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科研撞车之两篇谷子(Setaria italica)全基因组测序论文同时发表

已有 14870 次阅读 2012-5-14 23:58 |个人分类:论文阅读|系统分类:论文交流| 论文, 期刊, 科研选题, 科研撞车

据新闻【1，2】报道，中国科学家完成了谷子(英文名：foxtail millet, 拉丁学名：Setaria italica)【3】全基因组测序，成果发表于《自然-生物技术》杂志。具体的内容详见新闻，令我感到诧异的是，在我查找 Nature Biotechnology 上的原文时，居然在“Advanced online publication”上出现了两篇谷子全基因组测序的论文【4，5】(都是2012年5月13日在线发表)。

下面分别是两篇论文的题目和摘要。

题目：Reference genome sequence of the model plant Setaria

摘要：We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

题目：Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

摘要：Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C4 biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (~423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C4 photosynthesis pathway were also identified.

这是一个关于“科研撞车”的问题，两篇论文能在相同期刊发表，也算是一个很好的解决案例。不过，对于这样的事件的发生确实比较少见。过去，出现过两次全基因测序论文同时发表的事件，一次发生在2001年的人类全基因组测序论文，两篇文章相隔一天发表，一篇在Nature【6】上(2001年2月15日)，另一篇在Science【7】(2001年2月16日)上；另一次发生在2003年的水稻基因组测序上，一篇是粳稻(Oryza sativa L. ssp. japonica)基因组，一篇是籼稻(Oryza sativa L. ssp. indica)基因组，都发表在Science 2002年4月5日的一期杂志上【8，9】。

科学网上关于“科研撞车”话题讨论博文参见【10，11，12，13】。

参考资料
【1】华大基因，中国科学家完成谷子基因组测序，成果于《自然-生物技术》杂志发表

【2】南方日报，中国科学家完成谷子基因组测序

【3】维基百科——小米，Wikipedia--Foxtail millet

【4】Nature Biotechnology, Reference genome sequence of the model plant Setaria

【5】Nature Biotechnology, Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

【6】Nature, Initial sequencing and analysis of the human genome

【7】Science, The Sequence of the Human Genome

【8】Science, A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)

【9】Science, A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

【10】科学网，林涛，“出手慢，靠边站”——也说科研“撞车”

【11】科学网，陈沐，研究“撞车”之轻度、中度和重度