Genomes and Transcriptomes of Duckweeds.
Genomes and Transcriptomes of Duckweeds.
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浮萍的基因组和转录组
DOI：
10.3389/fchem.2018.00230
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发表时间：
2018
影响因子：
5.5
通讯作者：
Wang W
中科院分区：
文献类型：
--
作者：
An D;Li C;Zhou Y;Wu Y;Wang W
浮萍(Lemnaceae)是适应水环境的最小的开花植物。它们具有储存量高、繁殖快、全球分布等特点，被认为是一种很有前途的可持续发展的原料。浮萍基因组大小变化13倍，从多根螺旋藻的150Mb到华根狼尾藻的1881Mb不等。随着测序技术和生物信息学的发展，对蜘蛛目和浮萍属的5个浮萍基因组进行了测序和组装。基因组注释发现它们具有相似的蛋白质同源序列，而重复内容可以主要解释基因组大小的差异。负责细胞生长和扩张、木质素生物合成和开花的基因家族大大收缩。然而，谷氨酸合成酶的基因家族已经经历了扩张，这表明它们在氨同化和氮运输中具有重要意义。对蜘蛛属、长尾浮萍属和浮萍属的转录组进行了全面的测序，包括各种处理，如脱落酸、辐射、重金属和饥饿。对其潜在的分子机制和调控网络的分析将加速其在生物能源和植物修复领域的应用。比较基因组学研究表明，浮萍基因组包含的基因数量相对较少，而收缩的基因家族较多，这可能与浮萍的形态高度简化，只有一片单叶和初级根相平行。然而，由于Wolffiella和Wolffiia的基因组大小和多倍体的相似性，我们正在等待长读测序技术的进步，以解决未测序的Wolffiella和Wolffiia的复杂基因组和转录本。
Duckweeds (Lemnaceae family) are the smallest flowering plants that adapt to the aquatic environment. They are regarded as the promising sustainable feedstock with the characteristics of high starch storage, fast propagation, and global distribution. The duckweed genome size varies 13-fold ranging from 150 Mb in Spirodela polyrhiza to 1,881 Mb in Wolffia arrhiza. With the development of sequencing technology and bioinformatics, five duckweed genomes from Spirodela and Lemna genera are sequenced and assembled. The genome annotations discover that they share similar protein orthologs, whereas the repeat contents could mainly explain the genome size difference. The gene families responsible for cell growth and expansion, lignin biosynthesis, and flowering are greatly contracted. However, the gene family of glutamate synthase has experienced expansion, indicating their significance in ammonia assimilation and nitrogen transport. The transcriptome is comprehensively sequenced for the genera of Spirodela, Landoltia, and Lemna, including various treatments such as abscisic acid, radiation, heavy metal, and starvation. The analysis of the underlying molecular mechanism and the regulatory network would accelerate their applications in the fields of bioenergy and phytoremediation. The comparative genomics has shown that duckweed genomes contain relatively low gene numbers and more contracted gene families, which may be in parallel with their highly reduced morphology with a simple leaf and primary roots. Still, we are waiting for the advancement of the long read sequencing technology to resolve the complex genomes and transcriptomes for unsequenced Wolffiella and Wolffia due to the large genome sizes and the similarity in their polyploidy.