Construction of pseudomolecule sequences of Brassica rapa ssp. pekinensis inbred line CT001 and analysis of spontaneous mutations derived via sexual propagation

English version

Autoři: Jee-Soo Park ^aff001; Ji-Hyun Park ^aff001; Young-Doo Park ^aff001
Působiště autorů: Department of Horticultural Biotechnology, Kyung Hee University, Yongin, Korea ^aff001
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0222283

Souhrn

Chinese cabbage (Brassica rapa ssp. pekinensis) is a major crop that is widely cultivated, especially in Korea, Japan, and China. With the advent of next generation sequencing technology, the cost and time required for sequencing have decreased and the development of genome research accelerated. Genome sequencing of Chinese cabbage was completed in 2011 using the variety Chiifu-401-42, and since then the genome has been continuously updated. In the present study, we conducted whole-genome sequencing of Chinese cabbage inbred line CT001, a line widely used in traditional or molecular breeding, to improve the accuracy of genetic polymorphism analysis. The constructed CT001 pseudomolecule represented 85.4% (219.8 Mb) of the Chiifu reference genome, and a total of 38,567 gene models were annotated using RNA-Seq analysis. In addition, the spontaneous mutation rate of CT001 was estimated by resequencing DNA obtained from individual plants after sexual propagation for six generations to estimate the naturally occurring variations. The CT001 pseudomolecule constructed in this study will provide valuable resources for genomic studies on Chinese cabbage.

Klíčová slova:

Biology and life sciences – Genetics – Genomics – Plant genomics – Genome analysis – Plant genetics – Bioengineering – Biotechnology – Plant biotechnology – Plant science – Organisms – Eukaryota – Plants – Computational biology – Engineering and technology – Research and analysis methods – Animal studies – Experimental organism systems – Molecular biology – Sequence assembly tools – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – Molecular biology techniques – Mutation – DNA construction – DNA library construction – Genomic library construction – Artificial gene amplification and extension – Polymerase chain reaction – Substitution mutation – Brassica – Inbred strains

Zdroje

1. Warwick SI, Francis A, Al-Shehbaz IA. Brassicaceae: species checklist and database on CD-Rom. Plant Syst Evol. 2006;259:249–58.

2. Kim KS, Ha SO, Lee YH, Jang YS, Choi IH. Study on growth and flowering characteristics in the spring sowing for selection of rapeseed (Brassica napus L.) varieties. Korean J Plant Res. 2015;28(1):111–8.

3. Sun R. Economic/Academic Importance of Brassica rapa. In: Wang X, Kole C, editors. The Brassica rapa Genome. Berlin: Springer; 2015. p. 1–15.

4. Stein L. The case for cloud computing in genome informatics. Genome Biol. 2010;11:207. doi: 10.1186/gb-2010-11-5-207 20441614

5. Reuter JA, Spacek DV, Snyder MP. High-throughput sequencing technologies. Mol Cell. 2015;58(4):586–97. doi: 10.1016/j.molcel.2015.05.004 26000844

6. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315–27. doi: 10.1016/j.ygeno.2010.03.001 20211242

7. Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics. 2016;107(1):1–8. doi: 10.1016/j.ygeno.2015.11.003 26554401

8. Buermans HP, den Dunnen JT. Next generation sequencing technology: advances and applications. Biochim Biophys Acta. 2014;1842(10):1932–41. doi: 10.1016/j.bbadis.2014.06.015 24995601

9. Christenhusz MJ, Byng JW. The number of known plants species in the world and its annual increase. Phytotaxa. 2016;261(3):201–17.

10. Bolger ME, Arsova B, Usadel B. Plant genome and transcriptome annotations: from misconceptions to simple solutions. Brief Bioinform. 2017;19(3):437–49.

11. Lai K, Lorenc MT, Edwards D. Genomic databases for crop improvement. Agronomy. 2012;2(1):62–73.

12. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408(6814):796. doi: 10.1038/35048692 11130711

13. Beven M, Walsh S. The Arabidopsis genome: a foundation for plant research. Genome Res. 2005;15:1632–42. doi: 10.1101/gr.3723405 16339360

14. Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand K, et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 2011;477:419–23. doi: 10.1038/nature10414 21874022

15. Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, et al. The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet. 2007;115(6):777–92. doi: 10.1007/s00122-007-0608-z 17646962

16. Brassica rapa Genome Sequencing Project Consortium. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 2011;43(10):1035. doi: 10.1038/ng.919 21873998

17. Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, et al. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol. 2011;11:136. (BRAD, brassicadb.org/) doi: 10.1186/1471-2229-11-136 21995777

18. Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, et al. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res. 2007;36(suppl_1):D959–65.

19. Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, et al. Ensembl 2018. Nucleic Acids Res. 2017;46(D1):D754–61.

20. Dellaporta SL, Wood J, Hicks JB. A Plant DNA Minipreparation: Version II. Plant Mol Biol Rep. 1983;1:19–21.

21. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci. 2011;108(4):1513–8. doi: 10.1073/pnas.1017351108 21187386

22. Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 2002;30:2478–83. doi: 10.1093/nar/30.11.2478 12034836

23. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12. doi: 10.1186/gb-2004-5-2-r12 14759262

24. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, 2014; 30: 2114–20. doi: 10.1093/bioinformatics/btu170 24695404

25. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015. 12: 357–60. doi: 10.1038/nmeth.3317 25751142

26. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015, 33: 290–5. doi: 10.1038/nbt.3122 25690850

27. Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nat Protoc. 2016; 11, 1650–67. doi: 10.1038/nprot.2016.095 27560171

28. Niknafs YS, Pandian B, Iyer HK, Chinnaiyan AM, Iyer MK. TACO produces robust multisample transcriptome assemblies from RNA-seq. Nat Meth, 2017. 14:, 68–70.

29. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, et al. UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view. In Plant Bioinformatics (pp. 23–54). 2016 Humana Press, New York, NY.

30. Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J. 2017;89(4):789–804. doi: 10.1111/tpj.13415 27862469

31. El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2018;47(D1):D427–32.

32. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint. 2013;arXiv:1303.3997.

33. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303. doi: 10.1101/gr.107524.110 20644199

34. Ness RW, Morgan AD, Colegrave N, Keightley PD. Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii. Genetics. 2012;192(4):1447–54. doi: 10.1534/genetics.112.145078 23051642

35. Oppold AM, Pfenninger M. Direct estimation of the spontaneous mutation rate by short‐term mutation accumulation lines in Chironomus riparius. Evol Lett. 2017;1(2):86–92. doi: 10.1002/evl3.8 30283641

36. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005;436:793–800. doi: 10.1038/nature03895 16100779

37. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326:1112–5. doi: 10.1126/science.1178534 19965430

38. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457(7229):551–6. doi: 10.1038/nature07723 19189423

39. Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. The Plant Cell. 2006;18(6):1348–59. doi: 10.1105/tpc.106.041665 16632643

40. Jiang C, Mithani A, Gan X, Belfield EJ, Klingler JP, Zhu JK, et al. Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Curr Biol. 2011;21(16):1385–90. doi: 10.1016/j.cub.2011.07.002 21802297

41. Miyao A, Nakagome M, Ohnuma T, Yamagata H, Kanamori H, Katayose Y, et al. Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing. Plant Cell Physiol. 2011;53(1):256–64. doi: 10.1093/pcp/pcr172 22156226

42. Zhang D, Wang Z, Wang N, Gao Y, Liu Y, Wu Y, et al. Tissue culture-induced heritable genomic variation in rice, and their phenotypic implications. PloS one. 2014;9(5): e96879. doi: 10.1371/journal.pone.0096879 24804838

43. Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science. 2010;327(5961):92–4. doi: 10.1126/science.1180677 20044577

44. Greene EA, Codomo CA, Taylor NE, Henikoff JG, Till BJ, Reynolds SH, et al. Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics. 2003;164:731–40. 12807792

Construction of pseudomolecule sequences of Brassica rapa ssp. pekinensis inbred line CT001 and analysis of spontaneous mutations derived via sexual propagation

Souhrn

Klíčová slova:

Zdroje

PLOS One

Aktuální možnosti diagnostiky a léčby litiáz