A Comprehensive Collection of Chicken cDNAs

Abstract

Birds have played a central role in many biological disciplines, particularly ecology, evolution, and behavior. The chicken, as a model vertebrate, also represents an important experimental system for developmental biologists, immunologists, cell biologists, and geneticists. However, genomic resources for the chicken have lagged behind those for other model organisms, with only 1845 nonredundant full-length chicken cDNA sequences currently deposited in the EMBL databank. We describe a large-scale expressed-sequence-tag (EST) project aimed at gene discovery in chickens (http://www.chick.umist.ac.uk). In total, 339,314 ESTs have been sequenced from 64 cDNA libraries generated from 21 different embryonic and adult tissues. These were clustered and assembled into 85,486 contiguous sequences (contigs). We find that a minimum of 38% of the contigs have orthologs in other organisms and define an upper limit of 13,000 new chicken genes. The remaining contigs may include novel avian specific or rapidly evolving genes. Comparison of the contigs with known chicken genes and orthologs indicates that 30% include cDNAs that contain the start codon and 20% of the contigs represent full-length cDNA sequences. Using this dataset, we estimate that chickens have approximately 35,000 genes in total, suggesting that this number may be a characteristic feature of vertebrates.

Gene expression analysis of the hedgehog signaling cascade in the chick midbrain and spinal cord

“…Chick gene fragments for BOC were isolated by polymerase chain reaction from E6 chick ventral midbrain cDNA and subcloned into pCR-TOPO (Invitrogen). Primers were designed with Mac Vector 7.2 (Accelrys) based on sequences obtained from BLAST searches of chick expressed sequence tag and genomic databases (Boardman et al, 2002;Wong et al, 2004;Caldwell et al, 2005). The primer pair successfully used for cloning BOC cDNA was BOC-forward, 5Ј-GGAG-CAGCATTCATCTTCTACAACG-3Ј; BOC-reverse, 5Ј-TGGTCACAGGCTT-TGGTGGACTAC-3Ј.…”

Chicken genome: Current status and future opportunities

“…These arrays may be able to classify many avian species into unique clades, a notoriously difficult task (Edwards et al 2005). From the very start, ESTs and cDNA clones have been important (Boardman et al 2002;ChickEST), in particular for the prediction of chicken genes. ESTs have been used to create cDNA microarrays ) and design DNA chips (Affymetrix) for high-throughput gene expression assays.…”

“…A similar effort has started in the chicken using the large collection of sequenced chicken ESTs (Boardman et al 2002;ARK-Genomics;ChickEST). Data can be accessed at GEISHA and standard three-dimensional embryo reconstructions are under development (EMAP).…”

“…Avian genomics has its origins in genetic linkage mapping (Burt and Cheng 1998), but our knowledge of the chicken genome has been transformed in recent years, mostly through the analysis of large numbers of partial cDNA sequences (Abdrakhmanov et al 2000;Tirunagaru et al 2000;Boardman et al 2002) and culminating with the chicken genome sequence (Hillier et al 2004). These were landmark events in our understanding of avian biology, developmental biology, and the evolution of vertebrates and will facilitate applications in agriculture and medicine.…”

Identification of genes regulating sensory neuron genesis and differentiation in the avian dorsal root ganglia

“…Investigations into their function should provide considerable insight into the cellular and molecular mechanisms regulating sensory neurogenesis and differentiation in the DRG. With the completion of a draft sequence of the chicken genome in 2004, the compilation of several comprehensive EST resources, and the eventual generation of chick microarrays, combined with the ease of gene manipulation in the chick, the classic embryologic chick model system returns to the forefront of developmental biology (Swartz et al, 2001;Boardman et al, 2002;Burt and Pourquie, 2003).…”