A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics.
A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics.
复制标题
崎岖玫瑰 (Rosa rugosa) 的染色体水平基因组组装提供了对其进化、生态和花卉特征的深入了解
DOI：
10.1038/s41438-021-00594-z
复制
发表时间：
2021-06-18
影响因子：
8.7
通讯作者：
Cheng ZM
中科院分区：
文献类型：
--
作者：
Chen F;Su L;Hu S;Xue JY;Liu H;Liu G;Jiang Y;Du J;Qiao Y;Fan Y;Liu H;Yang Q;Lu W;Shao ZQ;Zhang J;Zhang L;Chen F;Cheng ZM
玫瑰，俗称蔷薇，是一种多年生观赏灌木。它能开出美丽的花朵，散发出温和的香味，并结出五颜六色的豆荚。与许多其他栽培玫瑰不同，R.皱藻适应广泛的生境类型和恶劣的环境条件，如盐、碱、阴、干旱、高湿度和寒冷的温度。在这里，我们生产和分析了高质量的基因组序列的R。rugosa了解其生态，花的特点和演变。PacBio HiFi reads最初用于构建R. rugosa，然后应用Hi-C测序将重叠群组装成7条染色体。我们获得了一个382.6 Mb的基因组，编码39，704个蛋白质编码基因。R. rugosa似乎是保守的，没有额外的全基因组复制后，γ全基因组三倍（WGT），这发生在约1亿年前的核心真双子叶植物的祖先。在对高质量的R. rugosa等蔷薇科优质植物基因组中发现了一个独特的大倒位片段。中国和草莓中由WGT后事件引起的逆行。我们还发现，花发育和胁迫反应信号相关的基因模块后WGT保留。两个MADS盒基因参与花发育和胁迫相关的转录因子DREB 2A相互作用蛋白2（DRIP 2）和肽转运蛋白3（PTR 3）被发现是积极的选择在进化中，这可能有助于该植物适应恶劣环境的独特能力。综上所述，本研究获得了高质量的R. rugosa为该植物的遗传研究和分子育种提供了图谱，并使蔷薇属的比较基因组研究在不久的将来成为可能。
Rosa rugosa, commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for R. rugosa to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of R. rugosa, and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of R. rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred~ 100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of R. rugosa and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose R. chinensis and a retroposition in strawberry caused by post-WGT events. We also found that floral development-and stress response signaling-related gene modules were retained after the WGT. Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 (DRIP2) and PEPTIDE TRANSPORTER 3 (PTR3) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of R. rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.
登录
查看更多内容
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
12.3
作者：
Haas, Brian J.;Salzberg, Steven L.;Zhu, Wei;Pertea, Mihaela;Allen, Jonathan E.;Orvis, Joshua;White, Owen;Buell, C. Robin;Wortman, Jennifer R.
通讯作者：
Wortman, Jennifer R.
被子植物基因组和基因组数据库测序。
影响因子：
5.6
作者：
Chen F;Dong W;Zhang J;Guo X;Chen J;Wang Z;Lin Z;Tang H;Zhang L
通讯作者：
Zhang L
影响因子：
48
作者：
Kim D;Langmead B;Salzberg SL
通讯作者：
Salzberg SL