Taeniopygia guttata Sequence Assembly Release Notes

The zebra finch DNA for shotgun sequencing, and for BAC and cosmid
libraries, derived from a single male (Black 17) domesticated zebra
finch from the laboratory of Arthur P. Arnold in the Department of
Physiological Science at UCLA, Los Angeles, CA, USA. The parents of
this male hatched in the same clutch in an aviary of group-housed
zebra finches, and therefore may have been brother-sister.  A male BAC
library was constructed from the same bird by Barbara Blackmon at the
Clemson University Genomics Institute (this library is NOT the same as
the BAC library available from the Arizona Genome Institute) made from
several individual females. The initial assembly was generated using
PCAP (Huang et al., 2006) from ~6X coverage in whole-genome shotgun
reads, a combination of plasmid, fosmid and bacterial artificial
chromosome (BAC)-end read pairs.  The sequence of 35 finished BAC
clones were incorporated into the final assembly. The T. guttata
physical map contains 108,725 clones for a ~10X depth of coverage and
is contained in 2,724 contigs.

Of the 1.2 Gb genome, 1.0Gb was ordered and oriented along 33 zebra
finch chromosomes and 3 linkage groups.  An additional 36 Mb was
localized to specific chromosomes or linkage groups, but was not
ordered and oriented. For the initial PCAP assembly, there were 92,299
major contigs (126,053 total contigs) with an N50 contig length of
39kb (n=8,037). There were 37,252 major supercontigs (37,698 total
supercontigs) with the N50 supercontig length of 10.4Mb (n=29).

The zebra finch chromosomes were named based on their homologous
chromosomes in Gallus gallus.  For those chromosomes where multiple
zebra finch chromosomes correspond to a single chicken chromosome, a
letter was appended to the chromosome name.  The lookup table can be
found below for cross-referencing the Gallus gallus homologous names
with the current naming convention for the zebra finch.  All
unanchored supercontigs have been concatenated into chromosome
"chrUn", separated by gaps of 25 bp. On all other chromosomes, unknown
gap sizes between supercontigs have been set to 100 bp.

AGP Generation Details

To create chromosomal sequences, data from the Sheffield Linkage Map
and the physical map were integrated with the WGS assembly data. Using
sequence comparison, T. guttata SNP marker sequences were assigned to
contigs (contiguous stretches of DNA) in the WGS assembly. Based on
these marker assignments, the supercontigs (sets of ordered/oriented
contigs linked by virtue of read pairing data) were assigned to a
chromosome based on a majority rule (>50% of markers assigned to the
same chromosome). The supercontigs were initially positioned along
chromosomes based on their median marker position, and initially
oriented based on relative marker order along the supercontig.  The
physical map was also linked to the sequence assembly by using BAC end
sequence links and in silico digests of the assembly to create
"ultracontigs", ordered/oriented lists of "supercontigs". Following
these initial placements, the WGS assembly read pairing data were
used, where possible, to aid in orientation and confirm order. For the
Z chromosome, marker order was also determined by FISH (Art Arnold,
personal commuication) and integrated again with the linkage map, physical
map and assembly.  All discrepancies betwen the various maps
were manually reviewed and a combined super/ultracontig order was
established based on reconciling the data from the Sheffield, assembly 
and physical maps. Available EST data were also used in reviewing the assembly.
Alignments with the chicken genome were also examined and used as aid
in orientation particularly when available other zebra finch-specific
data were inconclusive. The location of the centromere is known only for the Z
chromosome. Thus no other centromeres were placed in the current
chromosomal assemblies.


Cross-reference of zebra finch chromosome names used for this release,
chicken and finch chromosome name suggested by Itoh et al, 2005*.

TGU	GGA	Itoh et al., 2005
Tgu1	1	3
Tgu1A	1	4
Tgu1B	1	NA
Tgu2	2	1
Tgu3	3	2
Tgu4	4	5
Tgu4A	4	microchromosome
Tgu5	5	6
Tgu6	6	7
Tgu7	7	8
Tgu8	8	9
Tgu9	9	10
Tgu10	10	NA
Tgu11	11	NA
Tgu12	12	NA
Tgu13	13	NA
Tgu14	14	NA
Tgu15	15	NA
Tgu16	16	NA
Tgu17	17	NA
Tgu18	18	NA
Tgu19	19	NA
Tgu20	20	NA
Tgu21	21	NA
Tgu22	22	NA
Tgu23	23	NA
Tgu24	24	NA
Tgu25	25	NA
Tgu26	26	NA
Tgu27	27	NA
Tgu28	28	NA
TguLGE22	LGE22C19W28_E50C23 	NA
TguLGE22A	LGE22C19W28_E50C23 	NA
Tgun2	NA	NA
Tgun5	NA	NA
TguZ	Z	Z

***********************************************************************************

Taeniopygia guttata Sequence and Assembly Credits


DNA source - Art Arnold, Department of Physiological Science, UCLA
Genome Sequence - The Genome Center, Washington University School of
Medicine Sequence Assembly and Chromosomal Sequence Construction - The
Genome Center, Washington University School of Medicine Zebra finch
linkage map - Jessica Stapley, Tim Birkhead, Terry Burke and Jon
Slate, Department of Animal & Plant Sciences, University of Sheffield,
Sheffield, UK Z Map/FISH Mapping - Itoh Yuichiro and Art Arnold,
Department of Physiological Science, UCLA Fingerprint Map - The Genome
Center, Washington University School of Medicine T. guttata Finished
Clones - The Genome Center, Washington University School of Medicine
BAC library - Barbara Blackmon, Clemson University Genomics Institute
(CUGI) Fosmid Library - The Genome Center, Washington University
School of Medicine and Lucigen Corporation, Middleton, Wisconsin Finch
EST data - David Clayton, W.M. Keck Center for Comparative and
Functional Genomics at the University of Illinois at Urbana-Champaign,
and The Genome Center, Washington University School of Medicine

Funding for the sequence characterization of the zebra finch genome is
being provided by the National Human Genome Research Institute
(NHGRI), National Institutes of Health (NIH).

The T. guttata sequence is made freely available to the community by
The Genome Center, Washington University School of Medicine, with the
following understanding: 1. The data may be freely downloaded, used in
analyses, and repackaged in databases.  2. Users are free to use the
data in scientific papers analyzing particular genes and regions from
these data if the providers of this data (The Genome Center,
Washington University School of Medicine, and the International Zebra
finch Sequencing and Analysis Consortium) are properly
acknowledged. Any whole genome analyses of this assembly should
consult The Genome Center, Washington University School of Medicine,
and the International Zebra finch Sequencing and Analysis Consortium
prior to publication.  3. Any redistribution of the data should carry
this notice.

*Itoh Y, Arnold AP (2005) Chromosomal polymorphism and comparative
painting analysis in the zebra finch.  Chromosome
Res. 2005;13(1):47-56.


*** SIMPLE READ STATS ***
Total input reads: 12988460
Total input bases: 10657162288 bp
Total Q20 bases: 8429388296 bp
Average Q20 bases per read: 649 bp
Average read length: 821 bp
Placed reads: 12657512
(reads in scaffold: 11837360)
(reads in singleton: 820152)
Unplaced reads: 330948
Chaff rate: 2.55%
Q20 base redundancy: 6.3x
Total prefin reads input: 279
Total prefin reads unused: 3


*** Contiguity: Contig ***
Total contig number: 126053
Total contig bases: 1224525252 bp
Total Q20 bases: 1197969478 bp
Q20 bases %: 97.8%
Average contig length: 9714 bp
Average major (> 2000 bp) contig length: 12768
Maximum contig length: 424635 bp
N50 contig length: 38549 bp
N50 contig number: 8037

Major contig (> 2000 bp) number: 92299
Major_contig bases: 1178496641 bp
Major_contig Q20 bases: 1155793110 bp
Major_contig Q20 base percent: 98.1%

Top tier (up to 900000000 bp):
Contig number: 21151
Average length: 42551 bp
Longest length: 424635 bp
Contig bases in this tier: 900002090 bp
Q20 bases in this tier: 887183057 bp
Q20 base percentage: 98.5%
Top tier N50 contig length: 57749 bp
Top tier N50 contig number: 4606

Middle tier (900000000 bp -- 1200000000 bp):
Contig number: 83348
Average length: 3599 bp
Longest length: 11441 bp
Contig bases in this tier: 300001510 bp
Q20 bases in this tier: 288579601 bp
Q20 base percentage: 96.1%
Middle tier N50 contig length: 3941 bp
Middle tier N50 contig number: 24235

Bottom tier (1200000000 bp -- end):
Contig number: 21554
Average length: 1138 bp
Longest length: 1528 bp
Contig bases in this tier: 24521652 bp
Q20 bases in this tier: 22206820 bp
Q20 base percentage: 90.5%
Bottom tier N50 contig length: 1228 bp
Bottom tier N50 contig number: 8904


*** Contiguity: Supercontig ***
Total supercontig number: 37698
Average supercontig length: 32482 bp
Maximum supercontig length: 56620707 bp
N50 supercontig length: 10409499 bp
N50 supercontig number: 29

Major supercontig (> 2000 bp) number: 37252
Major_supercontig bases: 1223725179 bp
Major_supercontig Q20 bases: 1197282719 bp
Major_supercontig Q20 base percent: 97.8%

Scaffolds > 1M: 132
Scaffold 250K--1M: 49
Scaffold 100K--250K: 64
Scaffold 10--100K: 3100
Scaffold 5--10K: 8699
Scaffold 2--5K: 25182
Scaffold 0--2K: 472

Top tier (up to 900000000 bp):
Supercontig number: 78
Average length: 11544469 bp
Longest length: 56620707 bp
Contig bases in this tier: 900468551 bp
Q20 bases in this tier: 884996675 bp
Q20 base percentage: 98.2%
Top tier N50 supercontig length: 16225236 bp
Top tier N50 supercontig number: 16

Middle tier (900000000 bp -- 1200000000 bp):
Supercontig number: 26792
Average length: 11197 bp
Longest length: 3213145 bp
Contig bases in this tier: 300000509 bp
Q20 bases in this tier: 290386571 bp
Q20 base percentage: 96.7%
Middle tier N50 supercontig length: 26915 bp
Middle tier N50 supercontig number: 407

Bottom tier (1200000000 bp -- end):
Supercontig number: 10828
Average length: 2222 bp
Longest length: 2551 bp
Contig bases in this tier: 24056192 bp
Q20 bases in this tier: 22586232 bp
Q20 base percentage: 93.8%
Bottom tier N50 supercontig length: 2242 bp
Bottom tier N50 supercontig number: 4940


*** Fosmid Coverage ***
Total fosmids assembled in scaffold: 702580
Total length of these reads: 646072624
Paired reads: 555942 (79.1%)
Estimated fosmid coverage (total fosmids Q20 bases over genome): 0.41%


*** BES Coverage ***
Total BES assembled in scaffold: 396722
Total length of these reads: 357829671
Paired reads: 338936 (85.4%)
Estimated BES coverage (total fosmids Q20 bases over genome): 0.41%