ArticleBMC genomics2020
A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
- Transposable elements and their epigenetic modifications mediate gene expression and subgenome dominance in Brassica carinata.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Review
- An NGS approach for the identification of precise homoeologous recombination sites between A and C genomes inBreeding science · 2024Article
- Chromosome-scale reference genome of broccoli (Horticulture research · 2024Article
- Applications of Molecular Markers for Developing Abiotic-Stress-Resilient Oilseed Crops.Life (Basel, Switzerland) · 2022Review
- Performance and Characterization of Bi-Metal Compound on Activated Carbon for Hydrogen Sulfide Removal in Biogas.Molecules (Basel, Switzerland) · 2022Article
- The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency.The Plant journal : for cell and molecular biology · 2022Article
- Genome-wide identification of biotin carboxyl carrier subunits of acetyl-CoA carboxylase in Brassica and their role in stress tolerance in oilseed Brassica napus.BMC genomics · 2022Article
- BRAD V3.0: an upgraded Brassicaceae database.Nucleic acids research · 2022Article
- Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis ofFrontiers in plant science · 2022Article
- Subgenome Discrimination inCells · 2021Article
- Challenges and prospects for a potential allohexaploid Brassica crop.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes.Plant biotechnology journal · 2021Article
- Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants.Applications in plant sciencesArticle
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3 authors.
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Abstract
backgroundBrassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U's triangle and is one of the progenitor species of B. juncea (AABB), an important oilseed crop of the Indian subcontinent. We report the genome assembly of B. nigra variety Sangam.
resultsThe genome assembly was carried out using Oxford Nanopore long-read sequencing and optical mapping. A total of 1549 contigs were assembled, which covered ~ 515.4 Mb of the estimated ~ 522 Mb of the genome. The final assembly consisted of 15 scaffolds that were assigned to eight pseudochromosomes using a high-density genetic map of B. nigra. Around 246 Mb of the genome consisted of the repeat elements; LTR/Gypsy types of retrotransposons being the most predominant. The B genome-specific repeats were identified in the centromeric regions of the B. nigra pseudochromosomes. A total of 57,249 protein-coding genes were identified of which 42,444 genes were found to be expressed in the transcriptome analysis. A comparison of the B genomes of B. nigra and B. juncea revealed high gene colinearity and similar gene block arrangements. A comparison of the structure of the A, B, and C genomes of U's triangle showed the B genome to be divergent from the A and C genomes for gene block arrangements and centromeric regions.
conclusionsA highly contiguous genome assembly of the B. nigra genome reported here is an improvement over the previous short-read assemblies and has allowed a comparative structural analysis of the A, B, and C genomes of the species belonging to the U's triangle. Based on the comparison, we propose a new nomenclature for B. nigra pseudochromosomes, taking the B. rapa pseudochromosome nomenclature as the reference.
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