Evaluation of genome sequencing quality in selected plant species using expressed sequence tags.
Evaluation of genome sequencing quality in selected plant species using expressed sequence tags.
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使用表达序列标签评估选定植物物种的基因组测序质量
DOI：
10.1371/journal.pone.0069890
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Fang J
中科院分区：
文献类型：
--
作者：
Shangguan L;Han J;Kayesh E;Sun X;Zhang C;Pervaiz T;Wen X;Fang J
背景随着30多种植物基因组测序计划的完成，大量的基因组序列已经产生并存储在在线数据库中。测序技术的进步已经降低了全基因组测序的成本和时间，使得越来越多的植物能够进行基因组测序。尽管如此，尚未评估多个植物的基因组序列质量。方法/主要发现计算完整性和准确性以评估32种植物的基因组序列质量。基因组序列的完整性由染色体大小与基因组大小的比率（或支架大小与基因组大小之间的比率）表示，其范围从55.31%到接近100%。基因组测序的准确性以匹配EST和筛选EST的比率表示，其中随机选择的干净EST中，52.93%~ 98.28%和89.02%~ 98.85%分别可定位到染色体和支架序列上。根据各植物种类的完整性、准确性等分析，将13种植物分为4个等级。结果表明，品质最好的是拟南芥、水稻和玉米，其次是二穗短柄草、大叶杨、葡萄属和大豆、二色高粱、番茄和野草莓、百脉根、蒺藜苜蓿和苹果。将支架序列组装成染色体序列应该是剩下的19个物种的首要任务。低GC含量和重复DNA影响基因组序列组装。结论植物基因组序列的质量低于预期，因此基因组测序计划的快速发展以及生物信息学工具和基因组序列组装算法的研究应该提供更多的处理和校正已经发表的基因组序列。
Background With the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. Advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. Despite this, genome sequence qualities of multiple plants have not been evaluated. Methodology/Principal Finding Integrity and accuracy were calculated to evaluate the genome sequence quality of 32 plants. The integrity of a genome sequence is presented by the ratio of chromosome size and genome size (or between scaffold size and genome size), which ranged from 55.31% to nearly 100%. The accuracy of genome sequence was presented by the ratio between matched EST and selected ESTs where 52.93% ∼ 98.28% and 89.02% ∼ 98.85% of the randomly selected clean ESTs could be mapped to chromosome and scaffold sequences, respectively. According to the integrity, accuracy and other analysis of each plant species, thirteen plant species were divided into four levels. Arabidopsis thaliana, Oryza sativa and Zea mays had the highest quality, followed by Brachypodium distachyon, Populus trichocarpa, Vitis vinifera and Glycine max, Sorghum bicolor, Solanum lycopersicum and Fragaria vesca, and Lotus japonicus, Medicago truncatula and Malus × domestica in that order. Assembling the scaffold sequences into chromosome sequences should be the primary task for the remaining nineteen species. Low GC content and repeat DNA influences genome sequence assembly. Conclusion The quality of plant genome sequences was found to be lower than envisaged and thus the rapid development of genome sequencing projects as well as research on bioinformatics tools and the algorithms of genome sequence assembly should provide increased processing and correction of genome sequences that have already been published.
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影响因子：
14.9
作者：
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通讯作者：
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影响因子：
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作者：
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影响因子：
14.9
作者：
Fedurco, M;Romieu, A;Williams, S;Lawrence, I;Turcatti, G
通讯作者：
Turcatti, G
影响因子：
7
作者：
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通讯作者：
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DOI：
10.1073/pnas.0509473102
发表时间：
2005-12-27
影响因子：
11.1
作者：
Devos, KM;Ma, JX;Bennetzen, JL
通讯作者：
Bennetzen, JL