Supporting data for "The genome of common long-arm octopus Octopus minor"

Dataset type: Genomic, Transcriptomic
Data released on September 17, 2018

Kim B; Kang S; Ahn D; Jung S; Rhee H; Yoo JS; Lee J; Lee S; Han Y; Ryu K; Cho S; Park H; An HS (2018): Supporting data for "The genome of common long-arm octopus Octopus minor" GigaScience Database. http://dx.doi.org/10.5524/100503

DOI10.5524/100503

The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioural repertoire to diverse environmental conditions makes the species a promising model to understand genomic adaptation and evolution in cephalopods.
The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using PacBio RS II platform. We identified 30,010 genes and 44.43% of the genome is composed of repeat elements. The genome-widw phylogenetic tree indicated the divergence time between O. minor and O. bimaculoides was estimated to be 43 million years ago (Mya) based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the bilaterian species.
We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.

Additional details

Read the peer-reviewed publication(s):

Kim, B.-M., Kang, S., Ahn, D.-H., Jung, S.-H., Rhee, H., Yoo, J. S., … An, H. S. (2018). The genome of common long-arm octopus Octopus minor. GigaScience. doi:10.1093/gigascience/giy119

Accessions (data generated as part of this study):

BioProject: PRJNA421033





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN08131172515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from the yolk of Callstoctopus min...
Common name:long arm octopus
Tissue:yolk [UBERON:2000084]
...
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SAMN08131173515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from the embryo of Callstoctopus m...
Common name:long arm octopus
Tissue:embryo [UBERON:0000922]
...
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SAMN08131174515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from stage 10 of Callstoctopus min...
Common name:long arm octopus
Tissue:embryo [UBERON:0000922]
...
+
SAMN08131175515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from stage 12 of Callstoctopus min...
Common name:long arm octopus
Tissue:embryo [UBERON:0000922]
...
+
SAMN08131176515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from stage 14 of Callstoctopus min...
Common name:long arm octopus
Tissue:embryo [UBERON:0000922]
...
+
SAMN08131177515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from stage 16 of Callstoctopus min...
Common name:long arm octopus
Tissue:embryo [UBERON:0000922]
...
+
SAMN08131178515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from stage 18 of Callstoctopus min...
Common name:long arm octopus
Tissue:embryo [UBERON:0000922
...
+
SAMN08131179515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from the arms of Callstoctopus min...
Common name:long arm octopus
Tissue:arm [CEPH:0000015]
...
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SAMN08131180515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from the brain of Callstoctopus mi...
Common name:long arm octopus
Tissue:brain [UBERON:0000955]
...
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SAMN08131181515824Korean common octopus long arm octopusCallistoctopus minor Description:RNA from the branchial heart of Callst...
Common name:long arm octopus
Tissue:heart [UBERON:0000948]
...
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Displaying 1-10 of 27 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
textTEXT47.18 KB2018-09-04
textTEXT0.65 KB2018-09-04
textTEXT0.64 KB2018-09-04
ScriptTEXT0.29 KB2018-09-19
alignmentzip1.73 MB2018-09-12
BLASTTEXT2.47 MB2018-09-04
Genome sequenceFASTA1.29 GB2018-09-04
annotationUNKNOWN4.8 GB2018-09-04
protein sequenceFASTA5.06 MB2018-09-04
Repeat sequenceUNKNOWN6.08 GB2018-09-04
Displaying 1-10 of 15 File(s).
Funding body Awardee Award ID Comments
MABIK 2018M00900
Date Action
October 4, 2018 Manuscript Link added : 10.1093/gigascience/giy119
September 17, 2018 Dataset publish
September 17, 2018 Link updated : BioProject:PRJNA421033
September 17, 2018 Link updated : BioProject:PRJNA421033
November 29, 2018 File chimera_removal.sh updated