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Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species.

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.

SUBMITTER: Yin K

PROVIDER: S-EPMC5979438 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND AND AIMS: Trees with a partial leaf-shedding pattern and other morphological features a priori considered intermediate between those of the deciduous Nothofagus antarctica (G. Forster) Oersted and the evergreen N. dombeyi (Mirb.) Oersted (Nothofagaceae) were found in natural stands. The hybridization between a deciduous and an evergreen species of Nothofagus has not been reported so far in natural communities. METHODS: The putative hybrids and the two presumed parental species were compared using 14 enzyme systems as well as shoot, leaf and reproductive morphology. KEY RESULTS: Six enzyme systems showed good resolution (MDH-B, IDH, SKDH, 6-PGDH, GOT and PGI) and in four of them (PGI, MDH-B, SKDH and 6-PGDH) the putative hybrids showed intermediate zymogram patterns between N. antarctica and N. dombeyi. Both principal coordinates analysis on isozyme data and principal components analysis (PCA) on quantitative morphological traits of shoots and leaves separated both parental species and located the putative hybrids closer to N. antarctica than to N. dombeyi. In the PCA, the number of basal cataphylls and the length : width ratio of leaves were the variables most discriminating among shoots of the three entities. The putative hybrids were intermediate between both species regarding leaf vernation, outline and venation, variation in leaf shape (length/width) with position on the parent shoot and in staminate inflorescence and cupule morphology. For other morphological traits, the putative hybrids resembled one of the parental species or differed from both species (e.g. valve morphology). CONCLUSIONS: Isoenzymatic and morphological data sets support the idea of the hybrid nature (probably F1 generation) of the semi-deciduous trees found. Nothofagus antarctica and N. dombeyi are probably more closely related than previously assumed. The relevance of pollen type in revealing evolutionary relationships between Nothofagus species is supported, and that of leaf-shedding pattern is rejected.

Dataset Information

Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species.

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