plotsr: visualizing structural similarities and rearrangements between multiple genomes

Goel, Manish; Schneeberger, Korbinian

doi:10.1093/bioinformatics/btac196

Cited by 141 publications

(97 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The resulting alignments were processed with SyRI v1.5.4 [ 100 , 101 ] to identify syntenic regions and structural rearrangements. The syntenic regions and structural rearrangements for the four chelonian genomes were visualized with plotsr v0.5.3 [ 102 , 103 ]. Among genomes, we found 1.5 to 1.6 Gbp of syntenic regions and 15.3 to 54.6 Mbp of rearrangements corresponding to 89–94% and 0.8–3% of the compared genome portions, respectively.…”

Section: Data Descriptionmentioning

confidence: 99%

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Çilingir

A'Bear²,

Hansen

et al. 2022

GigaScience

View full text Add to dashboard Cite

Background The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is listed as Vulnerable on the International Union for Conservation of Nature Red List (v2.3) due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts for both wild and ex situpopulations. A high-quality genome would also open avenues to investigate the genetic basis of the species’ exceptionally long life span. Findings We produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture. We produced a 2.37-Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNA sequencing–assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. To assess the utility of the high-quality assembly for species conservation, we performed a low-coverage resequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. We further identified putatively deleterious mutations to be monitored. Conclusions We establish a high-quality chromosome-level reference genome for A. gigantea and one of the most complete turtle genomes available. We show that low-coverage whole-genome resequencing, for which alignment to the reference genome is a necessity, is a powerful tool to assess the population structure of the wild population and reveal the geographic origins of ex situ individuals relevant for genetic diversity management and rewilding efforts.

show abstract

Section: Data Descriptionmentioning

confidence: 99%

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Çilingir

A'Bear²,

Hansen

et al. 2022

GigaScience

View full text Add to dashboard Cite

show abstract

“…Structural variations were identified using SyRI (Goel et al ., 2019) from the alignment of each pair of individual genomes and visualized using PlotSR (Goel et al ., 2022) (Figure 4). The visualization shows a relatively large number of structural rearrangements between the seven cowpea genomes, which are more abundant in the centromeric and pericentromeric regions of all chromosomes.…”

Section: Resultsmentioning

confidence: 99%

“…Structural variants including inversions and translocations were identified from the alignment files using SyRI (Goel et al ., 2019). Figures were produced using PlotSR (Goel et al ., 2022). Depth analyses were carried out using Mosdepth (Pedersen & Quinlan 2018).…”

Section: Methodsmentioning

confidence: 99%

A view of the pan-genome of domesticated cowpea (Vigna unguiculata[L.] Walp.)

Liang

Muñoz‐Amatriaín

Shu

et al. 2022

Preprint

View full text Add to dashboard Cite

Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America and East/Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six sub-populations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. A total of 44,861 genes were identified in the resulting pan-genome, including 21,330 core and 23,531 non-core genes. Therefore, the total number of genes in the domesticated cowpea pan-genome is more than double the number of genes in any of the individual genomes. GO-Terms associated with response to stress, defense response in particular, were highly enriched among the non-core genes, while core genes were significantly enriched in terms associated with catabolic processes, transport and cellular homeostasis, among others. Over 5 million SNPs relative to each individual assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs and Vu04 had the most structural variants of all sizes. While similar numbers of synonymous SNPs and in-frame indels were found in core and non-core genes, non-core genes had much higher numbers of missense, stop gain, and frameshift mutations. These results suggest that non-core genes make a large contribution to diversity within domesticated cowpeas, and may be particularly important in terms of the contribution of large-effect variants.

show abstract

“…A detailed view of an inversion between Han1 (top, in blue color) and CHM13 (bottom, in orange color), spanning the region from approximately 7.5Mbp to 11.5Mbp on the chromosome 8. Figure created with Plotsr (Goel and Schneeberger 2022)…”

Section: Resultsmentioning

confidence: 99%

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

Chao

Zimin

Pertea

et al. 2022

Preprint

View full text Add to dashboard Cite

We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. We organized the sequence into chromosomes and filled in gaps using the recently completed CHM13 genome as a guide, yielding a gap-free genome, Han1, containing 3,099,707,698 bases. Using the CHM13 annotation as a reference, we mapped all genes onto the Han1 genome and identified additional gene copies, generating a total of 60,708 genes, of which 20,003 are protein coding. A comprehensive comparison between the genes revealed that 235 protein-coding genes were substantially different between the individuals, with frameshifts or truncations affecting the protein-coding sequence. Most of these were heterozygous variants in which one gene copy was unaffected. This represents the first gene-level comparison between two finished, annotated individual human genomes.

show abstract

plotsr: visualizing structural similarities and rearrangements between multiple genomes

Cited by 141 publications

References 24 publications

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

A view of the pan-genome of domesticated cowpea (Vigna unguiculata[L.] Walp.)

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

Contact Info

Product

Resources

About