Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly.
Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly.
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DOI：
10.1186/s12864-014-1196-3
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发表时间：
2015-01-22
期刊：
影响因子：
4.4
通讯作者：
Garcia-Mas J
中科院分区：
文献类型：
--
作者：
Argyris JM;Ruiz-Herrera A;Madriz-Masis P;Sanseverino W;Morata J;Pujol M;Ramos-Onsins SE;Garcia-Mas J
最近对甜瓜 (Cucumis melo L.) 双单倍体系 DHL92 的基因组进行了测序，其中 87.5% 和 80.8% 的支架组件分别锚定并定向于 12 个连锁群。然而，标记覆盖率不足和缺乏重组导致一些大型的、富含基因的支架未锚定，并且一些锚定的支架未定向。为了改善甜瓜基因组组装的锚定和方向，我们使用 DHL92 亲本系之间的重测序数据，从未锚定的支架中开发了一组新的 SNP 标记。由 580 个 SNP 组成的高分辨率遗传图谱用于将 354.8 Mb 的序列锚定到 12 个甜瓜染色体上，该序列包含在 141 个支架（平均大小 2.5 Mb）中，相当于支架组装的 98.2%。超过 325.4 Mb (90%) 的程序集已定向。遗传图谱揭示了有利于 SC 等位基因的分离扭曲区域以及与假定的着丝粒、45S 和 5S rDNA 位点一致的重组抑制区域。通过将额外的 38.3 Mb 锚定序列（代表 55 个支架中包含的 1,837 个预测基因）合并到之前的 v3.5 版本中，创建了新的染色体规模的假分子。利用产生染色体特异性信号的 BAC 荧光原位杂交 (FISH)，鉴定了对应于 12 个连锁群的甜瓜染色体，并开发了甜瓜自交系 T111 的标准化核型。通过利用重测序数据和靶向 SNP 选择以及大型 F2 作图群体，我们显着提高了锚定和定向甜瓜支架基因组组装的数量。利用基因组信息与 FISH 作图相结合，提供了臭味甜瓜类型的第一个细胞遗传学图谱。有了这些结果，就可以通过将重组抑制区域与着丝粒以及 45S 和 5S 异染色质区域相关联来推断甜瓜染色体结构。这项研究代表了将高分辨率遗传和细胞遗传学图谱与甜瓜基因组序列整合的第一步，这将提供有关基因组组织的更多信息，并允许改进甜瓜基因组草图序列。本文的在线版本 (doi:10.1186/s12864-014-1196-3) 包含补充材料，可供授权用户使用。
The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds. A high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed. By utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence. The online version of this article (doi:10.1186/s12864-014-1196-3) contains supplementary material, which is available to authorized users.
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影响因子：
56.9
作者：
Chamala, Srikar;Chanderbali, Andre S.;Barbazuk, W. Brad
通讯作者：
Barbazuk, W. Brad
影响因子：
56.9
作者：
Boualem, Adnane;Fergany, Mohamed;Bendahmane, Abdelhafid
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影响因子：
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DOI：
10.1007/978-3-642-20450-0_6
发表时间：
2011-01-01
期刊：
WILD CROP RELATIVES: GENOMIC AND BREEDING RESOURCES - VEGETABLES
影响因子：
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作者：
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通讯作者：
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影响因子：
14.9
作者：
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通讯作者：
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