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Horticulture Research:甜樱桃高质量参考基因组

已有 604 次阅读 2020-8-10 15:04 |个人分类:每日摘要|系统分类:论文交流

Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing

第一作者Jiawei Wang


通讯作者Qingzhong Liu


背景回顾Sweet cherry (Prunus avium) is an economically significant fruit species in the genus Prunus. However, in contrast to other important fruit trees in this genus, only one draft genome assembly is available for sweet cherry, which was assembled using only Illumina short-read sequences.

提出问题:The incompleteness and low quality of the current sweet cherry draft genome limit its use in genetic and genomic studies. A high-quality chromosome-scale sweet cherry reference genome assembly is therefore needed.

结果-三代+二代测序:A total of 65.05 Gb of Oxford Nanopore long reads and 46.24 Gb of Illumina short reads were generated, representing ~190x and 136x coverage, respectively, of the sweet cherry genome.

结果-组装:The final de novo assembly resulted in a phased haplotype assembly of 344.29 Mb with a contig N50 of 3.25 Mb.

结果-染色体挂载:Hi-C scaffolding of the genome resulted in eight pseudochromosomes containing 99.59% of the bases in the assembled genome.

结果-基因组注释:Genome annotation revealed that more than half of the genome (59.40%) was composed of repetitive sequences, and 40,338 protein-coding genes were predicted, 75.40% of which were functionally annotated.

结果-基因家族扩张:With the chromosome-scale assembly, we revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry.

结果-果实发育:Four auxin-responsive genes (two GH3s and two SAURs) were induced in the late stage of fruit development, indicating that auxin is crucial for the sweet cherry ripening process.

结果-抗性育种:In addition, 772 resistance genes were identified and functionally predicted in the sweet cherry genome.

结论:The high-quality genome assembly of sweet cherry obtained in this study will provide valuable genomic resources for sweet cherry improvement and molecular breeding.

 摘  要 

甜樱桃是李属中一个具有重要经济效应的水果物种。然而,相比于该属其它重要水果作物,甜樱桃目前只有一个基于二代Illumina测序完成的基因组草图可供参考。目前的甜樱桃参考基因组连续性和组装质量都未达到较高水平,严重限制了甜樱桃的遗传和基因组研究。因此,亟需通过新的测序技术获得一个高质量、染色体水平的甜樱桃基因组。本文中,作者通过结合65.05 Gb的Oxford纳米孔长reads和46.24 Gb的Illumina短reads,获得了总大小约为344.29 Mb,contig N50长约3.25Mb的甜樱桃基因组组装。进一步通过Hi-C技术,将99.59%的组装挂载到了8条假染色体上。基因组注释显示超过一半的甜樱桃基因组由重复序列组成,共预测了40338个蛋白编码基因,其中75.40%的基因具有功能注释信息。基于染色体级别的甜樱桃基因组,作者发现基因复制事件作用于水杨酸/茉莉酸羧基甲基转移酶和锚定蛋白重复域蛋白基因家族在甜樱桃基因组中的扩张。两个GH3s和两个SAURs,共四个生长素响应基因在甜樱桃果实发育后期被诱导表达,说明生长素对于甜樱桃果实的成熟具有关键作用。另外,作者还进一步鉴定了甜樱桃基因组上772个抗性基因。本文的所报道了甜樱桃高质量参考基因组将有助于未来甜樱桃的遗传改良和分子育种工作。







doi: 10.1038/s41438-020-00343-8

Journal: Horticulture Research

Published date: August 01, 2020


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