First De novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar 'Emma White'.

GigaByte (Hong Kong, China) Pub Date : 2022-08-09 eCollection Date: 2022-01-01 DOI:10.46471/gigabyte.66

Rubina Sherpa, Ramgopal Devadas, Penna Suprasanna, Sadashiv Narayan Bolbhat, Tukaram Dayaram Nikam

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Abstract

The Dendrobium hybrid cultivar 'Emma White' is an ornamental, successfully commercialised orchid. We used a gamma ray-induced early flowering mutant and the Illumina HiSeqX10 sequencing platform to generate the first draft de novo whole genome sequence and assembly. The draft sequence was 678,650,699 bp in length, comprising 447,500 contigs with an N50 of 1423 and 33.48% GC content. Comparing 95,529 predicted genes against the Uniprot database revealed 60,741 potential genes governing molecular functions, biological processes and cellular components. We identified 216,232 simple sequence repeats and 138,856 microsatellite markers. Chromosome-level genome assembly of Dendrobium huoshanense was used to RagTag-scaffold available contigs of the mutant, revealing a total length of 687,254,899 bp with an N50 of 2096. The longest final contiguous length was 18,000,059 bp from 30,571 bp. BUSCO genome completeness was 93.6%. This study is valuable for investigating the mechanisms of mutation, and developing Dendrobium hybrid cultivars using mutation breeding.

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首次对突变的铁皮石斛杂交栽培品种'Emma White'进行全新全基因组测序和组装。

铁皮石斛杂交栽培品种'Emma White'是一种成功商业化的观赏兰花。我们利用伽马射线诱导的早花突变体和Illumina HiSeqX10测序平台生成了第一个全新的全基因组序列和组装草案。该序列草案长度为 678,650,699 bp，由 447,500 个等位基因组成，N50 为 1423，GC 含量为 33.48%。将 95,529 个预测基因与 Uniprot 数据库进行比较，发现了 60,741 个潜在的基因，这些基因控制着分子功能、生物过程和细胞成分。我们确定了 216232 个简单序列重复序列和 138856 个微卫星标记。我们使用染色体级的霍山石斛基因组组装技术对突变体的现有等位基因进行了RagTag-scaffold处理，结果发现突变体的等位基因总长度为687,254,899 bp，N50为2096。最长的最终连续长度为 18,000,059 bp，来自 30,571 bp。BUSCO 基因组的完整性为 93.6%。这项研究对于研究突变机制以及利用突变育种技术开发铁皮石斛杂交栽培品种具有重要价值。

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