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Astyanax_mexicanus-2.0

Organism name:
Astyanax mexicanus (Mexican tetra)
Isolate:
Rio Sabinas/Rio Valles surface cross
Sex:
female
BioSample:
SAMN02981523
BioProject:
PRJNA89115
Submitter:
Washington University School of Medince
Date:
2017/09/25
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000372685.2 (latest)
RefSeq assembly accession:
GCF_000372685.2 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
APWO02
Assembly method:
wtdbg v. 1.1.006
Genome coverage:
65x
Sequencing technology:
PacBio_RSII

IDs: 1225811 [UID] 5087688 [GenBank] 5110888 [RefSeq]

See Genome Information for Astyanax mexicanus

History (Show revision history)

Comment

Assembly Release Notes for cavefish, Astyanax mexicanus 2.0:
 Background:
 The Astyanax mexicanus DNA sample was obtained from a female fish that is a reared cross of wild-caught Astyanax mexicanus surface populations from the Rio Sabinas and the Rio Valles ... surface localities in the lab of Dr. Richard Borowsky, New York University. 
 Total assembled sequence coverage of PacBio_RSII reads was 65X using a genome size estimate of 1.3Gb. The combined sequence reads were assembled using wtdbg v1.1.006 (Ruan). This draft assembly was referred to as Astyanax mexicanus 2.0. To create a chromosomal version of the 2.0 assembly we used Chromonomer (http://catchenlab.life.illinois.edu/chromonomer/) and marker sequences associated with a SNP-based genetic linkage map (Carlson et al. 2015) to order and orient all possible scaffolds. The assembly is made up of a total of 2,416 scaffolds with an N50 scaffold length of over 35Mb (N50 contig length was 1.77Mb). The assembly spans nearly 1.34Gb.
 This work was supported by NIH grant R24 RR032658-01 to WCW, McDonnell Genome Institute at Washington University School of Medicine.
 For questions regarding this Astyanax mexicanus 2.0 assembly please contact Dr. Wesley Warren, McDonnell Genome Institute, Washington University School of Medicine (wwarren@wustl.edu). Funding for the sequence characterization of the Astyanax mexicanus genome was provided by the Office of Director, National Institutes of Health (NIH).
 Credits:
 DNA source - Dr. Nicolas Rohner, Stowers Institute for Medical Research, Kansas City, MO; Dr. Richard Borowsky, New York University, New York, NY.
 Sequencing - The McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO. 
 Sequence assembly and chromosome build - The McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.

 SNP linkage map - Joshua Gross, University of Cincinnati, Cincinnati, OH.
 BioNano map - The McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.

 Assembly Stats
 SCAFFOLDS
 COUNT 2416 
 LENGTH 1335246584 
 AVG 552668 
 N50 35377769
 LARGEST 74127438 
 (ID: CHR3_Scaffold, BASES_ONLY_LENGTH: 72042632)
 Scaffolds > 1M: 97 ( 1117144449 bp )
 Scaffolds 250K--1M: 229 ( 98692424 bp )
 Scaffolds 100K--250K: 314 ( 48158559 bp )
 Scaffolds 10K--100K: 1649 ( 70476946 bp )
 Scaffolds 5K--10K: 78 ( 580101 bp )
 Scaffolds 2K--5K: 48 ( 192239 bp )
 Scaffolds 0--2K: 1 ( 1866 bp )
 CONTIGS
 COUNT 3031 
 LENGTH 1291603821 
 AVG 426131 
 N50 1767240
 LARGEST 11197471 
 Contigs > 1M: 381 ( 896099441 bp )
 Contigs 250K--1M: 517 ( 268177590 bp )
 Contigs 100K--250K: 356 ( 55979097 bp )
 Contigs 10K--100K: 1650 ( 70573487 bp )
 Contigs 5K--10K: 78 ( 580101 bp )
 Contigs 2K--5K: 48 ( 192239 bp )
 Contigs 0--2K: 1 ( 1866 bp )

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Global statistics

Total sequence length1,335,239,194
Total ungapped length1,291,596,431
Gaps between scaffolds0
Number of scaffolds2,415
Scaffold N5035,377,769
Scaffold L5016
Number of contigs3,030
Contig N501,767,240
Contig L50198
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)2,415

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCF_000372695.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM008300.1=NC_035897.10
Chromosome 2CM008301.1=NC_035898.10
Chromosome 3CM008302.1=NC_035899.10
Chromosome 4CM008303.1=NC_035900.10
Chromosome 5CM008304.1=NC_035901.10
Chromosome 6CM008305.1=NC_035902.10
Chromosome 7CM008306.1=NC_035903.10
Chromosome 8CM008307.1=NC_035904.10
Chromosome 9CM008308.1=NC_035905.10
Chromosome 10CM008309.1=NC_035906.10
Chromosome 11CM008310.1=NC_035907.10
Chromosome 12CM008311.1=NC_035908.10
Chromosome 13CM008312.1=NC_035909.10
Chromosome 14CM008313.1=NC_035910.10
Chromosome 15CM008314.1=NC_035911.10
Chromosome 16CM008315.1=NC_035912.10
Chromosome 17CM008316.1=NC_035913.10
Chromosome 18CM008317.1=NC_035914.10
Chromosome 19CM008318.1=NC_035915.10
Chromosome 20CM008319.1=NC_035916.10
Chromosome 21CM008320.1=NC_035917.10
Chromosome 22CM008321.1=NC_035918.10
Chromosome 23CM008322.1=NC_035919.10
Chromosome 24CM008323.1=NC_035920.10
Chromosome 25CM008324.1=NC_035921.10
unplacedn/an/an/a2,390

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All1,335,239,1942,4151,291,596,43135,377,7696150
Chromosome 126,953,843125,386,26126,953,843210
Chromosome 234,292,151132,461,25134,292,151230
Chromosome 374,127,438172,042,63274,127,438510
Chromosome 425,652,880124,976,04725,652,880110
Chromosome 540,584,741138,807,48240,584,741200
Chromosome 652,532,229151,390,86452,532,229290
Chromosome 740,813,162137,919,80140,813,162360
Chromosome 827,092,187125,802,13427,092,187180
Chromosome 942,966,623141,445,50542,966,623210
Chromosome 1035,377,769135,264,57435,377,769150
Chromosome 1111,650,534111,496,69011,650,53480
Chromosome 1231,403,898130,086,85531,403,898220
Chromosome 1344,161,018143,387,48144,161,018210
Chromosome 1438,842,236137,817,66638,842,236150
Chromosome 1535,718,434133,654,80335,718,434210
Chromosome 1641,032,606139,479,94441,032,606270
Chromosome 1728,317,440126,962,74328,317,440200
Chromosome 1841,377,133139,903,96841,377,133230
Chromosome 1935,429,340134,459,21135,429,340230
Chromosome 2036,262,418135,802,79136,262,418180
Chromosome 2121,661,149119,677,69621,661,149170
Chromosome 2232,506,130132,158,37132,506,130200
Chromosome 2338,085,671135,921,06338,085,671230
Chromosome 2447,266,144145,111,23747,266,144260
Chromosome 2546,505,145145,343,72046,505,145330
unplaced404,626,8752,390394,835,641710,873530
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