Closing target trimming and CTTdocker programs for discovering hidden superfamily loci in genomes
Closing target trimming and CTTdocker programs for discovering hidden superfamily loci in genomes
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DOI：
10.1371/journal.pone.0209468
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发表时间：
2019-07-02
期刊：
影响因子：
3.7
通讯作者：
Early, Matthew J.
中科院分区：
文献类型：
--
作者：
Hua, Zhihua;Early, Matthew J.
基因组序列分析的当代能力明显落后于快速发展的测序技术。从不断增加的基因组数据中检索生物学上有意义的信息对于功能基因组学研究将是非常有益的。例如，超家族基因的复制、组织、进化和功能在生命的许多方面都很重要。然而，许多测序基因组中注释的不完整性往往导致在超家族的比较基因组研究中得出有偏见的结论。在这里，我们提出了一个Perl软件，称为关闭目标修剪（CTT），自动识别大多数，如果不是全部，基因家族的成员在任何测序的基因组在CentOS 7平台上。为了在其他操作系统上更广泛地应用，我们还创建了一个Docker应用程序包CTTdocker。我们对F-box基因超家族的测试数据显示，在两个注释良好的植物基因组中，拟南芥和水稻，分别有78.2%和79%的基因发现准确率。为了进一步证明该计划的有效性，我们通过18个植物基因组和5个非植物基因组来比较F-box和BTB超家族的扩展。该计划发现，平均12.7%和9.3%的F-box和BTB成员分别是植物基因组中的新位点，而在脊椎动物基因组中只发现了少量新成员。因此，Cullin-RING泛素连接酶在植物和动物中可能存在不同的进化和调节机制。我们还注释和比较了广泛的生物体中的Pkinase家族成员，包括从Ensembl数据库中随机选择的10种真菌，10种后生动物，10种脊椎动物和10种其他植物。我们的CTT注释在这40个基因组中平均多恢复了14%的Pkinase超家族的基因座，包括假基因，证明了其在注释任何基因组中的超家族成员时的稳健的可复制性和可扩展性。
The contemporary capacity of genome sequence analysis significantly lags behind the rapidly evolving sequencing technologies. Retrieving biological meaningful information from an ever-increasing amount of genome data would be significantly beneficial for functional genomic studies. For example, the duplication, organization, evolution, and function of superfamily genes are arguably important in many aspects of life. However, the incompleteness of annotations in many sequenced genomes often results in biased conclusions in comparative genomic studies of superfamilies. Here, we present a Perl software, called Closing Target Trimming (CTT), for automatically identifying most, if not all, members of a gene family in any sequenced genomes on CentOS 7 platform. To benefit a broader application on other operating systems, we also created a Docker application package, CTTdocker. Our test data on the F-box gene superfamily showed 78.2 and 79% gene finding accuracies in two well annotated plant genomes, Arabidopsis thaliana and rice, respectively. To further demonstrate the effectiveness of this program, we ran it through 18 plant genomes and five non-plant genomes to compare the expansion of the F-box and the BTB superfamilies. The program discovered that on average 12.7 and 9.3% of the total F-box and BTB members, respectively, are new loci in plant genomes, while it only found a small number of new members in vertebrate genomes. Therefore, different evolutionary and regulatory mechanisms of Cullin-RING ubiquitin ligases may be present in plants and animals. We also annotated and compared the Pkinase family members across a wide range of organisms, including 10 fungi, 10 metazoa, 10 vertebrates, and 10 additional plants, which were randomly selected from the Ensembl database. Our CTT annotation recovered on average 14% more loci, including pseudogenes, of the Pkinase superfamily in these 40 genomes, demonstrating its robust replicability and scalability in annotating superfamiy members in any genomes.