Sequencing and comparative analysis of the gorilla MHC genomic sequence

Wilming, Laurens G.; Coggill, Penny; Horton, Roger W.; Gilbert, James; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David J.; Beck, Stephan; Harrow, Jennifer

doi:10.1093/database/bat011

Cited by 15 publications

(16 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We identified eight putatively functional MHC IIB exon 2 variants (Sica-DAB*01-*08), and we found one putative pseudogene (Sica-DAB*09). Pseudogenes have been reported in other taxa, including birds (Hess et al 2000, Aguilar et al 2005 and mammals (Hughes 1995, Wilming et al 2013. More extensive sampling using next-generation sequencing methods is ongoing (Jaeger et al, unpublished) which may clarify this result.…”

Section: Discussionmentioning

confidence: 97%

Initial Characterization of Major Histocompatibility Complex (Mhc) Class Iib Exon 2 in an Endangered Rattlesnake, the Eastern Massasauga (Sistrurus Catenatus)

Jaeger¹,

King²,

Duvall³

2014

jnah

View full text Add to dashboard Cite

Genes of the major histocompatibility complex (MHC) play an important role in the vertebrate immune system and exhibit remarkably high levels of polymorphism, maintained by strong balancing selection. While the conservation implications of MHC variation have been explored in a variety of vertebrates, non-avian reptiles (most notably snakes) have received less attention. To address this gap and take the first steps toward more extensive population-level analyses, we cloned and sequenced MHC IIB exon 2 in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus). Based on three individuals, we found evidence of at least four putatively functional loci. These sequences exhibited relatively high levels of variation and significantly higher rates of nonsynonymous to synonymous substitutions, especially within the antigen-binding sites, indicating strong positive selection. Phylogenetic analysis revealed a pattern of trans-species polymorphism, also suggesting positive selection. These results contribute to our understanding of MHC variation in non-avian reptiles and form a basis for more studies of MHC variation in snakes of conservation concern.

show abstract

Section: Discussionmentioning

confidence: 97%

Initial Characterization of Major Histocompatibility Complex (Mhc) Class Iib Exon 2 in an Endangered Rattlesnake, the Eastern Massasauga (Sistrurus Catenatus)

Jaeger¹,

King²,

Duvall³

2014

jnah

View full text Add to dashboard Cite

show abstract

“…Broken lines indicate absence of linkage between genes; and dashed boxes indicate unknown linkage as a result of unmapped scaffolds in the saltwater crocodile and green anole. MHC gene mapping in fowl (chicken, quail, black grouse, golden pheasant, and turkey), eutherians (human, chimpanzee, gorilla, rat, mouse, dog, cat, cattle, sheep, pig, and horse), green anoles, and opossums is generated using data from Kelley et al [5] , Wang et al [31] , Ye et al [13] , Chaves et al [12] , Wilming et al [61] , Yuhki et al [92] , Gao et al [14] , Gonidez et al (manuscript in revision), and Belov et al [15] .…”

Section: Discussionmentioning

confidence: 99%

Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC

et al. 2014

View full text Add to dashboard Cite

The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2–6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

show abstract

“…In non‐human primates, chimpanzees have a single MIC gene designated MICA/B , which is a hybrid gene resulting from the fusion of MICA and MICB genes . Gorillas also have a MICA/MICB fusion gene, but this fusion is supposed to have taken place independently in the gorilla lineage . Orangutans ( Pongo abelii ) have both MICA and MICB genes.…”

Section: Comparative Genomics Of the Mic Gene Familymentioning

confidence: 99%

Comparative genomics of the NKG2D ligand gene family

Kasahara

Sutoh

2015

Immunological Reviews

View full text Add to dashboard Cite

NKG2D ligands (NKG2DLs) are a group of stress-inducible major histocompatibility complex (MHC) class I-like molecules that act as a danger signal alerting the immune system to the presence of abnormal cells. In mammals, two families of NKG2DL genes have been identified: the MIC gene family encoded in the MHC region and the ULBP gene family encoded outside the MHC region in most species. Some mammals have a third family of NKG2DL-like class I genes which we named MILL (MHC class I-like located near the leukocyte receptor complex). Despite the fact that MILL genes are more closely related to MIC genes than ULBP genes are to MIC genes, MILL molecules do not function as NKG2DLs, and their function remains unknown. With the progress of mammalian genome projects, information on the MIC, ULBP, and MILL gene families became available in many mammalian species. Here, we summarize such information and discuss the origin and evolution of the NKG2DL gene family from the viewpoint of host-pathogen coevolution.

show abstract

Sequencing and comparative analysis of the gorilla MHC genomic sequence

Cited by 15 publications

References 81 publications

Initial Characterization of Major Histocompatibility Complex (Mhc) Class Iib Exon 2 in an Endangered Rattlesnake, the Eastern Massasauga (Sistrurus Catenatus)

Initial Characterization of Major Histocompatibility Complex (Mhc) Class Iib Exon 2 in an Endangered Rattlesnake, the Eastern Massasauga (Sistrurus Catenatus)

Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC

Comparative genomics of the NKG2D ligand gene family

Contact Info

Product

Resources

About