Green plant genomes: What we know in an era of rapidly expanding opportunities.
Green plant genomes: What we know in an era of rapidly expanding opportunities.
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DOI：
10.1073/pnas.2115640118
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发表时间：
2022-01-25
影响因子：
11.1
通讯作者：
Soltis PS
中科院分区：
文献类型：
--
作者：
Kress WJ;Soltis DE;Kersey PJ;Wegrzyn JL;Leebens-Mack JH;Gostel MR;Liu X;Soltis PS
绿色植物在生态系统、人类健康和农业中发挥着重要作用。正如地球生物基因组计划所倡导的那样，正在为所有已知的真核物种生成从头开始的基因组，因此增加关于绿色陆地植物的基因组信息是至关重要的。然而，对植物科学家来说，为表征绿色生命谱系的一组复杂基因组的生成和存储设定标准是一个重大挑战。这样的标准需要适应绿色植物基因组大小、转座元素含量和结构复杂性的巨大差异，同时能够研究导致这种巨大基因组差异的分子和进化过程。在这里，我们提供了绿色植物基因组知识的现状的概述和评估。到目前为止，在绿色植物分支中估计有45万到50万个物种，只产生了不到300个完整的染色体规模的基因组组合，代表不到900个物种。这些基因组的大小从12Mb到27.6 GB不等，偏向于拥有绿色生命树大分支的农作物，不受基因组规模测序的影响。寻找大多数植物物种的合适组织样本，特别是那些来自极端环境的分类群，仍然是增加我们基因组库存的最大障碍之一。此外，植物基因组的注释目前正在进行密集的改进。我们希望这一新的概述将有助于制定基因组质量标准，以便在我们为未来扩大规模时，对绿色植物基因组进行有凝聚力和有意义的合成。
Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.
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影响因子：
14.9
作者：
Arita M;Karsch-Mizrachi I;Cochrane G
通讯作者：
Cochrane G
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影响因子：
9.2
作者：
Cheng S;Melkonian M;Smith SA;Brockington S;Archibald JM;Delaux PM;Li FW;Melkonian B;Mavrodiev EV;Sun W;Fu Y;Yang H;Soltis DE;Graham SW;Soltis PS;Liu X;Xu X;Wong GK
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影响因子：
12.3
作者：
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通讯作者：
Ermini L
影响因子：
3
作者：
Folk, Ryan A.;Sun, Miao;Guralnick, Robert P.
通讯作者：
Guralnick, Robert P.
影响因子：
12.3
作者：
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通讯作者：
Gillis, Jesse A.