干旱区生态环境知识资源中心(Arid): 新疆沙冬青基因组调查测序与基因组大小预测

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	新疆沙冬青基因组调查测序与基因组大小预测
其他题名	Genomic Survey Sequencing and Estimation of Genome Size of Ammopiptanthus mongolicus
	王雪; 周佳熠; 孙会改; 禹瑞敏; 高飞; 周宜君
来源期刊	植物遗传资源学报
ISSN	1672-1810
出版年	2018
卷号	19 期号:1 页码:143-149
中文摘要	新疆沙冬青是中国荒漠地区代表性常绿阔叶植物,属于第三纪孑遗植物。其极强的逆境耐受性受到了研究者的广泛关注,但由于缺乏基因组序列,分子生物学研究水平进展缓慢。本研究对新疆沙冬青进行了基因组调查测序,共得到65 Gb大小的双端测序数据。结合基于K-mer分析和流式细胞分析的方法,预测基因组大小、杂合率和GC含量等特征,估计基因组大小为770 ~ 787 Mb。测序数据拼接构建得到contigs的N50为684 bp,总读长为0.538 Gb;进一步组装后scaffolds的N50为12.09 kb,总读长为0.602 Gb。对拼接数据进行SSR分子标记预测,共得到151858个SSR,其中二核苷酸重复单元比例最高为56.39%,在二核苷酸重复单元中,AT/TA组成形式占多数。本研究首次报道了荒漠植物新疆沙冬青的基因组特征,为后续基因组学研究提供参考。
英文摘要	Ammopiptanthus mongolicus(Maxim. ex Kom.) Cheng f.,one of the tertiary relict plants, is a rare evergreen broad-leaved shrub distributed in desert region of central Asia. A. mongolicus(Maxim. ex Kom.) Cheng f. grows in environment with extremely high level of drought and freezing stresses,and the plant species can be used as an ideal model for stress tolerance research in plant. Previous studies revealed that A. mongolicus(Maxim. ex Kom.) Cheng f. showed high levels of tolerance to various abiotic stresses. Several genes presumed to play important roles in stress tolerance of A. mongolicus(Maxim. ex Kom.) Cheng f. were cloned and characterized, including AnGobs1,An- PLD,AnMCSD,AnBADH,and AnAFP. However, research in A. mongolicus(Maxim. ex Kom.) Cheng f. at the molecular level was hindered by the lack of genome information. There were several genome size prediction methods, including Feulgen densitometry, field gel electrophoresis,quantitative reverse transcription PCR(qRT-PCR), flow cytometry analysis,and K-mer analysis. Flow cytometry was the standard method for estimating genome size. K-mer analysis not only predicted genome size accurately,but also provideed more information about genome, such as heterozygosity and GC percentage. In the present study, flow cytometry analysis was performed to predict the genome size of A. mongolicus(Maxim. ex Kom.) Cheng f.. Genomic survey sequencing of A. mongolicus(Maxim. ex Kom.) Cheng f. was then conducted,and a total of 65 Gb sequencing reads was obtained. K-mer analysis using these sequencing reads was conducted to predict the genome size,heterozygosity and GC content of A. mongolicus(Maxim. ex Kom.) Cheng f.. Based on the results of flow cytometry and K-mer analyses, the genome size of A. mongolicus(Maxim. ex Kom.) Cheng f. was estimated to be 770-787 Mb. The genome size of A. mongolicus(Maxim. ex Kom.) Cheng f. was close to that of Cicer arietinum L.,and was smaller than that of Glycine max L.. The total reads length of contigs was 0.538 Gb,with N50 of 684 bp,and after further assembly, the N50 of scaffolds was 12.09 Kb with a total reads length of 0.602 Gb. The predicted heterozygosity was 0.0844% and the GC content was 36.51%. The low heterozygosity of A. mongolicus(Maxim. ex Kom.) Cheng f. will facilitate the whole genome sequencing of A. mongolicus(Maxim. ex Kom.) Cheng f.,and subsequent gene annotation and comparative genomics study. Simple sequence repeat(SSR) molecular markers were predicted using the assembled genome sequences and 151858 SSRs were obtained. Of all SSR categories, the dinucleotide repeat unit was the largest category,with a percentage of 56.39%,and the AT /TA components was the dominant dinucleotide repeat unit. Our study reported the genome size prediction of A. mongolicus(Maxim. ex Kom.) Cheng f. for the first time and provided a large number of genomic sequences for further research in A. mongolicus(Maxim. ex Kom.) Cheng f.. The large number of SSR molecular markers identified in the present study will promote the study of genome mapping,evolutionary biology,and population genetics in A. mongolicus(Maxim. ex Kom.) Cheng f.
中文关键词	新疆沙冬青 ; 基因组大小 ; 流式细胞分析 ; K-mer分析 ; SSr分子标记
英文关键词	Ammopiptanthus mongolicus(Maxim. ex Kom.) Cheng f. genome size flow cytometry K-mer SSR molecular marker
语种	中文
国家	中国
收录类别	CSCD
WOS类目	FORESTRY
WOS研究方向	Forestry
CSCD记录号	CSCD:6159338
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/238643
作者单位	中央民族大学生命与环境科学学院, 北京 100081, 中国
推荐引用方式 GB/T 7714	王雪,周佳熠,孙会改,等. 新疆沙冬青基因组调查测序与基因组大小预测[J],2018,19(1):143-149.
APA	王雪,周佳熠,孙会改,禹瑞敏,高飞,&周宜君.(2018).新疆沙冬青基因组调查测序与基因组大小预测.植物遗传资源学报,19(1),143-149.
MLA	王雪,et al."新疆沙冬青基因组调查测序与基因组大小预测".植物遗传资源学报 19.1(2018):143-149.