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橡胶树基因组从头杂交组装揭示了 Hevea 物种中古老四倍体的证据。

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species.

机构信息

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.

Rubber Authority of Thailand, Bang Khun Non, Bangkok, Thailand.

出版信息

Sci Rep. 2017 Feb 2;7:41457. doi: 10.1038/srep41457.

DOI:10.1038/srep41457
PMID:28150702
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5288721/
Abstract

Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range "Chicago" technique to obtain a final assembly of 1.26 Gb (N50 = 96.8 kb). The assembled genome contains 69.2% repetitive sequences and has a GC content of 34.31%. Using a high-density SNP-based genetic map, we were able to anchor 28.9% of the genome assembly (363 Mb) associated with over two thirds of the predicted protein-coding genes into rubber tree's 18 linkage groups. These genetically anchored sequences allowed comparative analyses of the intragenomic homeologous synteny, providing the first concrete evidence to demonstrate the presence of paleotetraploidy in Hevea species. Additionally, the degree of macrosynteny conservation observed between rubber tree and cassava strongly supports the hypothesis that the paleotetraploidization event took place prior to the divergence of the Hevea and Manihot species.

摘要

巴西橡胶树（Hevea brasiliensis）是一种重要的经济树种，因为它是唯一商业化生产高品质天然橡胶的树种。在这里，我们报告了 BPM24 品系的从头杂交组装，该品系表现出对东南亚主要真菌病原体的抗性。深度覆盖的 454/Illumina 短读和 Pacific Biosciences (PacBio) 长读序列数据被用来生成一个初步的草案，随后使用远程“芝加哥”技术将其支架化，以获得最终的 12.6Gb 组装体（N50=96.8kb）。组装的基因组包含 69.2%的重复序列，GC 含量为 34.31%。利用高密度 SNP 遗传图谱，我们能够将基因组组装的 28.9%（363Mb）与超过三分之二的预测蛋白编码基因锚定到橡胶树的 18 条连锁群中。这些遗传锚定序列允许对基因组内同源同线性进行比较分析，首次提供了确凿的证据表明巴西橡胶树种存在古四倍体现象。此外，橡胶树和木薯之间观察到的宏同线性保守程度强烈支持古四倍体化事件发生在巴西橡胶树和 Manihot 物种分化之前的假设。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/92b7da3eaf68/srep41457-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/5b24bd641260/srep41457-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/2d6d2795f211/srep41457-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/50a08617aad5/srep41457-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/4a0c06ef77a4/srep41457-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/c1d666898b2a/srep41457-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/92b7da3eaf68/srep41457-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/5b24bd641260/srep41457-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/2d6d2795f211/srep41457-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/50a08617aad5/srep41457-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/4a0c06ef77a4/srep41457-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/c1d666898b2a/srep41457-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7e68/5288721/92b7da3eaf68/srep41457-f6.jpg

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