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甘蔗高度复杂基因组的镶嵌单倍体参考序列。

A mosaic monoploid reference sequence for the highly complex genome of sugarcane.

机构信息

CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.

AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France.

出版信息

Nat Commun. 2018 Jul 6;9(1):2638. doi: 10.1038/s41467-018-05051-5.

DOI:10.1038/s41467-018-05051-5
PMID:29980662
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6035169/
Abstract

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.

摘要

甘蔗（Saccharum spp.）是生产糖和生物能源的主要作物。其高度多倍体、非整倍体、杂合和种间基因组给产生参考序列带来了重大挑战。我们利用与高粱的共线性关系，产生了基于 BAC 的甘蔗单倍体基因组序列。根据全基因组分析，选择了最佳覆盖高粱基因组基因丰富部分的最小平铺路径 4660 个甘蔗 BAC，对其进行测序，并在高质量序列的单个平铺路径中组装成 382-Mb 序列。共预测到 25316 个蛋白质编码基因模型，其中 17%与高粱的直系同源物没有共线性。我们表明，参与现代品种的两个物种，甘蔗和甘蔗野生种，其转座元件和少数大的染色体重排不同，这解释了它们不同的基因组大小和不同的基本染色体数，同时也表明多倍化是在它们分化后出现在两个谱系中的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/344cf784296c/41467_2018_5051_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/800303d42aac/41467_2018_5051_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/eb912d6e7a13/41467_2018_5051_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/6e1a3fc551de/41467_2018_5051_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/64f4fc8af9b8/41467_2018_5051_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/344cf784296c/41467_2018_5051_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/800303d42aac/41467_2018_5051_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/eb912d6e7a13/41467_2018_5051_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/6e1a3fc551de/41467_2018_5051_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/64f4fc8af9b8/41467_2018_5051_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76ad/6035169/344cf784296c/41467_2018_5051_Fig5_HTML.jpg

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