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Plant Biotechnol J:二倍体野生黄毛草莓基因组

已有 462 次阅读 2020-2-3 01:13 |个人分类:每日摘要|系统分类:论文交流

The high‐quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation


First author: Junxiang Zhang; Affiliations: Shenyang Agricultural University (沈阳农业大学): Shenyang, China

Corresponding author: Zhihong Zhang


Fragaria nilgerrensis is a wild diploid strawberry species endemic to east and southeast region in Asia and provides a rich source of genetic variations for strawberry improvement. Here, we present a chromosome‐scale assembly of F. nilgerrensis using single‐molecule real‐time (SMRT) Pacific Biosciences sequencing and chromosome conformation capture (Hi‐C) genome scaffolding. The genome assembly size was 270.3 Mb, with a contig N50 of ~8.5 Mb. A total of 28,780 genes and 117.2 Mb of transposable elements were annotated for this genome. Next, detailed comparative genomics with the high‐quality F. vesca reference genome was conducted to obtain the difference among transposable elements, SNPs, Indels, and so on. The genome size of F. nilgerrensis was enhanced by around 50 Mb relatively to F. vesca, which is mainly due to expansion of transposable elements. In comparison to the Fvesca genome, we identified 4,561,825 SNPs, 846,301 Indels, 4,243 inversions, 35,498 translocation, and 10,099 relocation. We also found a marked expansion of genes involved in phenylpropanoid biosynthesis, starch and sucrose metabolism, cyanoamino acid metabolism, plant‐pathogen interaction, brassinosteroid biosynthesis, and plant hormone signal transduction in F. nilgerrensis, which may account for its specific phenotypes and considerable environmental adaptability. Interestingly, we found sequence variations in the upstream regulatory region of FnMYB10, a core transcriptional activator of anthocyanin biosynthesis, resulted in the low expression level of the FnMYB10 gene, which is likely responsible for white fruit phenotype of F. nilgerrensis. The high‐quality F. nilgerrensis genome will be a valuable resource for biological research and comparative genomics research.




黄毛草莓(Fragaria nilgerrensis)是野生二倍体草莓物种,为亚洲东部和东南部地区所特有,为草莓的育种改良提供了分布的遗传资源。本文中,作者基于单分子实时测序Pacbio和染色体构象捕获Hi-C技术报道了一个染色体级别的黄毛草莓参考基因组。黄毛草莓基因组组装大小约为270.3Mb,contig N50长8.5Mb。黄毛草莓基因组共编码了28780个蛋白编码基因,并且包含了117.2Mb的转座子元件。接着,作者通过与野草莓(Fragaria vesca)的比较基因组分析,鉴定了这两个草莓物种在转座子元件、SNP以及Indel等方面的差异。黄毛草莓的基因组大约要比野草莓多出50Mb的序列,多是由于转座子元件的扩张所引起。相比于野草莓,作者鉴定了4,561,825个SNPs,846,301个Indels,4,243个倒置,35,498个易位,10,099个迁移。作者发现参与苯丙烷类生物合成、淀粉和蔗糖代谢、氰基氨基酸代谢、植物与病原体互作、油菜素类固醇生物合成以及植物激素信号转导相关基因在黄毛草莓基因组中存在明显的扩张,这可能与黄毛草莓特异的表型以及很好的环境适应性有关。有趣的是,作者发现一个花青素生物合成的核心转录激活因子FnMYB10基因上游调控区域存在的序列变异导致了该基因的表达量保持在较低水平,这有可能与黄毛草莓的白色果实表型有关。本文所报道的高质量黄毛草莓基因组为草莓属物种的生物学研究以及比较基因组学研究提供了宝贵的遗传资源。



通讯:张志宏 (https://yyxy.syau.edu.cn/info/1022/1119.htm)


个人简介1987-1991年,沈阳农业大学,学士;1991-1996,沈阳农业大学,博士;2000-2001年,日本国家蔬菜茶业研究所,博士后。


研究方向果树重要性状形成的分子机理研究



doi: https://doi.org/10.1111/pbi.13351


Journal: Plant Biotechnology Journal

First Published: January 31, 2020


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