Genome sequence of the model rice variety KitaakeX

doi:10.1186/s12864-019-6262-4

. 2019 Nov 27;20(1):905.

doi: 10.1186/s12864-019-6262-4.

Genome sequence of the model rice variety KitaakeX

Rashmi Jain^{1

2}, Jerry Jenkins^{3

4}, Shengqiang Shu³, Mawsheng Chern^{1

2}, Joel A Martin³, Dario Copetti^{5

6

7}, Phat Q Duong^{1

2}, Nikki T Pham¹, David A Kudrna^{5

8}, Jayson Talag^{5

8}, Wendy S Schackwitz³, Anna M Lipzen³, David Dilworth³, Diane Bauer³, Jane Grimwood^{3

4}, Catherine R Nelson¹, Feng Xing⁹, Weibo Xie⁹, Kerrie W Barry³, Rod A Wing^{5

8

10}, Jeremy Schmutz^{3

4}, Guotian Li^{11

12

13}, Pamela C Ronald^{14

15}

Affiliations

¹ Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.
² Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
³ U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
⁴ HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
⁵ Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
⁶ Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.
⁷ Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
⁸ BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
⁹ National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
¹⁰ International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
¹¹ Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. li4@mail.hzau.edu.cn.
¹² Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. li4@mail.hzau.edu.cn.
¹³ The Provincial Key Lab of Plant Pathology of Hubei Province and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. li4@mail.hzau.edu.cn.
¹⁴ Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. pcronald@ucdavis.edu.
¹⁵ Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. pcronald@ucdavis.edu.

PMID: 31775618
PMCID: PMC6882167
DOI: 10.1186/s12864-019-6262-4

Free PMC article

Genome sequence of the model rice variety KitaakeX

Rashmi Jain et al. BMC Genomics. 2019.

Free PMC article

. 2019 Nov 27;20(1):905.

doi: 10.1186/s12864-019-6262-4.

Authors

Affiliations

¹ Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.
² Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
³ U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
⁴ HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
⁵ Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
⁶ Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.
⁷ Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
⁸ BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
⁹ National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
¹⁰ International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
¹¹ Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. li4@mail.hzau.edu.cn.
¹² Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. li4@mail.hzau.edu.cn.
¹³ The Provincial Key Lab of Plant Pathology of Hubei Province and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. li4@mail.hzau.edu.cn.
¹⁴ Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. pcronald@ucdavis.edu.
¹⁵ Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. pcronald@ucdavis.edu.

PMID: 31775618
PMCID: PMC6882167
DOI: 10.1186/s12864-019-6262-4

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Abstract

Background: The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species.

Results: Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics.

Conclusions: The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.

Keywords: De novo genome assembly; Kitaake; KitaakeX; Nipponbare; Rice; Whole genome sequence; XA21 immune receptor; Zhenshan97.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1

The early flowering rice variety KitaakeX; a KitaakeX and selected sequenced rice varieties under long-day conditions. Scale bar = 10 cm; b Flowering time of KitaakeX and selected rice varieties under long-day conditions. DAG, days after germination. Asterisks indicate significant differences using the unpaired Student’s t-test (P c KitaakeX in the unweighted neighbor-joining tree comprising 3010 accessions of the 3 k rice genomes project and indicated varieties. It includes four XI clusters (XI-1A from East Asia, XI-1B of modern varieties of diverse origins, XI-2 from South Asia and XI-3 from Southeast Asia); three GJ clusters [primarily East Asian temperate (named GJ-tmp), Southeast Asian subtropical (named GJ-sbtrp) and Southeast Asian Tropical (named GJ-trp)]; and two groups for the mostly South Asian cA (circum-Aus) and cB (circum-Basmati) accessions, 1 group Admix (accessions that fall between major groups were classified as admixed) Branch length indicates the genetic distance between two haplotypes

Fig. 2

Genome wide analysis of KitaakeX genome and its comparison with other rice varieties; a Circles indicate the 12 KitaakeX chromosomes represented on a Mb scale; b, c SNPs and InDels between KitaakeX and Nipponbare (b) and KitaakeX and Zhenshan97 (c); d Repeat density; e GC content; f Gene density; g Homologous genes in the KitaakeX genome. Window size used in the circles is 500 kb

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References

1. Gross BL, Zhao Z. Archaeological and genetic insights into the origins of domesticated rice. Proc Natl Acad Sci U S A. 2014;111(17):6190–6197. doi: 10.1073/pnas.1308942110. - DOI - PMC - PubMed
1. Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang FJN. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557(7703):43. doi: 10.1038/s41586-018-0063-9. - DOI - PMC - PubMed
1. Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) 2013;6(1):4. doi: 10.1186/1939-8433-6-4. - DOI - PMC - PubMed
1. Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang XJ. A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science. 2002;296(5565):79–92. doi: 10.1126/science.1068037. - DOI - PubMed
1. Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban EJG. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 2014;15(11):506. - PMC - PubMed

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[1] Gross BL, Zhao Z. Archaeological and genetic insights into the origins of domesticated rice. Proc Natl Acad Sci U S A. 2014;111(17):6190–6197. doi: 10.1073/pnas.1308942110. - DOI - PMC - PubMed

[2] Gross BL, Zhao Z. Archaeological and genetic insights into the origins of domesticated rice. Proc Natl Acad Sci U S A. 2014;111(17):6190–6197. doi: 10.1073/pnas.1308942110. - DOI - PMC - PubMed

[3] Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang FJN. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557(7703):43. doi: 10.1038/s41586-018-0063-9. - DOI - PMC - PubMed

[4] Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang FJN. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557(7703):43. doi: 10.1038/s41586-018-0063-9. - DOI - PMC - PubMed

[5] Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) 2013;6(1):4. doi: 10.1186/1939-8433-6-4. - DOI - PMC - PubMed

[6] Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) 2013;6(1):4. doi: 10.1186/1939-8433-6-4. - DOI - PMC - PubMed

[7] Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang XJ. A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science. 2002;296(5565):79–92. doi: 10.1126/science.1068037. - DOI - PubMed

[8] Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang XJ. A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science. 2002;296(5565):79–92. doi: 10.1126/science.1068037. - DOI - PubMed

[9] Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban EJG. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 2014;15(11):506. - PMC - PubMed

[10] Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban EJG. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 2014;15(11):506. - PMC - PubMed

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Genome sequence of the model rice variety KitaakeX

Affiliations

Genome sequence of the model rice variety KitaakeX

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Similar articles

Cited by 2 articles

References

MeSH terms

Grant support

LinkOut - more resources

Full Text Sources

Miscellaneous

Abstract

Conflict of interest statement

Figures

Similar articles

Cited by 2 articles

References

MeSH terms

Related information

Grant support

LinkOut - more resources

Full Text Sources

Miscellaneous