The Southern Modern Forestry Collaborative Innovation Center, the Key Lab of Tree Genetics and Biotechnology of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, China.
Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Nat Plants. 2021 Jun;7(6):748-756. doi: 10.1038/s41477-021-00933-x. Epub 2021 Jun 14.
Gymnosperms are a unique lineage of plants that currently lack a high-quality reference genome due to their large genome size and high repetitive sequence content. Here, we report a nearly complete genome assembly for Ginkgo biloba with a genome size of 9.87 Gb, an N50 contig size of 1.58 Mb and an N50 scaffold size of 775 Mb. We were able to accurately annotate 27,832 protein-coding genes in total, superseding the inaccurate annotation of 41,840 genes in a previous draft genome assembly. We found that expansion of the G. biloba genome, accompanied by the notable extension of introns, was mainly caused by the insertion of long terminal repeats rather than the recent occurrence of whole-genome duplication events, in contrast to the findings of a previous report. We also identified candidate genes in the central pair, intraflagellar transport and dynein protein families that are associated with the formation of the spermatophore flagellum, which has been lost in all seed plants except ginkgo and cycads. The newly obtained Ginkgo genome provides new insights into the evolution of the gymnosperm genome.
裸子植物是一类独特的植物谱系，由于其基因组较大且重复序列含量高，目前缺乏高质量的参考基因组。在这里，我们报告了银杏近乎完整的基因组组装，其基因组大小为 98.7Gb，N50 连体型大小为 1.58Mb，N50 支架型大小为 775Mb。我们总共能够准确注释 27832 个蛋白质编码基因，超过了之前草案基因组组装中 41840 个基因的不准确注释。我们发现，银杏基因组的扩张伴随着内含子的显著延长，主要是由于长末端重复序列的插入，而不是最近发生的全基因组复制事件，这与之前的一份报告的发现相反。我们还在中心对、鞭毛内运输和动力蛋白蛋白家族中鉴定到了与精泡鞭毛形成相关的候选基因，而所有种子植物（除了银杏和苏铁）都已经失去了这种鞭毛。新获得的银杏基因组为裸子植物基因组的进化提供了新的见解。
