In this report, key features and limitations of the draft chicken genome …

• Abstract
• Chicken genome
• New tools for genome analysis
• Applications of the chicken genome sequence
• Conclusions
• References
• Tables

Biology Articles » Genetics » Genomics » Chicken genome: Current status and future opportunities » Tables

Tables

- Chicken genome: Current status and future opportunities

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Table 1. General characteristics of macro- and microchromosomes

Feature	Macrochromosomes	Microchromosomes	Reference
Cytogenetic band type	G-band	R-band	Ponce de Leon et al. 1992
Gene density (per Mb)	9.0 to 15.4	13.8 to 41.2	Hillier et al. 2004
Intron length (bp)	4066 to 5742	1867 to 4128	Hillier et al. 2004
Exon length (bp)	164 to 171	157 to 172	Hillier et al. 2004
Intergenic gap length (kb)	18 to 31	8 to 24	Hillier et al. 2004
Intron length/exon length	24.6 to 34.6	11.7 to 23.2	Hillier et al. 2004
%G + C content	38.4 to 40.1	40.9 to 50.1	Hillier et al. 2004
CpG island density (per Mb)	29 to 49	73 to 266	Hillier et al. 2004
LINEs (%)	6.0 to 11.9	2.5 to 10.0	Hillier et al. 2004
SINEs (%)	~ none	~ none	Hillier et al. 2004
Synonymous rate	0.090 to 0.125	0.111 to 0.156	Axelsson et al. 2005
Nonsynonymous rate	0.011 to 0.021	0.007 to 0.016	Axelsson et al. 2005
Ka/Ks ratio	0.128 to 0.360	0.066 to 0.177	Axelsson et al. 2005
GC3%	49 to 53	56 to 65	Hillier et al. 2004
DNA replication	late	early	Ponce de Leon et al. 1992
Recombination rate (cM/Mb)	2.5 to 3.2	2.5 to 17.1	Hillier et al. 2004

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Table 2. Frequency and class of gene/protein predictions (Ensembl, June 2004)

Gene family	Number	Function
tRNA	280	Transfer RNA, adaptor in translation
5S rRNA	12	Ribosomal RNA, component of ribosome
5.8S RNAa	~145	Ribosomal RNA, component of ribosome
18S rRNAa	~145	Ribosomal RNA, component of ribosome
28S rRNAa	~145	Ribosomal RNA, component of ribosome
snRNP U1	18	Major spliceosome
snRNP U2	6	Major spliceosome
snRNP U4	4	Major spliceosome
snRNP U5	9	Major and minor spliceosomes
snRNP U6	15	Major spliceosome
snRNP U4atac	1	Minor spliceosome
snRNP U6atac	4	Minor spliceosome
snRNP U11	1	Minor spliceosome
snRNP U12	1	Minor spliceosome
miRNA	121	Translation repression
snoRNA	83	Small nucleolar RNA, takes part in processing of rRNA
RNaseP	1	Ribozyme, processes tRNA
snRNP U7	1	3'-end processing of replication-dependent histone pre-mRNAs
SRP	3	RNA component of signal recognition particle
7SK	4	Binds P-TEFb, which activates transcription by phosphorylating C-terminal domain of RNA Pol II. This process is negatively regulated by the 7SK RNP.
Y RNA	2	Component of the Ro RNP, in association with Ro60 and La, function of Ro RNP not known.
Telomerase RNA	1	Provides the template for telomeric DNA addition
BIC	1	Cooperates with c-myc in B lymphomagenesis and erythroleukemogenesis
Total RNA genes	571 (1441 incl. rRNA genes)
Total pseudogenes	75
Total protein coding genes	17,709

^a Ribosomal DNA 40-kb repeat (18S, 5.8S, 28S); Muscarella et al. (1985)

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Table 3. Online resources for avian genomics

Web site	Description
http://bacpac.chori.org/	BPRC: BAC resources center.
http://chick.umist.ac.uk/	ChickEST: BBSRC chicken EST database.
http://chicken.genomics.org.cn/index.jsp	ChickVD: chicken variation database.
http://geisha.biosci.arizona.edu/	GEISHA: Gallus gallus EST and in situ hybridization analysis.
http://genex.hgu.mrc.ac.uk/intro.html	EMAP: Edinburgh mouse atlas project.
http://genome.ucsc.edu/cgi-bin/hgGateway	UCSC genome browser.
http://genomeold.wustl.edu/	WASHU: Washington University genome sequencing center.
http://www.affymetrix.com/	Affymetrix.
http://www.animalsciences.nl/ChickFPC/	ChickFPC: Chicken FPC BAC map.
http://www.ark-genomics.org/	ARK-Genomics: Center for functional genomics in farm animals.
http://www.chicken-genome.org/	AvianNET: the avian genome information network.
http://www.crbtrader.com/fund/articles/eggs.asp	CRB: commodity research bureau.
http://www.ensembl.org/Gallus_gallus/index.html	Ensembl genome browser.
http://www.fas.usda.gov/currwmt.asp	FAS: USDA foreign agricultural service.
http://www.gmod.org/	GMOD: Generic Model Organism Database.
http://www.nature.com/nature/focus/avianflu/index.html	Avian flu: Web Focus.
http://www.ncbi.nlm.nih.gov/genome/guide/chicken/	NCBI genome browser.
http://www.thearkdb.org/browser?species=chicken	ARKdb: genetic mapping databases.
http://acedb.asg.wur.nl/	ChickACE: Wageningen Animal Sciences Group ACEbrowser.

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Source: Genome Research 15:1692-1698, 2005