cp) genome of Q. aquifolioides with those of three closely related species. The analysis revealed a cp genome ranging in size from 160,415 to 161,304 bp and with a typical quadripartite structure, composed of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. The genome organization, gene number, gene order, and GC content of these four Quercus cp genomes are similar to those of many angiosperm cp genomes. We also analyzed the Q. aquifolioides repeats and microsatellites. Investigating the effects of selection events on shared protein-coding genes using the Ka/Ks ratio showed that significant positive selection had acted on the atpF gene of Q. aquifolioides compared to two deciduous oak species, and that there had been significant purifying selection on the atpF gene in the chloroplast of evergreen sclerophyllous oak trees. In addition, site-specific selection analysis identified positively selected sites in 12 genes. Phylogenetic analysis based on shared protein-coding genes from 14 species defined Q. aquifolioides as belonging to sect. Heterobalanus and being closely related to Q. rubra and Q. aliena. Our findings provide valuable genetic information for use in accurately identifying species, resolving taxonomy, and reconstructing the phylogeny of the genus Quercus.
Highlights
The chloroplast is an organelle which plays an important role in photosynthesis and carbon fixation in plant cells
The cp genome is between 120 and 160 kb in size and has a structure composed of two copies of a large inverted repeat (IR) region, a large single copy (LSC) region, and a small single copy (SSC) region [2]
The Q. aquifolioides cp genome is a typical circular double-stranded DNA molecule with a length of 160,415 bp, which falls within the normal angiosperm length range [23,24]
Summary
The chloroplast (cp) is an organelle which plays an important role in photosynthesis and carbon fixation in plant cells. Oaks are dominant in various habitats, such as temperate deciduous forest, oak-pine forest and temperate and subtropical evergreen forest [5] They are intimately associated with many other organisms, including fungi, ferns, birds, mammals, and insects [4]. We studied the phylogeography of Quercus aquifolioides, which is endemic to the Hengduanshan Biodiversity Hotspot, based on 58 populations distributed throughout the species range, using four chloroplast DNA fragments and 11 nuclear microsatellite loci [21]. Our findings will enrich the complete cp genome resources available for the genus Quercus and provide abundant genetic information for use in subsequent taxonomic and phylogenetic identification of members of the genus, and assist geneticists and breeders in improving commercially-grown oak trees
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