High contiguity long read assembly ofBrassica nigraallows localization of active centromeres and provides insights into the ancestralBrassicagenome

Perumal, Sampath; Koh, Chu Shin; Jin, Lingling; Buchwaldt, Miles; Higgins, Erin E.; Zheng, Chunfang; Sankoff, David; Robinson, Stephen J.; Kagale, Sateesh; Navabi, Zahra-Katy; Tang, Lily; Horner, Kyla; He, Zhesi; Bancroft, Ian; Chalhoub, Boulos; Sharpe, Andrew; Parkin, Isobel A. P.

doi:10.1101/2020.02.03.932665

Cited by 11 publications

(16 citation statements)

References 77 publications

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“…Likewise, hAT superfamilies of MITEs were identified and characterized in various species including B. rapa and B. oleracea, Oryza species, Musa species, and Beta vulgaris and were found to be present at high copy numbers (Bundock and Hooykaas, 2005;Muehlbauer et al, 2006;Nouroz et al, 2015b). MITEs comprised approximately 1% of the B. nigra genome (Perumal et al, 2020), and in our analysis we identified two hAT families that are largely specific to the B-genome. Genome or lineage specific amplification of transposons including MITEs has been observed for many species (Feschotte et al, 2002;Choi et al, 2014) and has been suggested to play a role not only in increasing genome size but more specifically in genome adaptation (Parisod et al, 2010;Belyayev, 2014).…”

Section: Discussionsupporting

confidence: 51%

Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome

et al. 2020

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Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II transposons which have been shown to influence genome evolution. Brassica nigra L. (Bgenome) is one of three Brassica diploids cultivated primarily as an oil crop, which harbors novel alleles important for breeding. Two new high copy hAT MITE families (BniHAT-1 and BniHAT-2) from the B-genome were characterized and their prevalence assessed in the genomes of the related diploids, rapa L. (A) and Brassica oleracea L. (C). Both novel MITE families were present at high copy numbers in the B-genome with 434 and 331 copies of BniHAT-1 and BniHAT-2, respectively. Yet less than 20 elements were identified in the genome assemblies of the A, and C-genomes, supporting B-genome specific proliferation of these MITE families. Although apparently randomly distributed across the genome, 68 and 70% of the B-genome MITEs were present within 2 kb flanking regions of annotated genes suggesting they might influence gene expression and/or function. In addition, MITE derived microRNAs and transcription factor binding sites suggested a putative role in gene regulation. Age of insertion analysis revealed that the major proliferation of these elements occurred during 2-3 million years ago. Additionally, site-specific polymorphism analyses showed that 44% MITEs were undergoing active amplification into the B-genome. Overall, this study provides a comprehensive analysis of two high copy MITE families, which were specifically amplified in the B-genome, suggesting a potential role in shaping the Brassica B-genome.

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Section: Discussionsupporting

confidence: 51%

Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome

et al. 2020

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“…In contrast, the previous studies reported that five MATE subfamilies were identified in tomato [ 4 ] and C . sinensis [ 25 ], six were identified in potato [ 36 ], and seven were identified in maize [ 22 ], indicating a functional diversification among plant species in the complex plant processes. In addition, phylogenetic analysis revealed that all of the MATE family genes from Brassicaceae are closely associated with AtMATE genes within the same groups ( Figure 1 ) and exhibited similar exon–intron structures ( Figure 4 ), indicating that members within the subfamily have highly conserved and might have similar functions in the same groups [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

“…However, no systematic and comprehensive study of this family is reported among Brassicaceae species. To date, with the completion of five Brassicaceae species ( B. napus , B. oleracea , B. rapa , B. juncea , and B. nigra ) genome sequencing [ 29 , 32 , 33 , 34 , 35 , 36 ], an investigation of the MATE gene family in Brassicaceae is now feasible and can not only provide insights into the evolutionary mechanisms of hybridization (allopolyploidy) among these species, but also lay a theoretical basis for a clearer understanding of the mechanisms involved in plant stress defense.…”

Section: Introductionmentioning

confidence: 99%

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Qiao

Yang

Wan

et al. 2020

Plants

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The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.

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“…SMARTdenovo has been available since 2015 on github, but its performance not only remains comparable with current assemblers, and but also has several advantages as described. Furthermore, given its excellent performance for use on corrected long sequence reads, it continues to be widely used in for genome assembly projects today [33][34][35][36][37][38][39][40][41][42].…”

Section: Discussionmentioning

confidence: 99%

SMARTdenovo: A de novo Assembler Using Long Noisy Reads

Liu¹,

Wu²,

Li³

et al. 2020

Preprint

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Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It also has been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler— SMARTdenovo, which is an SMS assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a fast assembler that did not require highly accurate raw reads for error correction, unlike other, contemporaneous SMS assemblers. It has performed well for evaluating congeneric assemblers and has been successful for a variety of assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015, and here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

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High contiguity long read assembly ofBrassica nigraallows localization of active centromeres and provides insights into the ancestralBrassicagenome

Abstract: High contiguity long read assembly of Brassica nigra allows localization of activecentromeres and provides insights into the ancestral Brassica genome.

Cited by 11 publications

References 77 publications

Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome

Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

<strong>SMARTdenov</strong><strong>o: A <em>de novo</em> Assembler Using Long Noisy Reads</strong>

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