XENLA Genome

Genome browser

• XenBase - JGIv6
  • http://www.xenbase.org/fgb2/gbrowse/Xenopus_laevis_6_0/?source=Xenopus_laevis_6_0
• NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)
  • http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway
• NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2
  • http://xenopus.lab.nig.ac.jp/cgi-bin/gb2/gbrowse/xl_v2soap/

Genome version

In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'.

Sequences 'in public' are available at ftp://ftp.xenbase.org/pub/Genomics/JGI/

Name	Release Date	Concat. Length (bp)	N50 (bp)	Scaffolds > 10kbp	Remarks
JGIv1	2010 Dec.	2.30 Gbp	8 kbp	385,933	Internal Use Only.
JGIv5	2011 Oct.	2.84 Gbp	0.28 Mbp	16,625	Released in Xenopus PI Meeting.
JGIv6	2012 Jul.	2.75 Gbp	0.70 Mbp	8,426	Officially released in XenBase.
JGIv6a	2012 Jul.	2.75 Gbp	0.70 Mbp	8,426	Officially released in XenBase; Minor update of JGIv6.
NIGv1	2012 Nov.	2.88 Gbp	0.34 Mbp	14,260	Original name is 'xl.v1soap'; Internal Use Only.
NIGv1ap	2012 Nov.	3.27 Gbp	0.17 Mbp	39,283	Original name is 'xl.v3ap'(AllPath?); Internal Use Only.
NIGv1m	2012 Nov.	2.84 Gbp	0.28 Mbp	82,132	Original name is 'xl.v5m'; Internal Use Only.
NIGv2	2013 Feb.	2.89 Gbp	0.72 Mbp	5,394	Original name is 'xl.v2soap'; Internal Use Only.
NIGv2c	2013 Feb.	2.88 Gbp	0.71 Mbp	5,377	Original name is 'xl.v2soap,GapClosed'; Can browse at NIG gbrowser.
JGIv7a	2013 Mar.	2.72 Gbp	1.15 Mbp	5,714	JGI7;Released in public.
JGIv7b	2013 May	2.78 Gbp	3.49 Mbp	2,598	JGI7.1;Released in public. Minor updates of 7.0.

J-strain Genomic Data Summary

Whole genome shotgun sequencing, JGI/UC Berkeley, USA

J strain

• JBL_009 Illumina paired-end (225 bp insertion), 2x150: 320 M reads, 48 G bases
• JBL_010 Illumina paired-end (450 bp insertion), 2x150: 264 M reads, 40 G bases
• JBL_011 Illumina paired-end (900 bp insertion), 2x150: 424 M reads, 64 G bases
• JBL_012 Illumina mate-pair (1,500 bp insertion), 2x100: 320 M reads, 32 G bases
• JBL_013 Illumina mate-pair (4,000 bp insertion), 2x100: 328 M reads, 33 G bases

F strain

• JBL_005 Illumina paired-end, 2x100: 416 M reads, 42 G bases
• JBL_005b Illumina paired-end, 2x150: 464 M reads, 70 G bases

F/J hybrid

• JBL_007 Illumina paired-end, 2x150: 344 M reads, 52 G bases

Whole genome shotgun sequencing, NIG/U Tokyo, Japan

J strain

• Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases
• Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases
• Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases
• Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases
• Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases
• Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases

Whole genome shotgun sequencing, UT Austin, USA

• SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases

Fosmid-end sequencing, JGI/Berkeley + UW, USA

• Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases

BAC-end sequencing, NIG/U Tokyo, Japan

• Sanger sequencing
• SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)
• HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)

Fosmid-end sequencing, NIG/U Tokyo, Japan

• Sanger sequencing
• 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp).

BAC full sequencing, NIG/U Tokyo, Japan

• Sanger sequencing.
• 30 BACs (mean length 112 kb).

Fosmid shotgun sequencing, JGI/Berkeley + UW, USA

• Illumina single-end: 102 M reads, 3.5 G bases

BAC shotgun sequencing, UT Austin, USA

• One plate of CHORI-210 (96 BACs).
• SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases
• SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases

See Also

XENLA_Transcriptome, XENLA_Proteome

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