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First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
University of Chinese Academy of Sciences, Beijing 100039, China
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
Wuhan Vegetable Research Station, Wuhan 430065, China
* Author to whom correspondence should be addressed.
Received: 7 January 2013; in revised form: 16 May 2013 / Accepted: 6 June 2013 / Published: 27 June 2013
Abstract: Epimedium sagittatum (Sieb. et Zucc) Maxim is a member of the Berberidaceae family of basal eudicot plants, widely distributed and used as a traditional medicinal plant in China for therapeutic effects on many diseases with a long history. Recent data shows that E. sagittatum has a relatively large genome, with a haploid genome size of ~4496 Mbp, divided into a small number of only 12 diploid chromosomes (2n = 2x = 12). However, little is known about Epimedium genome structure and composition. Here we present the analysis of 691 kb of high-quality genomic sequence derived from 672 randomly selected plasmid clones of E. sagittatum genomic DNA, representing ~0.0154% of the genome. The sampled sequences comprised at least 78.41% repetitive DNA elements and 2.51% confirmed annotated gene sequences, with a total GC% content of 39%. Retrotransposons represented the major class of transposable element (TE) repeats identified (65.37% of all TE repeats), particularly LTR (Long Terminal Repeat) retrotransposons (52.27% of all TE repeats). Chromosome analysis and Fluorescence in situ Hybridization of Gypsy-Ty3 retrotransposons were performed to survey the E. sagittatum genome at the cytological level. Our data provide the first insights into the composition and structure of the E. sagittatum genome, and will facilitate the functional genomic analysis of this valuable medicinal plant.
Keywords: Epimedium sagittatum; Chinese medicinal plant; structural genomics; genome composition; Gypsy-Ty3 retrotransposon; repetitive elements; FISH; chromosome
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Liu, D.; Zeng, S.-H.; Chen, J.-J.; Zhang, Y.-J.; Xiao, G.; Zhu, L.-Y.; Wang, Y. First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant. Int. J. Mol. Sci. 2013, 14, 13559-13576.
Liu D, Zeng S-H, Chen J-J, Zhang Y-J, Xiao G, Zhu L-Y, Wang Y. First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant. International Journal of Molecular Sciences. 2013; 14(7):13559-13576.
Liu, Di; Zeng, Shao-Hua; Chen, Jian-Jun; Zhang, Yan-Jun; Xiao, Gong; Zhu, Lin-Yao; Wang, Ying. 2013. "First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant." Int. J. Mol. Sci. 14, no. 7: 13559-13576.