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GigaScience:银杏基因组测序完成  

2016-12-05 14:09:40|  分类: 文献学习 |  标签: |举报 |字号 订阅

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被称为活化石银杏的基因组测序和信息分析工作已完成。据悉,该研究由华大基因、浙江大学和中国科学院的科学家团队完成,研究人员从头组装并分析了这个超大的基因组。其基因组信息可以在植物防御昆虫、病原体的研究、树木进化和生命进化的早期事件研究等方面提供广泛的研究资源。

GigaScience:银杏基因组测序完成 - 喜欢吃桃子 - wangyufeng的博客

 Phylogenetic relationships and comparative genomic analyses. a Phylogenetic relationships and number of gene families displaying expansion and contraction. b Comparison of the number of gene families in the five land plants Ginkgo bilobaCycacs revolutaPinus canariensisSelaginella moellendorffii and Arabidopsis thalianac Comparison of the longest 10% of introns in the five land plants. d Phylogenetic tree of three orthologous gene families indicating gene duplication and tandem distribution. The colors of solid circles represent species. Gene IDs of ginkgo start with ‘Gb’, and red and green text represents tandem distribution in different scaffolds. CREV, C. revoluta, PCAN, P. canariensis, SMOE, S. moellendorffii, OSAT, O. sativa, ATHA,A. thaliana

近日,开放期刊《GigaScience》发表论文介绍现存的最古老的树种——银杏的基因组。银杏被认为是活化石,也就是说从出现到现在的2.7亿年生存史中,它的形式和结构的变化都非常小,无论从历史学意义还是在生物学意义来看,银杏都有巨大的研究价值。

银杏基因组太大并存在大量的重复序列,组装全基因组序列是一项非常困难的工作。华大基因研究院生命大数据研究所负责人陈文彬表示,银杏基因组的测序产生了巨量的原始数据,如此大的数据量和基因组中高比例的重复序列极大地考验了研究人员在基因组组装时的内存优化和信息处理能力。

为了更好地了解银杏的防御机制,研究人员从注释的约四万个基因中分析了在植物中已知的与防御机制相关的基因家族。研究发现表明,银杏具有多重防御机制:基因家族的扩增,高剂量的特定基因,以及其防御基因的多样性。这些特点都可能与银杏非凡的恢复能力相关。这些信息也有助于研究者更好地理解植物防御机制用于改善粮食安全。








Abstract

Background

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.

Findings

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.

Conclusions

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.

参考文献:Draft genome of the living fossil Ginkgo biloba.  GigaScience20165:49 DOI: 10.1186/s13742-016-0154-1

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