文献类型: 外文期刊
作者: Xiang, Xiaoli 1 ; Li, Changsheng 2 ;
作者机构: 1.Sichuan Acad Agr Sci, Inst Biotechnol & Nucl Technol, Chengdu, Peoples R China
2.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Beijing, Peoples R China
期刊名称:DUCKWEED GENOMES
ISSN: 2199-4781
年卷期: 2020 年
页码:
收录情况: SCI
摘要: 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.
- 相关文献
作者其他论文 更多>>
-
Co-overexpression of AtSAT1 and EcPAPR improves seed nutritional value in maize
作者:Xiang, Xiaoli;Hu, Binhua;Pu, Zhigang;Wang, Lanying;Xiang, Xiaoli;Li, Changsheng;Leustek, Thomas
关键词:methionine; serine acetyltransferase1; 3'-phosphoadenosine-5'-phosphosulfate reductase; transcriptome profiling analysis; protein-protein interaction
-
Characterization and Evaluation of Transgenic Rice Pyramided with the Pi Genes Pib, Pi25 and Pi54
作者:Peng, Meifang;Lin, Xiaomin;Xiang, Xiaoli;Ren, Huibo;Fan, Xiaoli;Chen, Kegui
关键词:O; sativa; Pib; Pi25; Pi54; Blast disease; Transgenesis; Gene pyramiding; RNA-Seq; Transcriptome
-
Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
作者:Li, Changsheng;An, Dong;Wang, Wenqin;Li, Changsheng;Xiang, Xiaoli;Huang, Yongcai;Zhou, Yong;Wang, Qiong;Wu, Yongrui;Xiang, Xiaoli;Huang, Yongcai;Dong, Jiaqiang;Messing, Joachim;Zhao, Chenxi;Liu, Hongjun;Li, Yubin;Du, Chunguang;Larkins, Brian A.
关键词:
-
A single nucleotide mutation in the fourth exon of RBH1 is responsible for brown hull phenotype in rice
作者:Wang, Ping;Chen, Zhiqiang;Wang, Ping;Hu, Binhua;Xiang, Xiaoli;Wang, Mingxia;Bai, Yulu;Zhang, Baizhan;Zhang, Cong;Wang, Lanying;Pu, Zhigang
关键词:Oryza sativa L; Reddish brown hull; Mechanization of hybrid seed production; Breeding
-
AGO18b negatively regulates determinacy of spikelet meristems on the tassel central spike in maize
作者:Zhang, Dan;Cao, Zheng;Liu, Lei;Zhang, Zuxin;Xiang, Xiaoli;Zhai, Lihong
关键词:
-
Overexpression of serine acetyltransferase in maize leaves increases seed-specific methionine-rich zeins
作者:Leustek, Thomas;Xiang, Xiaoli;Wu, Yongrui;Wu, Yongrui;Planta, Jose;Messing, Joachim
关键词:serine acetyltransferase; seed storage protein; transgenic; zein; methionine; nutritional quality
-
The Maize Imprinted Gene Floury3 Encodes a PLATZ Protein Required for tRNA and 5S rRNA Transcription through Interaction with RNA Polymerase III
作者:Wang, Jiechen;Ye, Jianwei;Zheng, Xixi;Fu, Miaomiao;Wang, Qiong;Zhang, Zhiyong;Wu, Yongrui;Li, Qi;Zheng, Xixi;Fu, Miaomiao;Xiang, Xiaoli;Li, Changsheng
关键词: