Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. So far, the L. japonicus reference genome assembly has been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs. Here, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telomeric repeats at their extremes and large centromeric regions with low gene density. The new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be conserved in L. japonicus.

中文翻译：

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从染色体规模的莲花日本岐阜基因组序列洞察共生基因拷贝数和分布的演变

莲花是一种多年生草本植物，已被广泛用作遗传共生模型系统，用于解释共生固氮的分子遗传学。到目前为止，日本血吸虫参考基因组装配是基于来自日本血吸虫登录号MG-20的Sanger和Illumina测序读取，并且含有很大一部分未锚定的重叠群。在这里，我们使用了来自日本岐阜的长PacBio读数，并结合了Hi-C数据和新的高密度遗传图谱，从而为日本梧桐生成了高质量的染色体规模参考基因组。该程序集包含554个兆碱基，其中549个碱基被分配给六个假分子，这些假分子在其极值端粒重复序列和具有低基因密度的大着丝粒区域看来完整。新的L。日本岐阜的参考基因组和相关的表达数据代表了豆类功能和比较基因组学的宝贵资源。在这里，我们通过显示最近在苜蓿中的共生岛似乎在L. japonicus中不被保守来提供第一个例子。