Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

Tamazian, Gaik; Dobrynin, Pavel; Krasheninnikova, Ksenia; Komissarov, Aleksey; Koepfli, Klaus‐Peter; O’Brien, Stephen J.

doi:10.1186/s13742-016-0141-6

Cited by 66 publications

(73 citation statements)

References 23 publications

(25 reference statements)

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“…In order to facilitate comparisons between varieties, Chromosomer v 0.1.4a was used to align available contigs and scaffolds to the Zhongzhi13 reference genome and build chromosome‐level assemblies for the four sesame varieties (Baizhima, Mishuozhima,Yuzhi11 and Swetha) (Tamazian et al ., ). After reference‐assisted scaffolding, the original scaffold N50 sizes for the four sesame varieties were improved from Kb level (ranging from 47.354 Kb for Baizhima to 324.9 Kb for Yuzhi11) to Mb level (ranging from 16.33 Mb for Baizhima to 23.86 Mb for Swetha).…”

Section: Resultsmentioning

confidence: 97%

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Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

Golicz

et al. 2018

Plant Biotechnology Journal

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Summary Sesame ( Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces ( S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars ( S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference‐assisted assembly approach to improve the draft assemblies of four of the sesame varieties. We then constructed a sesame pan‐genome of 554.05 Mb. The pan‐genome contained 26 472 orthologous gene clusters; 15 409 (58.21%) of them were core (present across all five sesame genomes), whereas the remaining 41.79% (11 063) clusters and the 15 890 variety‐specific genes were dispensable. Comparisons between varieties suggest that modern cultivars from China and India display significant genomic variation. The gene families unique to the sesame modern cultivars contain genes mainly related to yield and quality, while those unique to the landraces contain genes involved in environmental adaptation. Comparative evolutionary analysis indicates that several genes involved in plant‐pathogen interaction and lipid metabolism are under positive selection, which may be associated with sesame environmental adaption and selection for high seed oil content. This study of the sesame pan‐genome provides insights into the evolution and genomic characteristics of this important oilseed and constitutes a resource for further sesame crop improvement.

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Section: Resultsmentioning

confidence: 97%

“…Chromosomer v 0.1.4a (Tamazian et al ., ) was used to construct chromosome‐level assemblies of S. indicum var. Yuzhi11, S. indicum var.…”

Section: Methodsmentioning

confidence: 99%

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

Golicz

et al. 2018

Plant Biotechnology Journal

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“…RACA produces, at best, subchromosomesized predicted chromosome fragments (PCFs) that require further verification and subsequent chromosome assembly. It is worth mentioning that, unlike RACA, other reference-assisted assembly algorithms, e.g., Ragout (Kolmogorov et al 2014) or Chromosomer (Tamazian et al 2016), do not use the target genome short-and long-range paired-read data to verify synteny breaks in/between scaffolds, meaning that the target species-specific rearrangements could be missed from the reconstructed PCFs/pseudochromosomes, making the reconstructed target chromosome structures more heavily biased to the reference genome(s) than when using RACA. RACA algorithm applied to the Tibetan antelope and blind mole rat genomes significantly improved continuities of these assemblies, but they still contain more than one large PCF for most chromosomes (Kim et al 2013;Fang et al 2014).…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

et al. 2016

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Most recent initiatives to sequence and assemble new species' genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE "deserts." This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.

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“…Furthermore, although reference-assisted assembly approaches may mask true genomic rearrangements (Liu et al 2018a), high-quality chromosome-level genomes of very close relatives can be used to improve draft assemblies, often employing alignment-based comparisons such as assisted assembly tools (Gnerre et al 2009), reference-assisted chromosome assembly (Kim et al 2013), CHROMOSOMER (Tamazian et al 2016), the Reference-based Genome Assembly and Annotation Tool (Liu et al 2018b), or the RAGOUT 2 reference-assisted assembly tool (Kolmogorov et al 2018). What role then is there for comparative genomics approaches that use evolutionary signals to predict scaffold adjacencies in draft assemblies?…”

Section: Discussionmentioning

confidence: 99%

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Waterhouse

Aganezov

Anselmetti

et al. 2018

Preprint

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Background: New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from 'finished'. Updating multiscaffold drafts to chromosome-level status can be achieved through experimental mapping or resequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results:We employed three gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.Conclusions: Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our comparisons show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

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Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

Cited by 66 publications

References 23 publications

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

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