The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates and is the primary laboratory model for approximately 9,600 extant bird species. The first construction of the chicken genome sequence appeared in March 2004, the first genome sequence of any livestock species. The sequence was primarily accomplished by whole-genome shotgun Sanger sequencing, using an extensive physical map of bacterial artificial chromosome (BAC) based read contigs to assemble sequence contigs and scaffolds and align them with known chicken chromosomes and linkage groups. Make a comparison. Many features of the chicken genome and its biology make it an ideal organism for developmental and evolutionary studies as well as agricultural and medical applications.

CD Genomics is a leading service provider for agricultural genomics research, offering reliable poultry genome sequencing services to support research and breeding efforts in the field of poultry genomics for clients worldwide. Our services contribute to the understanding of avian biology, developmental biology, and the mechanisms of vertebrate evolution and will facilitate applications in agriculture and medicine.

Our poultry genome sequencing service

CD Genomics offers comprehensive and customizable genome sequencing services for turkey and chicken. We utilize advanced next-generation sequencing and long-read sequencing technology platforms, as well as bioinformatics tools to perform whole-genome shotgun sequencing on different poultry breeds to provide reliable data support for genomic and other research on poultry genome structure, organization, and function.

Our services cover all stages of the sequencing process, from library preparation to data analysis. Strict quality control measures are adopted to ensure the accuracy and reliability of sequencing results, providing researchers with reliable poultry genome sequences. Strong competitive advantages provided by these sequences include：

• Routine resequencing of commercial and research lines.
• Determine genetic correlates of phenotypic changes (e.g. selectivity scans).
• Dramatically improve understanding of poultry diversity and linkage disequilibrium.
• Obtain high-density SNP typing and association analysis.
• Detailed transcriptomics and proteomics studies.
• Use genome-wide marker-assisted selection to enhance genetic gain in commercial stocks.

Applications of poultry genome sequencing

Our high-quality chicken genome sequences are widely used in comparative genomics, evolutionary biology and systematics, developmental and human disease modeling, and agriculture.

• Characterization of genes and non-coding elements

Our avian genome sequencing can be used to identify and characterize genes and non-coding elements within the avian genome. We help you identify genetic variation associated with specific traits, including single nucleotide polymorphisms (SNPs) and copy number variation (CNVs). These genetic variants are associated with phenotypic differences such as meat quality, egg production, disease resistance, and growth rate.

• Quantitative trait loci (QTL) analysis

Poultry genome sequences can facilitate the identification of QTL. We use SNP-generated high-density linkage and association mapping to enable precise QTL localization, helping you to better understand the genetic basis of complex traits.

• Genome-wide assisted selection (GWAS)

Our poultry genome sequencing enables GWAS by providing the necessary reference genome and SNP data, which eliminates the need to identify specific genes associated with a trait and utilizes high-density SNP profiles to directly measure breeding values.

• Transcriptomics and Proteomics

We offer technologies such as microarray and RNA-seq for transcriptome analysis to help you study gene expression patterns, selective splicing, and regulatory networks in poultry. Proteomics analysis complements transcriptomics developmental stages by providing a comprehensive view of proteins expressed in different tissues and developments.

• Comparative genomics and evolutionary studies

By comparing the genomes of different bird species, researchers can discover bird-specific conserved regions, evolutionary changes, and adaptations. The availability of avian genome sequences facilitates the identification of genetic elements responsible for unique avian traits such as feather development, flight, and vocalization.

Case study of poultry genome sequencing

Chicken is one of the most important vertebrate model organisms, and its genome is widely used in the study of vertebrate evolution and avian biology. Although karyotyping shows that the chicken genome contains 2n = 78, only 32 autosomes and two sex chromosomes (Z and W) have been assembled to date, indicating that 6 chromosomes are missing. A recent chicken pan-genome construction using PacBio reads has identified more than 1,000 novel genes enriched on minichromosomes. Creating a new reference chicken genome and assembling all chromosome models will reveal the complete gene repertoire and a complete picture of vertebrate karyotype evolution.

Researchers combined Nanopore ultralong reads and PacBio HiFi read sequencing technologies to generate the complete sequence of the chicken genome, revealing six chromosome models not present in previous genome assemblies. Unlike any other vertebrate chromosomes, the ten small microchromosomes have evolved unique genomic and epigenetic characteristics but remain stable and conserved in birds. Most chicken centromeres were found to contain higher-order repeats (HORs), similar to primate centromeric organization. A complete chicken chromosome model helps reconstruct the karyotype of vertebrate ancestors. We reveal the evolutionary trajectory of chromosomal changes from ancestral chordates to early vertebrates and amniotes through frequent fusion events before and after whole-genome duplication.

Fig. 1. A complete chicken genome with 10 dot chromosomes. (Huang et al., 2023)

CD Genomics is committed to providing reliable poultry genome sequencing services. Based on high-quality poultry genome sequences, we can unlock the secrets of poultry genetics, leading to improved breeding methods, increased productivity, and a deeper understanding of poultry biology. If you are interested, please feel free to contact us.

Reference

1. Huang, Zhen, et al. Evolutionary analysis of a complete chicken genome. Proceedings of the National Academy of Sciences. 120.8 (2023): e2216641120.