Chromosome level comparative analysis of Brassica genomes

Wang, Wenliang; Guan, Rui; Liu, Xing; Zhang, Haorui; Song, Bo; Xu, Qiwu; Fan, Guangyi; Chen, Wenbin; Wu, Xiaoming; Liu, Xin; Wang, Jianbo

doi:10.1007/s11103-018-0814-x

Cited by 20 publications

(24 citation statements)

References 55 publications

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“…Genetic exchanges may also be limited due to a strong mechanism in the B genome for suppression of pairing between the homeologous chromosomes 46,47 . B. nigra genome assembly reported here is an improvement over the previous B. nigra assemblies based on short-read sequencing 16,48 . The long-read Nanopore sequencing and optical mapping have provided highly contiguous genomes assembly, with five of the eight pseudochromosomes represented by a single scaffold.…”

Section: Discussionmentioning

confidence: 95%

A highly contiguous genome assembly ofBrassica nigra(BB) and revised nomenclature for the pseudochromosomes

Paritosh

Pradhan

Pental

2020

Preprint

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AbstractBrassica 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 here a highly contiguous genome assembly of B. nigra variety Sangam. The genome assembly has been carried out using Oxford Nanopore long-read sequencing and optical mapping. The resulting chromosome-scale assembly is a significant improvement over the previous draft assemblies of B. nigra; five out of the eight pseudochromosomes were represented by one scaffold each. The assembled genome was annotated for the transposons, centromeric repeats, and genes. The B. nigra genome was compared with the recently available contiguous genome assemblies of B. rapa (AA), B. oleracea (CC), and B. juncea (AABB). Based on the maximum homology among the three diploid genomes of U’s triangle, we propose a new nomenclature for B. nigra pseudochromosomes, taking the B. rapa pseudochromosome nomenclature as the reference.

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Section: Discussionmentioning

confidence: 95%

A highly contiguous genome assembly ofBrassica nigra(BB) and revised nomenclature for the pseudochromosomes

Paritosh

Pradhan

Pental

2020

Preprint

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“…The current nomenclature (Version 1) for the B. nigra LGs, recommended by the internationally agreed standard ( http://www.brassica.info ), is based on some early work on the comparative genetic mapping between At and B. nigra [ 26 ] . A total of 160 DNA fragments from the At genome, mostly anonymous and some cDNA fragments of known genes, were used as RFLP markers.…”

Section: Resultsmentioning

confidence: 99%

A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

2020

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Background Brassica 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. Results The 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. Conclusions A 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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“…The Rabl-like configuration is not restricted to beetles and flies; it is also found in the yeast genome (Jin et al 1998, Goto et al 2001, Mizuguchi et al 2015, Kim et al 2017) as well as in wheat, barley and Brassica (Santos and Shaw 2004, Mascher et al 2017, Concia et al 2020, Wang et al 2019), and was originally described from salamander cells (Rabl 1885). It is unclear how widespread the Rabl-like configuration is in Coleoptera.…”

Section: Discussionmentioning

confidence: 99%

The Easter Egg Weevil (Pachyrhynchus) genome reveals synteny in Coleoptera across 200 million years of evolution

Dam

Cabras

Henderson

et al. 2020

Preprint

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Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders? We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta. We find that synteny largely scales with clade age, with younger clades, such as Lepidoptera, having especially high synteny. However, we do find subtle differences in the maintenance of synteny and its rate of decay among the insect orders.

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Chromosome level comparative analysis of Brassica genomes

Cited by 20 publications

References 55 publications

A highly contiguous genome assembly ofBrassica nigra(BB) and revised nomenclature for the pseudochromosomes

A highly contiguous genome assembly ofBrassica nigra(BB) and revised nomenclature for the pseudochromosomes

A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

The Easter Egg Weevil (Pachyrhynchus) genome reveals synteny in Coleoptera across 200 million years of evolution

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