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Int. J. Mol. Sci. 2017, 18(11), 2307; https://doi.org/10.3390/ijms18112307

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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Received: 29 August 2017 / Revised: 27 September 2017 / Accepted: 20 October 2017 / Published: 2 November 2017
(This article belongs to the Special Issue Chloroplast)
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Abstract

The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC)—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus. View Full-Text
Keywords: Dendrobium; plastome assembly; selection; mutational biases; GC-biased gene conversion (gBGC); GCeq Dendrobium; plastome assembly; selection; mutational biases; GC-biased gene conversion (gBGC); GCeq
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Niu, Z.; Xue, Q.; Wang, H.; Xie, X.; Zhu, S.; Liu, W.; Ding, X. Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus. Int. J. Mol. Sci. 2017, 18, 2307.

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