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Chloroplast genome structure in Ilex (Aquifoliaceae)
Yao, Xin; Tan, Yun-Hong; Liu, Ying-Ying; ...; Corlett, Richard T.
2016
Source PublicationSCIENTIFIC REPORTS
Volume6Issue:xPages:28559
AbstractAquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. Most species are in East Asia or South America. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. The total length is 157,741 bp and there is one large single-copy region (LSC) with 87,109 bp, one small single-copy with 18,436 bp, and a pair of inverted repeat regions (IR) with 52,196 bp. A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers. This study will contribute to improved resolution of deep branches of the Ilex phylogeny and facilitate identification of Ilex species.
KeywordMultiple Sequence Alignment L. aquifoL.aceae High-throughput Dna History Organization Evolution Mitochondrial Angiosperms Plastome
Document Type期刊论文
Identifierhttp://ir.xtbg.org.cn/handle/353005/9999
Collection2012年后新成立研究组
Recommended Citation
GB/T 7714
Yao, Xin,Tan, Yun-Hong,Liu, Ying-Ying,et al. Chloroplast genome structure in Ilex (Aquifoliaceae)[J]. SCIENTIFIC REPORTS,2016,6(x):28559.
APA Yao, Xin,Tan, Yun-Hong,Liu, Ying-Ying,...,&Corlett, Richard T..(2016).Chloroplast genome structure in Ilex (Aquifoliaceae).SCIENTIFIC REPORTS,6(x),28559.
MLA Yao, Xin,et al."Chloroplast genome structure in Ilex (Aquifoliaceae)".SCIENTIFIC REPORTS 6.x(2016):28559.
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