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Strategies and Tools for Sequencing Duckweeds

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The Duckweed Genomes

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

Duckweeds belong to the smallest flowering plants that undergo fast vegetative growth in an aquatic environment. Due to their special plant characteristics, they are commonly used in wastewater treatment, biofuel, and animal feed. Sequencing duckweed genomes will promote their development in molecular biology and functional genomics, thereby facilitating its application in feed, energy, and environmental protection. In addition to extremely fast growth speed, the genome sizes of duckweeds are varied from 150 to 1881 Mb with a roughly 13-fold change. But with the rapid development of sequencing technology and dramatic decrease of sequencing cost, sequencing different kinds of duckweed genomes has become feasible. Here, we review the strategies and tools for sequencing and assembling duckweeds genomes. We introduce the platforms of the next-generation sequencing (NGS) (Illumina paired-end sequencing with short reads) and the third-generation sequencing (TGS) (PacBio and Nanopore sequencing with long reads) that are broadly applied in plant genomics. We also overview the recent widely used scaffolding technologies including Bionano, Hi-C, and 10X Genomics. Tools for de novo assembling duckweeds genomes are determined by the sequencing platforms that give short reads or long reads. The programs of SOAPdenovo and ALLPATHS-LG are sufficient to assemble Illumina short reads; whereas, the assemblers of FALCON, CANU, MECAT, and HGAP are broadly used in assembling plant genomes sequenced by the platforms of PacBio or Nanopore. The hybrid assembly tool such as MaSuRCA is required for the integration of short and long reads. We expect that the strategies and tools will accelerate the duckweed genomics and promote their industrial applications.

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Authors and Affiliations

  1. Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China

    Xiaoli Xiang

  2. Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Beijing, China

    Changsheng Li

Authors
  1. Xiaoli Xiang
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  2. Changsheng Li
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Correspondence to Changsheng Li .

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Editors and Affiliations

  1. Department of Plant Physiology, Institute of Biology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany

    Xuan Hieu Cao

  2. Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA

    Paul Fourounjian

  3. School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China

    Wenqin Wang

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Xiang, X., Li, C. (2020). Strategies and Tools for Sequencing Duckweeds. In: Cao, X., Fourounjian, P., Wang, W. (eds) The Duckweed Genomes. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-11045-1_6

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