Genome-wide synteny through highly sensitive sequence alignment: <i>Satsuma</i>

Grabherr, Manfred; Russell, Pamela J.; Meyer, Miriah; Mauceli, Evan; Alföldi, Jessica; Palma, Federica Di; Lindblad‐Toh, Kerstin

doi:10.1093/bioinformatics/btq102

Cited by 281 publications

(252 citation statements)

References 25 publications

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“…5). This rate is lower than the B2.1 and B1.9 rearrangements per million years (300 kbp resolution) in artiodactyl and primate genomes 43 , suggesting that a striking stability of the BMR chromosomal arms in evolution could compensate for a large number of chromosomal fusions and fissions observed in BMR chromosomal species and speciation.…”

Section: Resultsmentioning

confidence: 82%

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Fang¹,

Nevo²,

Han³

et al. 2014

Nat Commun

136

139

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The blind mole rat (BMR), Spalax galili, is an excellent model for studying mammalian adaptation to life underground and medical applications. The BMR spends its entire life underground, protecting itself from predators and climatic fluctuations while challenging it with multiple stressors such as darkness, hypoxia, hypercapnia, energetics and high pathonecity. Here we sequence and analyse the BMR genome and transcriptome, highlighting the possible genomic adaptive responses to the underground stressors. Our results show high rates of RNA/DNA editing, reduced chromosome rearrangements, an over-representation of short interspersed elements (SINEs) probably linked to hypoxia tolerance, degeneration of vision and progression of photoperiodic perception, tolerance to hypercapnia and hypoxia and resistance to cancer. The remarkable traits of the BMR, together with its genomic and transcriptomic information, enhance our understanding of adaptation to extreme environments and will enable the utilization of BMR models for biomedical research in the fight against cancer, stroke and cardiovascular diseases.

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Section: Resultsmentioning

confidence: 82%

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Fang¹,

Nevo²,

Han³

et al. 2014

Nat Commun

136

139

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show abstract

“…The most intuitive way to identify synteny would be to establish from selective genome alignments [35, 36], but levels of nucleotide divergence between species may make such methodologies challenging. Instead, many tools use orthologous relationships between protein-coding genes as anchors to position statistically significant local alignments.…”

Section: Introductionmentioning

confidence: 99%

“…We investigate the correlation between error rate (%) in detecting synteny and the level of assembly contiguation using five popular software packages (DAGchainer [37], i-ADHoRe [39], MCScanX [38], SynChro [40], and Satsuma [36]) on four nematodes: Caenorhabditis elegans, Caenorhabditis briggsae , Strongyloides ratti, and Strongyloides stercoralis . We also carried out and explored the effects of three scenarios associated with synteny analysis: gene ontology (GO) enrichment, reference-guided assembly scaffolding, and annotation quality.…”

Section: Introductionmentioning

confidence: 99%

Inferring synteny between genome assemblies: a systematic evaluation

2018

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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.

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“…The latter is more suitable for analyzing long sequences and searching for extended homologous fragments. Satsuma (Grabherr, 2010) is a sequence alignment program that finds sequence matches through cross-correlation implemented by fast Fourier transform (FFT).…”

Section: Related Workmentioning

confidence: 99%

A wavelet-based feature vector model for DNA clustering

Jp¹,

Ry²

2015

Genet. Mol. Res.

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ABSTRACT. DNA data are important in the bioinformatic domain. To extract useful information from the enormous collection of DNA sequences, DNA clustering is often adopted to efficiently deal with DNA data. The alignmentfree method is a very popular way of creating feature vectors from DNA sequences, which are then used to compare DNA similarities. This paper proposes a wavelet-based feature vector (WFV) model, which is also an alignment-free method. From the perspective of signal processing, a DNA sequence is a sequence of digital signals. However, most traditional alignment-free models only extract features in the time domain. The WFV model uses discrete wavelet transform to adaptively yield feature vectors with a fixed dimension based on the features in both the time and frequency domains. The level of wavelet transform is adjusted according to the length of the DNA sequence rather than a fixed manually set value. The WFV model prefers a 32-dimension feature vector, which greatly promotes system performance. We compared the WFV model with the other five alignment-free models, i.e., k-tuple, DMK, TSM, AMI, and CV, on several large-scale DNA datasets on the DNA clustering application by means of the K-means algorithm. The experimental results showed that the WFV 19163-19172 (2015) model outperformed the other models in terms of both the clustering results and the running time.

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Genome-wide synteny through highly sensitive sequence alignment: Satsuma

Abstract: Satsuma is part of the Spines software package, implemented in C++ on Linux. The latest version of Spines can be freely downloaded under the LGPL license from http://www.broadinstitute.org/science/programs/genome-biology/spines/.

Cited by 281 publications

References 25 publications

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Inferring synteny between genome assemblies: a systematic evaluation

A wavelet-based feature vector model for DNA clustering

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