Why is comparative genomics important

Scientists have found genes that increase muscling in cattle by twofold; they found the same genes in racing dogs, and such results may foster human performance studies. Comparisons of nearly 50 bird species' genomes revealed a gene network that underlies singing in birds and that may have an important role in human speech and language.

The bird researchers also found gene networks responsible for traits such as feathers and beaks. In recent years, researchers in the National Human Genome Research Institute NHGRI intramural program also have studied the genomics of various cancer types in dogs, including common cancers and other diseases, to try to develop new insights into the human form of the condition.

In some cases, they have mapped genes contributing to these disorders. In other studies, NHGRI researchers are comparing how genes affect body shape and size in dogs to better understand growth and development. Studies of dogs with sleep problems have revealed genes and pathways - and potential drug targets - to treat sleep problems. Researchers have sequenced the complete genomes of hundreds of animals and plants-more than animal species and 50 species of birds alone-and the list continues to grow almost daily.

In addition to the sequencing of the human genome, which was completed in , scientists involved in the Human Genome Project sequenced the genomes of a number of model organisms that are commonly used as surrogates in studying human biology. These include the rat, puffer fish, fruit fly, sea squirt, roundworm, and the bacterium Escherichia coli. Deha, P. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.

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Initial sequence of the chimpanzee genome and comparison with the human genome. Lindblad-Toh, K. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Insights into social insects from the genome of the honeybee Apis mellifera. Small, K. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol 8 , R41 Sodergren, E. The genome of the sea urchin Strongylocentrotus purpuratus.

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Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.

Nature : 82 — International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome.

The genomic basis of adaptive evolution in threespine sticklebacks. Nature : 55 — The sequence and de novo assembly of the giant panda genome. Genome sequence, comparative analysis and haplotype structure of the domestic dog. A high-resolution map of human evolutionary constraint using 29 mammals. Three periods of regulatory innovation during vertebrate evolution.

Genome Res 17 : — Human-specific loss of regulatory DNA and the evolution of human-specific traits. A high-coverage genome sequence from an archaic Denisovan individual. Nucleic Acids Res 41 : D64 — D Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.

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Genome analysis of the platypus reveals unique signatures of evolution. PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res 23 : — Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3 : e7. Evolutionary and functional analysis of celiac risk loci reveals SH2B3 as a protective factor against bacterial infection. Am J Hum Genet 86 : — This Article doi: Article Category Perspective.

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Annu Rev Genet. Chitin induces natural competence in Vibrio cholerae. Download references. The authors thank professor Brian Austin from University of Stirling for critical reading of the manuscript.

This work was supported by the National Natural Science Foundation of China through grants , , and The materials generated during the current study are available from the corresponding author on reasonable request.

You can also search for this author in PubMed Google Scholar. X-HZ designed the study, interpreted the data and thoroughly revised the manuscript. HL and MY performed the bioinformatics analysis and wrote the manuscript. XW isolated the strains and sequenced the genomic DNA and analyzed the genomic data. All authors edited and approved the final version of the manuscript. Correspondence to Xiao-Hua Zhang. Not applicable, as this study did not involve human or animal subjects, and the field sampling procedures met local guidelines.

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Table S1. General features of the 20 complete genomes of Vibrio species analyzed.

DOCX 48 kb. Table S2. General features of the 13 marine bacteria complete genomes used to compare with Vibrio. DOCX 34 kb. Figure S1. Pan and core plot of the 20 Vibrio species with complete genomes. Accumulation curves for A the number of genes in common or B total number of genes are plotted. The grey dots represent 10 different random input sequences of genomes, and the extrapolated limiting value for core genes is shown as a dashed line.

Equations which can be used to fit the curves are shown above the plot respectively. PDF kb. Figure S2. COGs classification of the specific genomes of V. Figure S3. Pan genome tree. The tree was created based on the presence or absence of gene clusters in the 20 complete Vibrio genomes. The color red and yellow are corresponding to the core genome tree, suggesting the discrepancy between core and pan genome trees.

Figure S4. Neighbor-joining phylogenetic tree of the 20 vibrios genomes based on 16S rRNA gene. Bar, 0. Figure S5. Heatmap presentation of pairwise average nucleotide identity of the 19 Vibrio species with complete genomes.

The genomes are hierarchical clustered according to the values of rows. The clusters present in blue and orange are corresponding to the core genome tree. Figure S6. Genes related to the chitin-degrading process in 20 vibrios with complete genomes.