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01 11, 2022;5 (1): 36.

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis.

Ning Yan, Ting Yang, Xiu-Ting Yu, Lian-Guang Shang, De-Ping Guo, Yu Zhang, Lin Meng, Qian-Qian Qi, Ya-Li Li, Yong-Mei Du, Xin-Min Liu, Xiao-Long Yuan, Peng Qin, Jie Qiu, Qian Qian, Zhong-Feng Zhang
Author Information
  1. Ning Yan: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China. yanning@caas.cn. ORCID
  2. Ting Yang: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
  3. Xiu-Ting Yu: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
  4. Lian-Guang Shang: Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China. ORCID
  5. De-Ping Guo: Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
  6. Yu Zhang: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China. ORCID
  7. Lin Meng: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
  8. Qian-Qian Qi: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China. ORCID
  9. Ya-Li Li: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
  10. Yong-Mei Du: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
  11. Xin-Min Liu: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
  12. Xiao-Long Yuan: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
  13. Peng Qin: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
  14. Jie Qiu: Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China. ORCID
  15. Qian Qian: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China. qianqian188@hotmail.com. ORCID
  16. Zhong-Feng Zhang: Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China. zhangzhongfeng@caas.cn. ORCID
PMID: 35017643 DOI: 10.1038/s42003-021-02993-3

Abstract

Chinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7-31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.

References

Molecules. 2019 Apr 30;24(9): [PMID: 31052148]
Microb Pathog. 2020 Jun;143:104107 [PMID: 32120003]
BMC Genomics. 2006 Dec 28;7:327 [PMID: 17194304]
Genome Biol. 2019 Nov 14;20(1):238 [PMID: 31727128]
Mol Biol Evol. 2015 Jan;32(1):268-74 [PMID: 25371430]
Genome Biol. 2019 Dec 16;20(1):275 [PMID: 31843001]
BMC Bioinformatics. 2004 May 14;5:59 [PMID: 15144565]
Genome Biol. 2004;5(2):R7 [PMID: 14759257]
Nucleic Acids Res. 2018 Nov 30;46(21):e126 [PMID: 30107434]
Syst Biol. 2007 Aug;56(4):564-77 [PMID: 17654362]
Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
Biomolecules. 2018 Dec 07;8(4): [PMID: 30544626]
Mol Plant. 2021 Jan 4;14(1):9-26 [PMID: 33316465]
BMC Plant Biol. 2010 Aug 26;10:190 [PMID: 20796287]
Plant Sci. 2013 Feb;199-200:48-60 [PMID: 23265318]
Mol Phylogenet Evol. 2010 Jun;55(3):1008-17 [PMID: 19944174]
Nucleic Acids Res. 2012 Apr;40(7):e49 [PMID: 22217600]
Nucleic Acids Res. 2016 May 19;44(9):e89 [PMID: 26893356]
PLoS One. 2014 May 02;9(5):e91929 [PMID: 24786468]
Nat Biotechnol. 2011 May 15;29(7):644-52 [PMID: 21572440]
Plant Mol Biol. 2017 Dec;95(6):533-547 [PMID: 29076026]
Trends Plant Sci. 2018 Dec;23(12):1102-1115 [PMID: 30293809]
Theor Appl Genet. 2006 Jul;113(2):196-205 [PMID: 16791687]
Nucleic Acids Res. 2012 Jan;40(Database issue):D565-70 [PMID: 22123736]
Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9 [PMID: 21109532]
Cytogenet Genome Res. 2005;110(1-4):462-7 [PMID: 16093699]
Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3 [PMID: 18428791]
Nucleic Acids Res. 1997 Mar 1;25(5):955-64 [PMID: 9023104]
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8 [PMID: 15961478]
Genome Res. 2004 May;14(5):988-95 [PMID: 15123596]
BMC Bioinformatics. 2018 May 30;19(1):189 [PMID: 29843602]
Mol Biol Evol. 2005 Apr;22(4):976-90 [PMID: 15647520]
Plant J. 2021 Sep;107(6):1802-1818 [PMID: 34310794]
Genome Res. 2009 Jan;19(1):143-9 [PMID: 18838612]
Plant Cell. 2009 Oct;21(10):3315-25 [PMID: 19825834]
Nat Commun. 2017 May 04;8:15324 [PMID: 28469237]
Theor Appl Genet. 2002 Nov;105(6-7):1075-1086 [PMID: 12582936]
Database (Oxford). 2019 Jan 1;2019: [PMID: 31560050]
J Chem Ecol. 2013 Feb;39(2):175-85 [PMID: 23385366]
Genome Res. 2017 May;27(5):737-746 [PMID: 28100585]
Molecules. 2018 Jun 28;23(7): [PMID: 29958396]
Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25 [PMID: 14534192]
Bioinformatics. 2015 Oct 1;31(19):3210-2 [PMID: 26059717]
Mol Plant. 2021 Jan 4;14(1):27-39 [PMID: 33346062]
Bioinformatics. 2019 Jun 1;35(12):2153-2155 [PMID: 30398564]
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12 [PMID: 16845082]
Nat Biotechnol. 2015 Mar;33(3):290-5 [PMID: 25690850]
Mol Plant Microbe Interact. 2021 Feb;34(2):168-185 [PMID: 33400553]
Nucleic Acids Res. 2015 Jul 13;43(12):e78 [PMID: 25870408]
Genome Res. 2009 Sep;19(9):1639-45 [PMID: 19541911]
Plant Cell. 2021 Apr 17;33(2):290-305 [PMID: 33793769]
Bioinformatics. 2007 May 1;23(9):1061-7 [PMID: 17332020]
Food Chem. 2020 Nov 30;331:127293 [PMID: 32554311]
Genome Res. 2017 May;27(5):722-736 [PMID: 28298431]
Plant J. 2016 Aug;87(3):293-304 [PMID: 27133567]
Theor Appl Genet. 2003 Sep;107(5):773-82 [PMID: 12904864]
Nucleic Acids Res. 2003 Jan 1;31(1):365-70 [PMID: 12520024]
Food Chem. 2021 May 15;344:128600 [PMID: 33221101]
Mol Plant Microbe Interact. 2010 Aug;23(8):1000-11 [PMID: 20615111]
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14 [PMID: 19274634]
Comput Appl Biosci. 1997 Oct;13(5):555-6 [PMID: 9367129]
Int J Biol Macromol. 2018 Feb;107(Pt A):882-890 [PMID: 28939508]
Nat Methods. 2015 Jan;12(1):59-60 [PMID: 25402007]
J Mol Biol. 1997 Apr 25;268(1):78-94 [PMID: 9149143]
Plant J. 2015 Aug;83(4):600-9 [PMID: 26072920]
Bioinformatics. 2005 Oct 1;21(19):3787-93 [PMID: 15817693]
Nat Methods. 2015 Apr;12(4):357-60 [PMID: 25751142]
Cell. 2021 Mar 4;184(5):1156-1170.e14 [PMID: 33539781]
PLoS One. 2014 Nov 19;9(11):e112963 [PMID: 25409509]
Am J Bot. 2015 Feb;102(2):239-47 [PMID: 25667077]
Food Chem. 2019 Mar 1;275:618-627 [PMID: 30724241]
Nat Biotechnol. 2013 Dec;31(12):1119-25 [PMID: 24185095]
J Biol Chem. 2007 Nov 23;282(47):34013-8 [PMID: 17872948]
Nucleic Acids Res. 2019 Jan 8;47(D1):D419-D426 [PMID: 30407594]
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8 [PMID: 17485477]
Genome Biol. 2008 Jan 11;9(1):R7 [PMID: 18190707]
Nucleic Acids Res. 2000 Jan 1;28(1):27-30 [PMID: 10592173]
Mol Biol Evol. 2013 Aug;30(8):1987-97 [PMID: 23709260]
Bioinformatics. 2019 Dec 15;35(24):5321-5322 [PMID: 31292621]
Nat Methods. 2017 Jun;14(6):587-589 [PMID: 28481363]
Mol Plant. 2019 May 6;12(5):615-631 [PMID: 30999078]
Genome Biol. 2015 Dec 01;16:259 [PMID: 26619908]
Molecules. 2018 Oct 26;23(11): [PMID: 30373196]
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8 [PMID: 15161969]
Nat Rev Genet. 2009 Oct;10(10):725-32 [PMID: 19652647]
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4 [PMID: 15608160]
Food Chem Toxicol. 1996 Apr;34(4):347-52 [PMID: 8641660]
Bioinformatics. 2004 Nov 1;20(16):2878-9 [PMID: 15145805]
Cell. 2006 Dec 29;127(7):1309-21 [PMID: 17190597]
J Mol Biol. 1990 Oct 5;215(3):403-10 [PMID: 2231712]

Grants

  1. 1610232018003/Chinese Academy of Agricultural Sciences (CAAS)
  2. 1610232020008/Chinese Academy of Agricultural Sciences (CAAS)
  3. 1610232021006/Chinese Academy of Agricultural Sciences (CAAS)
  4. ASTIP-TRIC05/Chinese Academy of Agricultural Sciences (CAAS)
  5. ASTIP-TRIC05/Chinese Academy of Agricultural Sciences (CAAS)
  6. U20A2043/National Natural Science Foundation of China (National Science Foundation of China)
  7. 31801336/National Natural Science Foundation of China (National Science Foundation of China)

MeSH Term

China
Chromosomes, Plant
Genome, Plant
Oryza
Phylogeny
Poaceae
Seeds
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GWH: GWHBFHI00000000 (Zizania latifolia)

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