ALLMAPS: robust scaffold ordering based on multiple maps

Tang, Haibao; Zhang, Xingtan; Miao, Chenyong; Zhang, Jisen; Ming, Ray; Schnable, James C.; Schnable, Patrick S.; Lyons, Eric; Lü, Jianguo

doi:10.1186/s13059-014-0573-1

Cited by 380 publications

(337 citation statements)

References 42 publications

Supporting

Mentioning

322

Contrasting

Unclassified

Order By: Relevance

“…ALLMAPS 43 was used to construct the initial pseudo-chromosomes of B. juncea from scaffolds using the genetic map (T84/DTC) constructed in the present study being integrated with a published genetic map (SY/PM) 23 . We sorted BjuA and BjuB subgenomes of B. juncea referred to the final genetic map (Supplementary Table 9).…”

Section: Competing Financial Interestsmentioning

confidence: 99%

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

View full text Add to dashboard Cite

2 2 5The Brassica genus contains a diverse range of oilseed and vegetable crops important for human nutrition 1 . Crops of particular agricultural importance include three diploid species, Brassica rapa (AA), Brassica nigra (BB) and Brassica oleracea (CC), and three allopolyploid species, B. napus (AACC), B. juncea (AABB) and Brassica carinata (BBCC). The evolutionary relationships among these Brassica species are described by what is called the 'triangle of U' model 2 , which proposes how the genomes of the three ancestral Brassica species, B. rapa, B. nigra and Brassica oleracae, combined to give rise to the allopolyploid species of this genus. B. juncea formed by hybridization between the diploid ancestors of B. rapa and B. nigra, followed by spontaneous chromosome doubling. Subsequent diversifying selection then gave rise to the vegetable-and oil-use subvarieties of B. juncea. These subvarieties include vegetable and oilseed mustard in China, oilseed crops in India, canola crops in Canada and Australia, and condiment crops in Europe and other regions 3 . Cultivation of B. juncea began in China about 6,000 to 7,000 years ago 4 , and flourished in India from 2,300 BC onward 5 .The genomes of B. rapa, B. oleracea and their allopolyploid offspring B. napus have been published recently [6][7][8] , and are often used to explain genome evolution in angiosperms [6][7][8] . The genomes of all Brassica species underwent a lineage-specific whole-genome triplication 6,7,9 , followed by diploidization that involved substantial genome reshuffling and gene losses 6,10-13 . In general, plant genomes are typically repetitive, polyploid and heterozygous, which complicates genome assembly 14 . The short read lengths of next-generation sequencing hinder assembly through complex regions, and fragmented draft and reference genomes usually lack skewed (G+C)-content sequences and repetitive intergenic sequences. Furthermore, in allopolyploid species, homoeolog expression dominance or bias, and specifically differential homoelog gene expression, has often been detected, for instance in Gossypium [15][16][17] Triticum 18,19 and Arabidopsis 20,21 , but the role of this phenomenon in selection for phenotypic traits remains mechanistically mysterious 22 .We reported here the draft genomes of an allopolyploid, B. juncea var. tumida, constructed by de novo assembly using shotgun reads, single-molecule long reads (PacBio sequencing), genomic (optical) mapping (BioNano sequencing) and genetic mapping, serving to resolve complicated allopolyploid genomes. The multiuse allopolyploid B. juncea genome offers a distinctive model to study the underlying genomic basis for selection in breeding improvement. These findings place this work into the broader context of plant breeding, highlighting The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-m...

show abstract

Section: Competing Financial Interestsmentioning

confidence: 99%

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Although assembly quality plays an important role in synteny analysis, it has been demonstrated that poor assembly contiguity of one species can be scaffolded by establishing synteny with a more contiguous assembly of a closely related species [42, 51–53]. However, we hypothesized that the true synteny relationship between two species may be incorrectly inferred when an assembly of one species is scaffolded based on another closely related species, by assuming the two genomes are syntenic.…”

Section: Resultsmentioning

confidence: 98%

“…However, we hypothesized that the true synteny relationship between two species may be incorrectly inferred when an assembly of one species is scaffolded based on another closely related species, by assuming the two genomes are syntenic. To investigate this, ALLMAPS [53] was used to order and orient sequences of 100 kb fragmented C. briggsae based on C. elegans as well as 100 kb fragmented S. stercoralis assembly based on S. ratti . ALLMAPS reduced the number of sequences in both fragmented assemblies impressively, increasing the N50 from 100 kb to 19 Mb and 15 Mb in C. briggsae and S. stercoralis, respectively (Additional file 8: Table S3).…”

Section: Resultsmentioning

confidence: 99%

Inferring synteny between genome assemblies: a systematic evaluation

2018

View full text Add to dashboard Cite

BackgroundGenome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis.ResultsWe fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous.ConclusionsOur results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2026-4) contains supplementary material, which is available to authorized users.

show abstract

“…Additionally, they present software called Stitch that automatically parses and interprets the output from a comparison between a consensus map and a reference genome to super scaffold a sequence assembly [51]. Another piece of software, ALLMAPS, performs a similar computational task as Stitch to link map data with draft genome sequence assemblies, although it is not written specifically for genome map data [52].…”

Section: Algorithms and Resourcesmentioning

confidence: 99%