NDLI: Genomic V exons from whole genome shotgun data in reptiles

Content Provider	Springer Nature Link
Author	Olivieri, D. N. Haeften, B. Sánchez Espinel, C. Faro, J. Gambón Deza, F.
Copyright Year	2014
Abstract	Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository ( http://vgenerepertoire.org ).
Starting Page	479
Ending Page	492
Page Count	14
File Format	PDF
ISSN	00937711
Journal	Immunogenetics
Volume Number	66
Issue Number	7-8
e-ISSN	14321211
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2014-06-04
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Immunologic repertoire Reptile evolution Immunoglobulin (IG) T cell receptor (TR) Variable (V) gene Immunology Human Genetics Gene Function Cell Biology Allergology
Content Type	Text
Resource Type	Article
Subject	Genetics Immunology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

V genes in primates from whole genome sequencing data

IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST

Immunoglobulin genes of the turtles

Molecular bases of genetic diversity and evolution of the immunoglobulin heavy chain variable region (IGHV) gene locus in leporids

Genomic variation in the porcine immunoglobulin lambda variable region

Characterization of the zebrafish T cell receptor β locus

TCRJ and BCRJ gene segments contain 5′ D-segment sequences that contribute to repertoire diversity

Analysis of the reptile CD1 genes: evolutionary implications

Bimodal evolution of the killer cell Ig-like receptor (KIR) family in New World primates

Genomic V exons from whole genome shotgun data in reptiles

Similar Documents

V genes in primates from whole genome sequencing data

IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST

Immunoglobulin genes of the turtles

Molecular bases of genetic diversity and evolution of the immunoglobulin heavy chain variable region (IGHV) gene locus in leporids

Genomic variation in the porcine immunoglobulin lambda variable region

Characterization of the zebrafish T cell receptor β locus

TCRJ and BCRJ gene segments contain 5′ D-segment sequences that contribute to repertoire diversity

Analysis of the reptile CD1 genes: evolutionary implications

Bimodal evolution of the killer cell Ig-like receptor (KIR) family in New World primates

Genomic V exons from whole genome shotgun data in reptiles