杂交葡萄藤'Chambourcin'的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-07-03 eCollection Date: 2023-01-01 DOI:10.46471/gigabyte.84
Sagar Patel, Zachary N Harris, Jason P Londo, Allison Miller, Anne Fennell
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引用次数: 0

摘要

Chambourcin'是一种法美种间杂交葡萄,生长在美国东部和中西部,用于酿造葡萄酒。像'Chambourcin'这样的杂交葡萄很少有基因组资源。在这里,我们利用 PacBio HiFi 长读数、Bionano 光学图谱和 Illumina 短读数测序技术组装了'Chambourcin'的基因组。我们为'Chambourcin'组装了 26 个支架,N50 长度为 23.3 Mb,BUSCO 的估计完整性为 97.9%。我们预测了 33,791 个基因模型,并在'Chambourcin'、V. vinifera 'PN40024' 12X.v2、VCOST.v3、Shine Muscat 和 V. riparia Gloire 之间发现了 16,056 个共同的直向同源物。我们发现了来自 58 个基因家族的 1,606 个植物转录因子。最后,我们还发现了 304,571 个简单序列重复(长度不超过 6 个碱基对)。我们的工作提供了'Chambourcin'的基因组组装、注释以及蛋白质和编码序列。我们的基因组组装是基因组比较、功能基因组分析和基因组辅助育种研究的宝贵资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Genome assembly of the hybrid grapevine <i>Vitis</i> 'Chambourcin'.

Genome assembly of the hybrid grapevine <i>Vitis</i> 'Chambourcin'.

Genome assembly of the hybrid grapevine <i>Vitis</i> 'Chambourcin'.

Genome assembly of the hybrid grapevine Vitis 'Chambourcin'.

'Chambourcin' is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like 'Chambourcin'. Here, we assembled the genome of 'Chambourcin' using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for 'Chambourcin' with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between 'Chambourcin', V. vinifera 'PN40024' 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of 'Chambourcin'. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research.

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CiteScore
2.60
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