Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal
Abstract Background Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usu...
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ftbiomed:oai:biomedcentral.com:1471-2164-14-52 2023-05-15T13:42:30+02:00 Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal Hoffman, Joseph I Thorne, Michael AS Trathan, Philip N Forcada, Jaume 2013-01-24 http://www.biomedcentral.com/1471-2164/14/52 en eng BioMed Central Ltd. http://www.biomedcentral.com/1471-2164/14/52 Copyright 2013 Hoffman et al.; licensee BioMed Central Ltd. Transcriptome Genomics Non-model organism Post mortem Immune gene Major Histocompatibility Complex (MHC) Microsatellite Single Nucleotide Polymorphism (SNP) Marine mammal Antarctic fur seal Arctocephalus gazella Pinniped Research article 2013 ftbiomed 2013-02-10T01:04:31Z Abstract Background Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usually requires a 'discovery pool' of individuals to be sacrificed in order to harvest mRNA from as many different types of tissue as possible. This hinders transcriptome development in large, charismatic and endangered species, many of which stand the most to gain from such approaches. To circumvent this problem in a model pinniped species, we 454 sequenced cDNA from testis, heart, spleen, intestine, kidney and lung tissues obtained from nine adult male Antarctic fur seals ( Arctocephalus gazella ) that died of natural causes at Bird Island, South Georgia. Results After applying stringent quality control criteria based on length and annotation, we obtained 12,397 contigs which, in combination with 454 data previously obtained from skin, gave a total of 23,096 unique contigs. Homology was found to 77.0% of dog ( Canis lupus familiaris ) transcripts, suggesting that the combined assembly represents a substantial proportion of this species' transcriptome. Moreover, only 0.5% of transcripts revealed sequence similarity to bacteria, implying minimal contamination, and the percentage of transcripts involved in cell death was low at 2.6%. Transcripts with immune-related annotations were almost five-fold enriched relative to skin and represented 13.2% of all spleen-specific contigs. By reference to the dog, we also identified transcripts revealing homology to five class I, ten class II and three class III genes of the Major Histocompatibility Complex and derived the putative genomic distribution of 17,121 contigs, 2,119 in silico mined microsatellites and 9,382 single nucleotide polymorphisms. Conclusions Our findings suggest that transcriptome development based on samples collected post mortem may greatly facilitate genomic studies, not only of marine mammals but also more generally of species that are of conservation concern. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Antarctic Fur Seals Arctocephalus gazella Bird Island Canis lupus BioMed Central Antarctic Bird Island ENVELOPE(-38.060,-38.060,-54.004,-54.004) |
institution |
Open Polar |
collection |
BioMed Central |
op_collection_id |
ftbiomed |
language |
English |
topic |
Transcriptome Genomics Non-model organism Post mortem Immune gene Major Histocompatibility Complex (MHC) Microsatellite Single Nucleotide Polymorphism (SNP) Marine mammal Antarctic fur seal Arctocephalus gazella Pinniped |
spellingShingle |
Transcriptome Genomics Non-model organism Post mortem Immune gene Major Histocompatibility Complex (MHC) Microsatellite Single Nucleotide Polymorphism (SNP) Marine mammal Antarctic fur seal Arctocephalus gazella Pinniped Hoffman, Joseph I Thorne, Michael AS Trathan, Philip N Forcada, Jaume Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal |
topic_facet |
Transcriptome Genomics Non-model organism Post mortem Immune gene Major Histocompatibility Complex (MHC) Microsatellite Single Nucleotide Polymorphism (SNP) Marine mammal Antarctic fur seal Arctocephalus gazella Pinniped |
description |
Abstract Background Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usually requires a 'discovery pool' of individuals to be sacrificed in order to harvest mRNA from as many different types of tissue as possible. This hinders transcriptome development in large, charismatic and endangered species, many of which stand the most to gain from such approaches. To circumvent this problem in a model pinniped species, we 454 sequenced cDNA from testis, heart, spleen, intestine, kidney and lung tissues obtained from nine adult male Antarctic fur seals ( Arctocephalus gazella ) that died of natural causes at Bird Island, South Georgia. Results After applying stringent quality control criteria based on length and annotation, we obtained 12,397 contigs which, in combination with 454 data previously obtained from skin, gave a total of 23,096 unique contigs. Homology was found to 77.0% of dog ( Canis lupus familiaris ) transcripts, suggesting that the combined assembly represents a substantial proportion of this species' transcriptome. Moreover, only 0.5% of transcripts revealed sequence similarity to bacteria, implying minimal contamination, and the percentage of transcripts involved in cell death was low at 2.6%. Transcripts with immune-related annotations were almost five-fold enriched relative to skin and represented 13.2% of all spleen-specific contigs. By reference to the dog, we also identified transcripts revealing homology to five class I, ten class II and three class III genes of the Major Histocompatibility Complex and derived the putative genomic distribution of 17,121 contigs, 2,119 in silico mined microsatellites and 9,382 single nucleotide polymorphisms. Conclusions Our findings suggest that transcriptome development based on samples collected post mortem may greatly facilitate genomic studies, not only of marine mammals but also more generally of species that are of conservation concern. |
format |
Article in Journal/Newspaper |
author |
Hoffman, Joseph I Thorne, Michael AS Trathan, Philip N Forcada, Jaume |
author_facet |
Hoffman, Joseph I Thorne, Michael AS Trathan, Philip N Forcada, Jaume |
author_sort |
Hoffman, Joseph I |
title |
Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal |
title_short |
Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal |
title_full |
Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal |
title_fullStr |
Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal |
title_full_unstemmed |
Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal |
title_sort |
transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal |
publisher |
BioMed Central Ltd. |
publishDate |
2013 |
url |
http://www.biomedcentral.com/1471-2164/14/52 |
long_lat |
ENVELOPE(-38.060,-38.060,-54.004,-54.004) |
geographic |
Antarctic Bird Island |
geographic_facet |
Antarctic Bird Island |
genre |
Antarc* Antarctic Antarctic Fur Seal Antarctic Fur Seals Arctocephalus gazella Bird Island Canis lupus |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Antarctic Fur Seals Arctocephalus gazella Bird Island Canis lupus |
op_relation |
http://www.biomedcentral.com/1471-2164/14/52 |
op_rights |
Copyright 2013 Hoffman et al.; licensee BioMed Central Ltd. |
_version_ |
1766168606083645440 |