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An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

Tørresen, Ole K., Star, Bastiaan, Jentoft, Sissel, Reinar, William B., Grove, Harald, Miller, Jason R., Walenz, Brian P., Knight, James, Ekholm, Jenny M., Peluso, Paul, Edvardsen, Rolf B., Tooming-Klunderud, Ave, Skage, Morten, Lien, Sigbjørn, Jakobsen, Kjetill S., Nederbragt, Alexander J.·2017·BMC Genomics
DOI 10.1186/s12864-016-3448-xPMC PMC5241972

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Fig. 1 Contig and scaffold N50 lengths of the different cod assemblies. gadMor2 was created by following the sequences in CA454ILM in a path through a graph created from a multiple alignment of the four original assemblies, and outputting the contig sequences from CA454PB for each alignment. NEWB454 and ALPILM were used to extend the scaffolds, see Table 1
Fig. 1 Contig and scaffold N50 lengths of the different cod assemblies. gadMor2 was created by following the sequences in CA454ILM in a path through a graph created from a multiple alignment of the four original assemblies, and outputting the contig sequences from CA454PB for each alignment. NEWB454 and ALPILM were used to extend the scaffolds, see Table 1CC BY · PubMed Central
Fig. 2 The HoxC cluster in gadMor1 and gadMor2. Blocks of dark and light blue are contig sequences, white blocks are gaps and red lines are tandem repeats. Gene models are sketched at the top of the figure. This region is a single contig in gadMor2 and 21 contigs in gadMor1. Tandem repeats are at the borders between almost all gaps and contigs in gadMor1
Fig. 2 The HoxC cluster in gadMor1 and gadMor2. Blocks of dark and light blue are contig sequences, white blocks are gaps and red lines are tandem repeats. Gene models are sketched at the top of the figure. This region is a single contig in gadMor2 and 21 contigs in gadMor1. Tandem repeats are at the borders between almost all gaps and contigs in gadMor1CC BY · PubMed Central
Fig. 3 The density of TRs and the size of the assembly for different cod assemblies. The different assemblies (black) are all similar in size, around 650 Mbp, with the exception of the much larger gadMor1, while the amount of sequence in contigs in the different assemblies (grey) differs substantially. The vertical distance between pairs of points for each assembly equals the amount of sequence in gaps
Fig. 3 The density of TRs and the size of the assembly for different cod assemblies. The different assemblies (black) are all similar in size, around 650 Mbp, with the exception of the much larger gadMor1, while the amount of sequence in contigs in the different assemblies (grey) differs substantially. The vertical distance between pairs of points for each assembly equals the amount of sequence in gapsCC BY · PubMed Central
Fig. 4 The number of tandem repeats categorized based on unit size. Only tandem repeats with unit size 1-20 bp are shown. A unit size of one indicates a mononucleotide tandem repeat, two a dinucleotide, three a trinucleotide, repeats etc. The horizontal axis denotes the unit sizes of the repeat, while the vertical axis shows the count of the particular repeat
Fig. 4 The number of tandem repeats categorized based on unit size. Only tandem repeats with unit size 1-20 bp are shown. A unit size of one indicates a mononucleotide tandem repeat, two a dinucleotide, three a trinucleotide, repeats etc. The horizontal axis denotes the unit sizes of the repeat, while the vertical axis shows the count of the particular repeatCC BY · PubMed Central
Fig. 5 The density of TRs in genome assemblies, promoters and coding regions. The assemblies shown here are from Ensembl release 81, excluding gadMor1, plus a human genome based on PacBio data, the California sea hare Aplysia californica and gadMor2 (n = 71). The panels show the density (percentage of bases) of TRs in the whole assembly, coding regions and promoter regions, respectively. The human PacBio assembly is not included in the gene and promoter analysis because it has no annotation, and the opossum is lacking for technical limitations. The species marked are Oc (Ochotona princeps, pika), Hs (Homo sapiens, human), Hs(PB) (Homo sapiens, human, PacBio based assembly), Cf (Canis familiaris, dog), Do (Dipodomys ordii, kangaroo rat), Xt (Xenopus tropicalis, frog), Pf (Poecilia formosa, Amazon molly), Dr (Danio rerio, zebrafish), Pm (Petromyzon marinus, lamprey), Sc (Saccharomyces cerevisiae, yeast), Ac (Aplysia californica, California sea hare) and Gm (Gadus morhua, Atlantic cod, gadMor2)
Fig. 5 The density of TRs in genome assemblies, promoters and coding regions. The assemblies shown here are from Ensembl release 81, excluding gadMor1, plus a human genome based on PacBio data, the California sea hare Aplysia californica and gadMor2 (n = 71). The panels show the density (percentage of bases) of TRs in the whole assembly, coding regions and promoter regions, respectively. The human PacBio assembly is not included in the gene and promoter analysis because it has no annotation, and the opossum is lacking for technical limitations. The species marked are Oc (Ochotona princeps, pika), Hs (Homo sapiens, human), Hs(PB) (Homo sapiens, human, PacBio based assembly), Cf (Canis familiaris, dog), Do (Dipodomys ordii, kangaroo rat), Xt (Xenopus tropicalis, frog), Pf (Poecilia formosa, Amazon molly), Dr (Danio rerio, zebrafish), Pm (Petromyzon marinus, lamprey), Sc (Saccharomyces cerevisiae, yeast), Ac (Aplysia californica, California sea hare) and Gm (Gadus morhua, Atlantic cod, gadMor2)CC BY · PubMed Central
Fig. 6 The intersections between contig termini and different annotated features. The percentage of contig termini (the position of the terminal nucleotides of each contig) intersecting different annotations of the genome
Fig. 6 The intersections between contig termini and different annotated features. The percentage of contig termini (the position of the terminal nucleotides of each contig) intersecting different annotations of the genomeCC BY · PubMed Central

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Metadata

Authors
Tørresen, O. K., Star, B., Jentoft, S., Reinar, W. B., Grove, H., Miller, J. R., Walenz, B. P., Knight, J., Ekholm, J. M., Peluso, P., Edvardsen, R. B., Tooming-Klunderud, A., Skage, M., Lien, S., Jakobsen, K. S., & Nederbragt, A. J.
ORCID
Nederbragt, Alexander J.
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2017-01-18
Volume
18
Issue
1
ISSN
1471-2164
DOI
10.1186/s12864-016-3448-x
PMC
PMC5241972
Cited by
137
References
8
Language
en
Funders
Norwegian Research Council (199806)

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