Draft genome of the living fossil Ginkgo biloba.
Draft genome of the living fossil Ginkgo biloba.
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DOI：
10.1186/s13742-016-0154-1
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发表时间：
2016-11-21
期刊：
影响因子：
9.2
通讯作者：
Chen W
中科院分区：
文献类型：
--
作者：
Guan R;Zhao Y;Zhang H;Fan G;Liu X;Zhou W;Shi C;Wang J;Liu W;Liang X;Fu Y;Ma K;Zhao L;Zhang F;Lu Z;Lee SM;Xu X;Wang J;Yang H;Fu C;Ge S;Chen W
银杏（Ginkgo biloba L.）是银杏科最具特色的植物之一。它具有一系列迷人的特征，包括大基因组，对非生物和生物胁迫的杰出抗性/耐受性，以及雌雄异株繁殖，使其成为生物学研究的理想模式物种。然而，缺乏高质量的基因组序列一直是我们理解其生物学和进化的障碍。本研究共组装了10.61 Gb的基因组序列，包含41840个注释基因。重复序列占组装序列的76.58%，其中长末端重复反转录转座子（long terminal repeat retrotransposons, LTR-RTs）尤为普遍。LTR-RTs的多样性和丰富性是由于它们在1600万至2400万年前逐渐积累和显著扩增，它们有助于长内含子和大基因组。全基因组复制（WGD）可能发生过两次，其中古代的WGD与其他种子植物中出现的WGD一致，而最近的一次事件仅发生在银杏中。串联重复产生的大量基因簇也很明显，扩展的基因家族的富集表明了一系列显著的化学和抗菌防御途径。银杏基因组主要由古代逐渐积累的LTR-RTs和两次WGD事件组成。银杏特有的多种防御机制是由古老的重复基因和银杏特异性基因集群的显著富集所促进的。目前的研究揭示了大基因组测序，并为进一步的遗传和进化研究开辟了一条途径。本文的在线版本（doi:10.1186/s13742-016-0154-1）包含补充材料，可供授权用户使用。
Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways. The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research. The online version of this article (doi:10.1186/s13742-016-0154-1) contains supplementary material, which is available to authorized users.
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