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Brassica juncea Genome Sequencing: Structural and Functional Insights

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The Brassica juncea Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

Indian mustard (Brassica juncea) is one of the oldest cultivated amphidiploid crops by human civilization. Natural interspecific crossing between diploid progenitors B. nigra (BB) and B. rapa (AA) resulted in evolution of this allotetraploid plant species with a total genome size of 1068 Mb. For genetic improvement of the desired traits, it is a prerequisite to unravel the whole genome sequence of this allotetraploid crop and its diploid progenitors. There are several genome and transcriptome sequencing initiatives conducted in this regard to unravel structure and functional annotation of genes in the genome. Similarly, this genomic information was used to obtain species specific molecular insights into the important agronomic traits such as fatty acid biosynthesis, anti-nutritional factors, resilience to climatic perturbations and pathogen resistance. The nuclear and organellar genome sequencing efforts in B. juncea, therefore, helped in improving our understanding of the complex allotetraploid architecture and building a foundation to utilize the information for translational genomics and precession breeding in the future.

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References

  • Anderson C (1993) Genome shortcut leads to problems. Science 259:1684–1688

    Article  CAS  PubMed  Google Scholar 

  • Bhatia G, Singh A, Verma D, Sharma S, Singh K (2020) Genome-wide investigation of regulatory roles of lncRNAs in response to heat and drought stress in Brassica juncea (Indian mustard). Environ Exp Bot 171:103922

    Google Scholar 

  • Cai C, Wang X, Liu B, Wu J, Liang J, Cui Y, Cheng F, Wang X (2017) Brassica rapa genome 2.0: a reference upgrade through sequence re-assembly and gene re-annotation. Mol Plant 10:649–651

    Article  CAS  PubMed  Google Scholar 

  • Cai Z, Chen Y, Liao J, Wang D (2020) Genome-wide identification and expression analysis of jasmonate ZIM domain gene family in tuber mustard (Brassica juncea var. tumida). PLoS One 15:e0234738

    Google Scholar 

  • Camilleri C, Lafleuriel J, Macadre C, Varoquaux F, Parmentier Y, Picard G, Caboche M, Bouchez D (1998) A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J 14:633–642

    Article  CAS  PubMed  Google Scholar 

  • Cavell A, Lydiate D, Parkin I, Dean C, Trick M (1998) A 30 centimorgan segment of Arabidopsis thaliana chromosome 4 has six collinear homologues within the Brassica napus genome. Genome 41:62–69

    Article  CAS  PubMed  Google Scholar 

  • Chang S, Yang T, Du T, Huang Y, Chen J, Yan J, He J, Guan R (2011) Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica. BMC Genomics 12:1–12

    Article  Google Scholar 

  • Choi S, Creelman RA, Mullet JE, Wing RA (1995) Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol Biol Rep 13(2):124–128

    Article  Google Scholar 

  • Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet 115(6):777–792

    Article  CAS  PubMed  Google Scholar 

  • Chyi Y-S, Hoenecke M, Sernyk J (1992) A genetic linkage map of restriction fragment length polymorphism loci for Brassica rapa (syn. campestris). Genome 35(5):746–757

    Google Scholar 

  • Ferreira M, Williams P, Osborn T (1994) RFLP mapping of Brassica napus using doubled haploid lines. Theor Appl Genet 89(5):615–621

    Article  CAS  PubMed  Google Scholar 

  • Gaikwad K, Baldev A, Kirti P, Mohapatra T, Bhat S, Chopra V, Prakash S (2006) Organization and expression of the mitochondrial genome in CMS (Moricandia) Brassica juncea: nuclear-mitochondrial incompatibility results in differential expression of the mitochondrial atpα gene. Plant Breed 125(6):623–628

    Article  CAS  Google Scholar 

  • Hauge BM, Giraudat J, Hanley S, Hwang I, Kohchi T, Goodman HM (1991) Physical mapping of the Arabidopsis genome and its applications. In: Plant Molecular Biology vol 2. Springer, pp 239–248

    Google Scholar 

  • He J, He X, Chang P, Jiang H, Gong D, Sun Q (2020) Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida. Peer J 8:e9130

    Google Scholar 

  • Heng S, Wei C, Jing B, Wan Z, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J (2014) Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288. BMC Genomics 15(1):1–12

    Article  Google Scholar 

  • Heng S, Gao J, Wei C, Chen F, Li X, Wen J, Yi B, Ma C, Tu J, Fu T (2018) Transcript levels of orf288 are associated with the hau cytoplasmic male sterility system and altered nuclear gene expression in Brassica juncea. J Exp Bot 69(3):455–466

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hong CP, Plaha P, Koo D-H, Yang T-J, Choi SR, Lee YK, Uhm T, Bang J-W, Edwards D, Bancroft I (2006) A Survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana. Molecules Cells (Springer Science and Business Media BV) 22(3)

    Google Scholar 

  • Hong CP, Kwon S-J, Kim JS, Yang T-J, Park B-S, Lim YP (2008) Progress in understanding and sequencing the genome of Brassica rapa. Int J Plant Genomics 2008

    Google Scholar 

  • Inturrisi F, Bayer PE, Yang H, Tirnaz S, Edwards D, Batley J (2020) Genome-wide identification and comparative analysis of resistance genes in Brassica juncea. Mol Breed 40(8):1–14

    Article  Google Scholar 

  • Jing B, Heng S, Tong D, Wan Z, Fu T, Tu J, Ma C, Yi B, Wen J, Shen J (2012) A male sterility-associated cytotoxic protein ORF288 in Brassica juncea causes aborted pollen development. Jexp Bot 63(3):1285–1295

    CAS  Google Scholar 

  • Kim JS, Chung TY, King GJ, Jin M, Yang T-J, Jin Y-M, Kim H-I, Park B-S (2006) A sequence-tagged linkage map of Brassica rapa. Genet 174(1):29–39

    Article  CAS  Google Scholar 

  • Kotani H, Nakamura Y, Sato S, Kaneko T, Asamizu E, Miyajima N, Tabata S (1997) Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones. DNA Res 4(4):291–293

    Google Scholar 

  • Lagercrantz U, Lydiate DJ (1995) RFLP mapping in Brassica nigra indicates differing recombination rates in male and female meioses. Genome 38(2):255–264

    Article  CAS  PubMed  Google Scholar 

  • Li P, Zhang S, Li F, Zhang S, Zhang H, Wang X, Sun R, Bonnema G, Borm TJ (2017) Front Plant Sci 8:111

    PubMed  PubMed Central  Google Scholar 

  • Li M, Sun B, Xie F, Gong R, Luo Y, Zhang F, Yan Z, Tang H (2019) Identification of the GRAS gene family in the Brassica juncea genome provides insight into its role in stem swelling in stem mustard. Peer J 7:e6682

    Google Scholar 

  • Li M, Xie F, Li Y, Gong L, Luo Y, Zhang Y, Chen Q, Wang Y, Lin Y, Zhang Y (2020a) Genome-wide analysis of the heat shock transcription factor gene family in Brassica juncea: structure, evolution, and expression profiles. DNA Cell Biol 39(11):1990–2004

    Article  CAS  PubMed  Google Scholar 

  • Li W, Chen F, Wang Y, Zheng H, Yi Q, Ren Y, Gao J (2020b) Genome-wide identification and functional analysis of ARF transcription factors in Brassica juncea var. tumida. PloS One 15(4):e0232039

    Google Scholar 

  • Luo M, Wing RA (2003) An improved method for plant BAC library construction. In: Plant functional genomics. Springer, pp 3–19

    Google Scholar 

  • Mir ZA, Ali S, Shivaraj S, Bhat JA, Singh A, Yadav P, Rawat S, Paplao PK, Grover A (2020) Genome-wide identification and characterization of Chitinase gene family in Brassica juncea and Camelina sativa in response to Alternaria brassicae. Genomics 112(1):749–763

    Article  CAS  PubMed  Google Scholar 

  • Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S (1999) A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet 22(3):271–275

    Article  CAS  PubMed  Google Scholar 

  • Mun J-H, Kwon S-J, Yang T-J, Kim H-S, Choi B-S, Baek S, Kim JS, Jin M, Kim JA, Lim M-H (2008) The first generation of a BAC-based physical map of Brassica rapa. BMC Genomics 9(1):1–11

    Article  Google Scholar 

  • Mun J-H, Kwon S-J, Seol Y-J, Kim JA, Jin M, Kim JS, Lim M-H, Lee S-I, Hong JK, Park T-H (2010) Sequence and structure of Brassica rapa chromosome A3. Genome Biol 11(9):1–12

    Article  Google Scholar 

  • Paritosh K, Pradhan AK, Pental D (2020) A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes. BMC Genomics 21(1):1–12

    Article  Google Scholar 

  • Paritosh K, Yadava SK, Singh P, Bhayana L, Mukhopadhyay A, Gupta V, Bisht NC, Zhang J, Kudrna DA, Copetti D (2021) A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes. Plant Biotechnol J 19(3):602

    Article  CAS  PubMed  Google Scholar 

  • Paritosh K, Gupta V, Yadava SK, Singh P, Pradhan AK, Pental D (2014) RNA-seq based SNPs for mapping in Brassica juncea (AABB): synteny analysis between the two constituent genomes A (from B. rapa) and B (from B. nigra) shows highly divergent gene block arrangement and unique block fragmentation patterns. BMC Genomics 15(1):1–14

    Google Scholar 

  • Perumal S, Koh CS, Jin L, Buchwaldt M, Higgins EE, Zheng C, Sankoff D, Robinson SJ, Kagale S, Navabi Z-K (2020) A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome. Nat Plants 6(8):929–941

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prabhudas SK, Raju B, Kannan Thodi S, Parani M, Natarajan P (2016) The complete chloroplast genome sequence of Indian mustard (Brassica juncea L.). Mitochondrial DNA A 27(6):4622–4623

    Google Scholar 

  • Prakash S, Chopra V (1991) Cytogenetics of crop Brassicas and their allies. In: Developments in Plant Genetics and Breeding, vol 2. Elsevier, pp 161–180

    Google Scholar 

  • Schmidt R, West J, Love K, Lenehan Z, Lister C, Thompson H, Bouchez D, Dean C (1995) Physical map and organization of Arabidopsis thaliana chromosome 4. Science 270(5235):480–483

    Article  CAS  PubMed  Google Scholar 

  • Schmidt R, Love K, West J, Lenehan Z, Dean C (1997) Description of 31 YAC contigs spanning the majority of Arabidopsis thaliana chromosome 5. Plant J 11(3):563–572

    Article  CAS  PubMed  Google Scholar 

  • Shizuya H, Birren B, Kim U-J, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci 89(18):8794–8797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Slocum M, Figdore S, Kennard W, Suzuki J, Osborn T (1990) Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea. TheorAppl Genet 80(1):57–64

    Article  CAS  Google Scholar 

  • Song K, Suzuki J, Slocum M, Williams P, Osborn T (1991) A linkage map ofBrassica rapa (syn. campestris) based on restriction fragment length polymorphism loci. Theor Appl Genet 82(3):296–304

    Google Scholar 

  • Tao Q, Zhao H, Qiu L, Hong G (1994) Construction of a full bacterial artificial chromosome (BAC) library of Oryza sativa genome. Cell Res 4(2):127–133

    Article  Google Scholar 

  • Thormann C, Ferreira M, Camargo L, Tivang J, Osborn T (1994) Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species. Theor Appl Genet 88(8):973–980

    Article  CAS  PubMed  Google Scholar 

  • Verma D, Lakhanpal N, Singh K (2019) Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa. BMC Genomics 20(1):1–18

    Google Scholar 

  • Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J-H, Bancroft I, Cheng F (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43(10):1035–1039

    Article  CAS  PubMed  Google Scholar 

  • Wang P, Zhao Z, Zhang Z, Cai Z, Liao J, Tan Q, Xiang M, Chang L, Xu D, Tian Q (2021) Genome-wide identification and analysis of NPR family genes in Brassica juncea var. tumida. Gene 769:145210

    Google Scholar 

  • Woo S-S, Jiang J, Gill BS, Paterson AH, Wing RA (1994) Construction and characterization of bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22(23):4922–4931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu Y, Tulsieram L, Tao Q, Zhang H-B, Rothstein SJ (2000) A binary vector-based large insert library for Brassica napus and identification of clones linked to a fertility restorer locus for Ogura cytoplasmic male sterility (CMS). Genome 43(1):102–109

    Article  CAS  PubMed  Google Scholar 

  • Wu Z, Hu K, Yan M, Song L, Wen J, Ma C, Shen J, Fu T, Yi B, Tu J (2019) Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea. BMC Genomics 20(1):1–15

    Article  Google Scholar 

  • Yang J, Liu X, Yang X, Zhang M (2010) Mitochondrially-targeted expression of a cytoplasmic male sterility-associated orf220 gene causes male sterility in Brassica juncea. BMC Plant Biol 10(1):1–10

    Article  Google Scholar 

  • Yang J, Liu D, Wang X, Ji C, Cheng F, Liu B, Hu Z, Chen S, Pental D, Ju Y (2016) The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 48(10):1225–1232

    Article  CAS  PubMed  Google Scholar 

  • Yang H, Bayer PE, Tirnaz S, Edwards D, Batley J (2021) Genome-wide identification and evolution of receptor-like kinases (RLKs) and receptor like proteins (RLPs) in Brassica juncea. Biology 10(1):17

    Article  Google Scholar 

  • Zachgo EA, Wang ML, Dewdney J, Bouchez D, Camilleri C, Belmonte S, Huang L, Dolan M, Goodman HM (1996) A physical map of chromosome 2 of Arabidopsis thaliana. Genome Res 6(1):19–25

    Article  CAS  PubMed  Google Scholar 

  • Zhang H-B, Wu C (2001) BAC as tools for genome sequencing. Plant Physiol Biochem 39(3–4):195–209

    Article  CAS  Google Scholar 

  • Zhang L, Cai X, Wu J, Liu M, Grob S, Cheng F, Liang J, Cai C, Liu Z, Liu B (2018) Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Hortic Res 5(1):1–11

    Article  Google Scholar 

  • Zhao N, Xu X, Wamboldt Y, Mackenzie SA, Yang X, Hu Z, Yang J, Zhang M (2016) MutS HOMOLOG1 silencing mediates ORF220 substoichiometric shifting and causes male sterility in Brassica juncea. J Exp Bot 67(1):435–444

    Article  CAS  PubMed  Google Scholar 

  • Zhao N, Li Z, Zhang L, Yang X, Mackenzie SA, Hu Z, Zhang M, Yang J (2021) MutS HOMOLOG1 mediates fertility reversion from cytoplasmic male sterile Brassica juncea in response to environment. PlantCell Environ 44(1):234–246

    CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Microbiology and Cell Sciences, IFAS, University of Florida, Gainesville, FL, 32611, USA

    Thakku R. Ramkumar

  2. The Energy and Resources Institute, TERI-Deakin Nano Biotechnology Centre, Gurugram, Haryana, 122003, India

    Sagar S. Arya, Divyani D. Kumari & Sangram K. Lenka

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  1. Thakku R. Ramkumar
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  2. Sagar S. Arya
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  3. Divyani D. Kumari
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  4. Sangram K. Lenka
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Editors and Affiliations

  1. President, International Climate Resilient Crop Genomics Consortium (ICRCGC), President, International Phytomedomics & Nutriomics Consortium (IPNC) and President, Genome India International (GII), New Delhi, India

    Chittaranjan Kole

  2. Secretary, Department of Agricultural Research and Education (DARE), Government of India; and Director General, Indian Council of Agricultural Research (ICAR), New Delhi, India

    Trilochan Mohapatra

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Ramkumar, T.R., Arya, S.S., Kumari, D.D., Lenka, S.K. (2022). Brassica juncea Genome Sequencing: Structural and Functional Insights. In: Kole, C., Mohapatra, T. (eds) The Brassica juncea Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-91507-0_12

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