Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

Zhang, Lei; Cai, Xiaohua; Wu, Jian; Liu, Min; Grob, Stefan; Cheng, Feng; Liang, Jiansheng; Cai, Chengcheng; Liu, Zhiyuan; Liu, Bo; Wang, Fan; Li, Song; Liu, Fuyan; Li, Xuming; Cheng, Lin; Yang, Wencai; Li, Mai-he; Grossniklaus, Ueli; Zheng, Hongkun; Wang, Xiaowu

doi:10.1038/s41438-018-0071-9

Cited by 262 publications

(298 citation statements)

References 48 publications

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“…We have reported a highly contiguous genome assembly of B. juncea variety Varuna, an oleiferous type belonging to the Indian gene pool of mustard, using long-read SMRT sequencing and optical mapping. The B. juncea assembly reported here has given contig N50 value of >5Mb, comparable to the other recent SMRT based genome assemblies [9][10][11][12][13][14] . We found recursive optical mapping with three different labeling reactions to be highly useful for correcting mis-assemblies.…”

Section: Discussionsupporting

confidence: 83%

“…Recent genome sequencing efforts have relied exclusively on high coverage SMRT sequencing, both for the de-novo genome assemblies and for improving earlier assembled draft genomes that used the second-generation technologies [8][9][10][11][12][13] . Amongst the Brassica species -assembly of B. rapa Chiifu has been improved by additional data from ~57x SMRT sequencing, BioNano optical mapping, and Hi-C reads 14 . Highly contiguous de-novo assemblies have been generated for two new lines of B. rapa and B. oleracea by Nanopore long-read sequencing and optical mapping 15 .…”

Section: Introductionmentioning

confidence: 99%

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A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

Paritosh

Yadava

Singh

et al. 2019

Preprint

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Brassica juncea (AABB; genome size ~920 Mb), commonly referred to as mustard, is a natural allopolyploid of two diploid species -B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100x PacBio single-molecule real-time (SMRT) reads providing contigs with an N50 value of >5Mb. Assembled contigs were corrected and scaffolded with BioNano optical mapping. Three different linkage maps containing a large number of GBS markers were developed and used to anchor scaffolds/contigs to the 18 linkage groups of B. juncea. The resulting chromosome-scale assembly is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content, and gene block associations. Both A and B genomes contain highly fragmented gene block arrangements. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The genome assembly reported here will provide a fillip to the breeding work on oleiferous types of mustard that are grown extensively in the dry land areas of South Asia and elsewhere.

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Section: Discussionsupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

Paritosh

Yadava

Singh

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…Continuity and completeness are important indicators of genome assembly. PacBio-based genome assembly plus error corrections based on Illumina data could greatly improve continuity and completeness [56][57][58][59] . Our genome assembly of I. indigotica by this strategy showed a highly resolved result with an N50 = 1.22 Mb and longest contig length = 8.99 Mb.…”

Section: Discussionmentioning

confidence: 99%

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

Kang

Yang

et al. 2020

Hortic Res

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Isatis indigotica (2n = 14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients. Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant. Here, we report a high-quality chromosome-scale genome assembly of I. indigotica with a total size of 293.88 Mb and scaffold N50 = 36.16 Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques. We annotated 30,323 highconfidence protein-coding genes. Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. In addition, we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications, which likely drove the production of these major active compounds and explained why I. indigotica has excellent antibacterial and antiviral activities. Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants. Data availabilityThe PacBio long reads and Illumina short reads were uploaded to the NCBI SRA database under BioProject PRJNA549758. The final chromosome-scale genome assembly was submitted to the NCBI with accession number VHIU00000000. The genome fasta and gff3 files were uploaded to Figshare.

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“…Another weakness of commonly used homology-based annota on pipelines is that they a empt to align an en re protein or mRNA sequence with a genomic sequence, a prac ce that is very likely to miss alterna ve splicing variants or pseudogenes, informa on concerning which is crucial in evolu onary studies (Danchin et al 2018;Zhang et al 2018) . In addi on, these pipelines have trouble annota ng tandem-array duplica ons, especially when there's high similarity between the copies (Zallot et al 2016;Nobre et al 2016) .…”

Section: New Approachmentioning

confidence: 99%

Reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty

Koludarov

Suranse³

et al. 2019

Preprint

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Gene duplica on is associated with the evolu on of many novel biological func ons at the molecular level. The dominant view, o en referred to as "neofunc onaliza on", is that duplica ons precede many novel gene func ons by crea ng func onally redundant copies which are less constrained than singletons. Numerous alterna ve models have been formulated, however, including several (such as "subfunc onaliza on" and "escape from adap ve constraints") in which novel func ons emerge prior to duplica on. Unfortunately, few studies have reconstructed the evolu onary history of a func onally diverse gene family sufficiently well to differen ate between these models. In order to understand how gene families evolve and to what extent they fit par cular evolu onary models, here we examined the evolu on of the g2 family of phospholipase A2 in 92 genomes from all major lineages of Vertebrata. This family is evolu onarily important and has been co-opted for a diverse range of func ons, including innate immunity and venom. The genomic region in which this family is located is remarkably syntenic. This allowed us to reconstruct all duplica on events over hundreds of millions of years of evolu onary history using a novel method to annotate gene clusters, which overcomes many limita ons of automa c annota on. Surprisingly, we found that even at this level of resolu on our data could not be unambiguously fit to exis ng models of gene family evolu on. This suggests that each model may describe a part-truth that doesn't capture the full complexity of gene family evolu on. Graphical abstract Introduc onPerhaps the most important goal in evolu onary biology remains the explana on of the origins of novelty -how do new func ons, traits, and ul mately organisms arise? Gene duplica on is widely considered one of the most important mechanisms facilita ng the evolu on of novel func ons (Ohno 1970;Innan and Kondrashov 2010) . However, duplica on itself is o en treated as a "black box" -a form of "random" muta on -and numerous apparently contradictory models have been ar culated to explain the fates of duplicate genes (Conant and Wolfe 2008;Innan and Kondrashov 2010) . Although discussion of duplica on and redundancy arguably goes back to Darwin (who had no knowledge of genes and spoke of redundant "organs") and has a rich history in the 20th Century (Taylor and Raes 2004) , the "neofunc onaliza on" model of Susumu Ohno has loomed large in the field of molecular evolu on since the publica on of the seminal text "Evolu on by Gene Duplica on" in 1970 (Ohno 1970) . Briefly, this model describes gene duplica on (a neutral process) facilita ng the genesis of novelty by crea ng func onally redundant gene copies which, no longer constrained by the func onal role of the molecule encoded by the "parent" gene, enjoy a period of relaxed selec on in which neutral muta ons may accumulate. Any poten ally beneficial muta ons acquired during this period of neutral change may then be fixed by posi ve selec on.

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Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

Cited by 262 publications

References 48 publications

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

Reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty

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