Knowledge Resource Center for Ecological Environment in Arid Area
DOI | 10.1093/gigascience/giy074 |
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub | |
Gao, Fei1; Wang, Xue1; Li, Xuming2; Xu, Mingyue2; Li, Huayun3; Abla, Merhaba1; Sun, Huigai1; Wei, Shanjun1; Feng, Jinchao1; Zhou, Yijun1 | |
通讯作者 | Zhou, Yijun |
来源期刊 | GIGASCIENCE
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ISSN | 2047-217X |
出版年 | 2018 |
卷号 | 7期号:7 |
英文摘要 | Background: Ammopiptanthus nanus is a rare broad-leaved shrub that is found in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here, we report a draft genome assembly using the Pacific Biosciences (PacBio) platform and gene annotation for A. nanus. Findings: A total of 64.72 Gb of raw PacBio sequel reads were generated from four 20-kb libraries. After filtering, 64.53 Gb of clean reads were obtained, giving 72.59x coverage depth. Assembly using Canu gave an assembly length of 823.74 Mb, with a contig N50 of 2.76 Mb. The final size of the assembled A. nanus genome was close to the 889 Mb estimated by k-mer analysis. The gene annotation completeness was evaluated using Benchmarking Universal Single-Copy Orthologs; 1,327 of the 1,440 conserved genes (92.15%) could be found in the A. nanus assembly. Genome annotation revealed that 74.08% of the A. nanus genome is composed of repetitive elements and 53.44% is composed of long terminal repeat elements. We predicted 37,188 protein-coding genes, of which 96.53% were functionally annotated. Conclusions: The genomic sequences of A. nanus could be a valuable source for comparative genomic analysis in the legume family and will be useful for understanding the phylogenetic relationships of the Thermopsideae and the evolutionary response of plant species to the Qinghai Tibetan Plateau uplift. |
英文关键词 | Ammopiptanthus nanus PacBio sequencing genome assembly genome annotation |
类型 | Article ; Data Paper |
语种 | 英语 |
国家 | Peoples R China |
收录类别 | SCI-E |
WOS记录号 | WOS:000439311000001 |
WOS关键词 | PROVIDES INSIGHTS ; MONGOLICUS ; PREDICTION ; TOOL ; CLASSIFICATION ; IDENTIFICATION ; ANNOTATION ; EVOLUTION |
WOS类目 | Biology ; Multidisciplinary Sciences |
WOS研究方向 | Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics |
资源类型 | 期刊论文 |
条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/209727 |
作者单位 | 1.Minzu Univ China, Coll Life & Evironm Sci, 27 Zhongguancun South St, Beijing 100081, Peoples R China; 2.Biomarker Technol Corp, Floor 8,Shunjie Bldg,12 Fuqian Rd, Beijing 101300, Peoples R China; 3.Annoroad Genom, Beijing Econ Technol Dev Area, Bldg B1,Yard 88,Kechuang Six Rd, Beijing 100176, Peoples R China |
推荐引用方式 GB/T 7714 | Gao, Fei,Wang, Xue,Li, Xuming,et al. Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub[J],2018,7(7). |
APA | Gao, Fei.,Wang, Xue.,Li, Xuming.,Xu, Mingyue.,Li, Huayun.,...&Zhou, Yijun.(2018).Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub.GIGASCIENCE,7(7). |
MLA | Gao, Fei,et al."Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub".GIGASCIENCE 7.7(2018). |
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