Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
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DOI：
10.1186/s12859-019-2945-8
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发表时间：
2019-06-24
影响因子：
3
通讯作者：
Tu, Jinxing
中科院分区：
文献类型：
--
作者：
Hu, Kaining;Xu, Kai;Tu, Jinxing
Helitron是一种滚环转座子，在植物进化中起着重要作用。然而，Helitron分布和贡献的进化在家庭水平上没有以前调查。ResultsWe开发的软件易于注释Helitron（EAHelitron），类Unix命令行，并用它来确定Helitrons在广泛的53植物基因组（包括13个豆科植物）。我们确定了Helitron密度（丰度/Mb），并可视化和检查Helitron分布模式。我们确定了超过104，653个Helitrons，包括许多其他软件没有预测到的新Helitrons。全基因组Helitron密度与基因组大小无关，在物种水平上具有稳定性。使用线性判别分析，从头基因组（下一代测序）被成功地分为拟南芥组。对于大多数菊科植物，Helitron密度与基因密度呈负相关，Helitron分布模式与A.A. thaliana.它们优先插入到着丝粒周围和基因间区的序列中。我们还将13个Helitron多态性位点与18个A.结论EAHelitron是鉴定新Helitron的一种快速有效的工具。全基因组Helitron密度可以作为植物分类的信息量。Helitron插入多态性可用于关联分析。
BackgroundHelitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated.ResultsWe developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes.ConclusionEAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis.