Strategies and Tools for Sequencing Duckweeds

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 Bio-nano, 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.