Identification and characterization of nucleotide variations in the genome of Ziziphus jujuba (Rhamnaceae) by next generation sequencing
Identification and characterization of nucleotide variations in the genome of Ziziphus jujuba (Rhamnaceae) by next generation sequencing
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DOI：
10.1007/s11033-014-3184-8
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发表时间：
2014-05-01
影响因子：
2.8
通讯作者：
Yin, Tongming
中科院分区：
文献类型：
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作者：
Ma, Qiuyue;Feng, Kai;Yin, Tongming
在这项研究中，单核苷酸多态性（SNPs）和插入/缺失（InDels）在枣基因组中进行了鉴定，使用Roche 454 GS-FLX测序仪产生的序列。总共产生了573，141个读段，平均读段长度为360 bp。在质量控制后，258，754个过滤的读段被组装成23，864个重叠群，并且293，458个保留为单例。使用重叠群组件作为参考，鉴定了17，160个SNP和478个InDel。在SNP中，转换发生的频率是颠换的三倍。在转换中，C/T和G/A转换的数量相似。在所有的颠换中，A/T颠换最为丰富，C/G颠换比其他类型的颠换少得多，仅占A/C、A/T和G/T颠换数量的一半左右。对于InDel，莫诺昔肽变化占InDel总数的64.4%。一般而言，检测到的InDel的频率随着InDel长度的增加而降低。本研究为枣属植物的遗传研究提供了宝贵的标记资源。
In this study, single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the genome of Ziziphus jujuba were identified using sequences generated by the Roche 454 GS-FLX sequencer. A total of, 573,141 reads were produced with an average read length of 360 bp. After quality control, 258,754 of the filtered reads were assembled into 23,864 contigs, and 293,458 remained as singletons. Using the contig assemblies as a reference, 17,160 SNPs and 478 InDels were identified. Among the SNPs, transitions occurred three times more frequently than transversions. In transitions, the number of C/T and G/A transitions was similar. Among the transversions, A/T was the most abundant, and C/G was much rarer than any of the other types of transversions, accounting for only about half the numbers of A/C, A/T and G/T transversions. For the InDels, mononucleotide changes amounted to 64.4 % of the total number of InDels. In general, the frequency of detected InDels decreased as the length of the InDels increased. This study provides valuable marker resources for future genetic studies of Ziziphus spp.