Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
BMC Genomics. 2013 Jul 24;14:502. doi: 10.1186/1471-2164-14-502.
Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species.
(i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome.
(i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a "fingerprint" to identify and characterize cacao accessions.
转座元件（TEs）和其他重复元件是真核生物基因组中一个庞大且不断进化的部分，尤其是在植物中，它们可能占基因组大小的很大一部分。它们的动态性质使它们有可能用于识别和表征作物种质资源。然而，它们的重复性质使得它们难以使用传统的分子生物学方法进行研究。下一代测序和新的计算工具极大地促进了物种内和近缘物种间 TE 变异的研究。
（i）我们为可可（Theobroma cacao）和相关物种的多个个体生成了低覆盖率的 Illumina 全基因组 shotgun 测序reads。这些reads 使用基于比对/映射的方法和从头（基于图的聚类）方法进行分析。（ii）一套标准的超保守直系同源序列（UCOS）标准化了样品之间的 TE 数据，并提供了样品亲缘关系的系统发育信息。（iii）映射方法在参考物种内非常有效，但与从头方法相比，在种间比较中低估了 TE 的丰度。（iv）个体可可品种具有独特的 TE 丰度模式，表明该基因组中的 TE 组成在该物种内正在积极进化。（v）LTR/Gypsy 元件是最丰富的，占基因组的 c.10%。（vi）在可可中，逆转录元件家族的序列变异性比 DNA 转座元件家族大一个数量级。（vii）Theobroma grandiflorum 的 TE 组成与可可相似，但相关属 Herrania 则大不相同，LTR 占基因组的比例较低，这可能是因为该基因组中存在大量独特的低复杂度卫星样重复（约 20%）。
（i）短读序列比对/映射到参考 TE 连续序列提供了一种简单有效的方法来研究 TE 组成的种内差异。它不适合于跨物种边界比较重复元件，对于这种情况，从头方法更为合适。（ii）个体可可品种具有独特的 TE 组成谱，表明该物种内 TE 丰度的活跃进化。TE 模式有可能被用作识别和表征可可品种的“指纹”。
