Vertebrate and Genome Annotation Project - Comparative Analysis

Comparative Analysis

In addition to full genomes, and unlike other browsers, VEGA also displays small finished regions of interest from genomes of other vertebrates, human haplotypes and mouse strains. Currently this comprises the finished sequence and annotation of the major histocompatibility complex (MHC) from different human haplotypes, and dog and pig Additionally there is mouse NOD (non-obese diabetes) strain annotation of IDD (insulin-dependent diabetes) candidate regions and two more pig regions.

Vega contains comparative pairwise analysis between specific genomic regions from either different species or from different haplotypes / strains. This is in contrast to Ensembl where many all genome versus all genome comparisons are performed. The analysis in Vega involves:

1. The identification of genomic alignments using LastZ. 2. Prediction of the orthologue pairs using the Ensembl gene tree pipeline. Note that although the pipeline generates phylogenetic genetrees, the limited scope of the Vega comparative analysis means that these will necessarily be incomplete and consequently only orthologs are shown on the website. 3. The manual identification of alleles in either different human haplotypes or mouse strains.

There are five sets of analyses:

1. The MHC region has been compared between dog, pig (two assemblies), gorilla, chimpanzee, wallaby, mouse and eight human haplotypes:

  • dog chromosome 12-MHC
  • gorilla chromosome 6-MHC
  • chimpanzee chromosome 6-MHC
  • wallaby chromosome 2-MHC
  • pig chromosome 7 on Sscrofa10.2 (24.7Mb to 29.8Mbp)
  • pig chromosome 7-MHC
  • mouse chromosome 17 (33.3Mbp to 38.9Mbp)
  • chromosome 6 on the human reference assembly (28Mbp to 34Mbp)
  • chromosome 6 MHC region in the human COX, QBL, APD, DBB, MANN, MCF and SSTO haplotypes (full length chromosome fragments)

2. Comparisons between the LRC regions of pig, gorilla and human (nine haplotypes):

  • pig chromosome 6 (53.6Mbp to 54.0Mbp)
  • gorilla chromosome 19-LRC
  • human chromosome 19q13.4 (54.6Mbp to 55.6Mbp) on the reference assembly.
  • chromosome 19 LRC region in the COX_1, COX_2, PGF_1, PGF_2, DM1A, DM1B, MC1A and MC1B haplotypes (full length chromosome fragments).
  • Insulin dependent diabetes (Idd) regions on six mouse chromosomes (1, 3, 4, 6, 11 and 17) have been compared between the CL57BL/6 reference and one or more of the DIL Non-Obese Diabetic (NOD), CHORI-29 NOD, and the 129 strains. Further details are described here

3. The regions of the CL57BL/6 reference assembly used in these comparisons are:

  • Idd3.1: chromosome 3, clones AC117584.11 to AC115749.12
  • Idd4.1: chromosome 11, clones AL596185.12 to AL663042.5
  • Idd4.2: chromosome 11, clones AL663082.5 to AL604065.7
  • Idd4.2Q: chromosome 11, clones AL596111.7 to AL645695.18
  • Idd5.1: chromosome 1, clones AL683804.15 to AL645534.20
  • Idd5.3: chromosome 1, clones AC100180.12 to AC101699.9
  • Idd5.4: chromosome 1, clones AC123760.9 to AC109283.8
  • Idd6.1 + Idd6.2: chromosome 6, clones AC164704.4 to AC164090.3
  • Idd6.3: chromosome 6, clones AC171002.2 to AC163356.2
  • Idd9.1: chromosome 4, clones AL627093.17 to AL670959.8
  • Idd9.1M: chromosome 4, clones AL611963.24 to AL669936.12
  • Idd9.2: chromosome 4, clones CR788296.8 to AL626808.28
  • Idd9.3: chromosome 4, clones AL607078.26 to AL606967.14
  • Idd10.1: chromosome 3, clones AC167172.3 to AC131184.4
  • Idd16.1: chromosome 17, clones AC125141.4 to AC167363.3
  • Idd18.1: chromosome 3, clones AL845310.4 to AL683824.8
  • Idd18.2: chromosome 3, clones AC123057.4 to AC129293.9

4. Comparisons between three specific regions:

  • pig chromosome 17 (58.2Mbp to 67.4Mbp)
  • human chromosome 20q13.13-q13.33 (45.8Mbp to 62.4Mbp)
  • mouse chromosome 2 (168.3Mbp to 179.0Mbp)

5. Pairwise comparisons between three pairs of full length mouse and human chromosomes:

  • human chromosome 1 and mouse chromosome 4
  • human chromosome 17 and mouse chromosome 11
  • human chromosome X and mouse chromosome X

Read more about this topic:  Vertebrate And Genome Annotation Project

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