Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales

The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a non-model system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from eleven exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that while some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.

比较基因组学（comparative genomics）研究领域正从聚焦单个基因，转向涵盖重复序列组分的更整体化研究视角。本研究旨在针对非模式生物体系，解析大型复杂基因组的重复序列组分的相对占比。单子叶植物天门冬目（Asparagales）涵盖洋葱、芦笋、龙舌兰等类群，包含部分已知体积最大的被子植物基因组，且在基因组大小与核型（karyotype）结构上均存在显著变异。研究团队对11个代表性天门冬目类群的匿名低覆盖度单端Illumina测序数据，采用从头组装（de novo）方法完成组装。所得重叠群（contigs）通过已公开的单子叶植物重复序列参考文库进行注释。将测序读段比对至重叠群，可估算出核基因组中每一类转座子（transposon）的相对占比。研究结果被归类为通用重复序列类型，并结合基因组大小估算值与系统发育背景开展整合分析，以描述这些演化支中转座元件的演化模式。核心研究结果表明：尽管天门冬目中部分类群的重复序列占比呈现演化保守性，但整体而言各类重复序列的类型与频率均存在广泛变异。该方法是在基因组资源匮乏的演化支中开展重复序列特征解析的适宜初步研究方案。