The chromosome-based genome provides insights into the evolution in water spinach
The chromosome-based genome provides insights into the evolution in water spinach
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DOI：
10.1016/j.scienta.2021.110501
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发表时间：
2021-08-18
影响因子：
4.3
通讯作者：
Wang, Zhiwei
中科院分区：
文献类型：
--
作者：
Hao, Yuanyuan;Bao, Wenlong;Wang, Zhiwei
空心菜（Ipomoeaaquatica）是亚洲最受欢迎的绿色叶菜之一，兼具水生和陆生特性。我们在这里报告了通过PacBio测序，短读测序，10 x Genomics和高密度遗传图谱的组合进行的高质量，染色体规模的基因组组装。该组装体包含1，392个支架（N50 = 2.75 Mb），覆盖估计的基因组（550.03 Mb）的93.3%。在组装体中，90%被锚定到含有162个支架（415.77 Mb）的15个假染色体。我们还组装了一个完整的叶绿体基因组，全长165，294 bp，包含111个基因，编码84个蛋白质，8个rRNA和19个tRNA。该物种包括30693个预测的蛋白质编码基因。基因组聚类结果表明，4种牵牛属植物共有3,431个基因家族，与牵牛属植物共有34个基因家族。sativa、美国苜蓿U.吉巴和我。水生植物这些基因可能与植物的水生特性有关。系统发育分析表明，I. aquatica and the lineage（I.尼勒岛Trifida和我triloba）在大约710万年前发生分歧。同线性分析表明，空心菜和菠菜的15条假染色体之间存在明显的一对一共线性。具有小规模的染色体间重排。与Copia相比，Gypsies在空心菜基因组中的含量更高，表明Gypsies在空心菜中具有种特异性的基因组扩增。4DTv分析证实了牵牛属谱系和菟丝子属谱系的祖先中的WGD事件。转录组分析表明，在根、花、叶和茎中共表达了23，828个基因。我们还发现重金属相关基因在基因组中扩展。该基因组序列为空心菜的功能基因组学研究和基因组辅助育种提供了宝贵的资源。
Water spinach (Ipomoea aquatica) is one of the most popular green leafy vegetables in Asia, with both aquatic and terrestrial characteristics. We report here its high-quality, chromosome-scale genome assembly through a combination of PacBio sequencing, short-read sequencing, 10 x Genomics and a high-density genetic map. This assembly contains 1,392 scaffolds (N50 = 2.75 Mb) covering 93.3% of the estimated genome (550.03 Mb). Of the assembly, 90% was anchored to 15 pseudo-chromosomes containing 162 scaffolds (415.77 Mb). We also assembled a complete chloroplast genome of 165, 294 bp with 111 genes, encoding 84 proteins, 8 rRNA, and 19 tRNA. This species includes 30, 693 predicted protein-coding genes. By clustering results of the genomes, there are 3,431 gene families specific to the four Ipomoea species and 34 gene families in common of O. sativa, U. gibba and I. aquatica. These genes from the 34 gene familes may be related to the aquatic characteristics of plants. Phylogenetic analysis reveals that I. aquatica and the lineage (I. nil, I. trifida and I. triloba) diverged around 7.1 million years ago. Synteny analysis revealed obvious one-to-one collinearity for all 15 pseudo-chromosomes between the genomes of water spinach and I. triloba, with small-scale interchromosomal rearrangements. Compared with Copia, there are more Gypsies in the genome of water spinach suggesting species-specific genome expansion of Gypsy in water spinach. The 4DTv analysis confirmed the WGD event in the ancestor of the Ipomoea lineage and Cuscuta lineage. Transcriptome analysis reveals that there are 23,828 genes co-expressed in roots, flowers, leaves and stems. We also found that heavy metal associated genes were expanded in the genome. The genome sequence is a valuable resource for functional genomics and the genome assisted breeding of water spinach.