An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes

The current melon (Cucumis melo L.) reference genome has still 41.6 Mb (Megabases) of sequences unassigned to pseudo-chromosomes and about 57 Mb of gaps. Although different approaches have been undertaken to improve the melon genome assembly in the recent years, the high percentage of repeats (~40%) and limitations due to read length have made it difficult to resolve gaps and scaffold's misassignments to pseudomolecules, especially in the heterochromatic regions. Taking advantage of the PacBio single- molecule Real-Time (SMRT) sequencing technology, an improvement of the melon genome was achieved. About 90% of the gaps were filled and the unassigned sequences were drastically reduced. A lift-over of the latest annotation v4.0 allowed to re-collocate protein-coding genes belonging to the unassigned sequences to the pseudomolecules. A direct proof of the improvement reached in the new melon assembly was highlighted looking at the improved annotation of the transposable element fraction. By screening the new assembly, we discovered many young, polymorphic LTR-retrotransposons that were not captured in the previous reference genome. These elements sit mostly in the pericentromeric regions, but some of them are inserted in the upstream region of genes suggesting that they can have regulatory potential. This improved reference genome will provide an invaluable tool for identifying new gene or transposon variants associated with important phenotypes.

当前甜瓜（Cucumis melo L.）参考基因组仍存在41.6 Mb（兆碱基）的序列未锚定至伪染色体，且带有约57 Mb的序列缺口。尽管近年来已开展多种策略优化甜瓜基因组组装，但由于重复序列占比高达约40%，加之测序读长存在局限，填补基因组缺口、解决支架序列锚定至假分子的错误仍颇具挑战，在异染色质区域尤为突出。本研究借助PacBio单分子实时（SMRT）测序技术，实现了甜瓜基因组的优化升级。约90%的基因组缺口得以填补，未锚定序列的数量大幅缩减。通过对最新的v4.0版本注释信息进行注释迁移（lift-over），我们将原本未锚定序列所编码的蛋白编码基因重新锚定至伪染色体上。通过分析转座元件组分的优化注释，可直观验证新型甜瓜基因组组装的改进效果。对新组装基因组进行筛选后，我们发现了大量此前参考基因组未捕获到的年轻、多态性LTR-反转录转座子（LTR-retrotransposon）。这些转座元件大多分布于着丝粒周边区域，其中部分插入至基因上游区域，提示其具备潜在的调控功能。这款优化后的参考基因组将为鉴定与重要性状相关的新型基因或转座子变异提供极具价值的研究工具。