Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar )
Abstract Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly s...
Published in: | BMC Genomics |
---|---|
Main Authors: | , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BMC
2009
|
Subjects: | |
Online Access: | https://doi.org/10.1186/1471-2164-10-502 https://doaj.org/article/40777f5516fa4ed79d61b71a52405553 |
id |
ftdoajarticles:oai:doaj.org/article:40777f5516fa4ed79d61b71a52405553 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:40777f5516fa4ed79d61b71a52405553 2023-05-15T15:30:41+02:00 Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar ) Lunner Sigbjørn Andreassen Rune Høyheim Bjørn 2009-10-01T00:00:00Z https://doi.org/10.1186/1471-2164-10-502 https://doaj.org/article/40777f5516fa4ed79d61b71a52405553 EN eng BMC http://www.biomedcentral.com/1471-2164/10/502 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-10-502 1471-2164 https://doaj.org/article/40777f5516fa4ed79d61b71a52405553 BMC Genomics, Vol 10, Iss 1, p 502 (2009) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2009 ftdoajarticles https://doi.org/10.1186/1471-2164-10-502 2022-12-31T03:29:44Z Abstract Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: <ext-link ext-link-type="gen" ext-link-id="BT043497">BT043497</ext-link> - <ext-link ext-link-type="gen" ext-link-id="BT044056">BT044056</ext-link>]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We ... Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles BMC Genomics 10 1 502 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Biotechnology TP248.13-248.65 Genetics QH426-470 Lunner Sigbjørn Andreassen Rune Høyheim Bjørn Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar ) |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: <ext-link ext-link-type="gen" ext-link-id="BT043497">BT043497</ext-link> - <ext-link ext-link-type="gen" ext-link-id="BT044056">BT044056</ext-link>]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We ... |
format |
Article in Journal/Newspaper |
author |
Lunner Sigbjørn Andreassen Rune Høyheim Bjørn |
author_facet |
Lunner Sigbjørn Andreassen Rune Høyheim Bjørn |
author_sort |
Lunner Sigbjørn |
title |
Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar ) |
title_short |
Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar ) |
title_full |
Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar ) |
title_fullStr |
Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar ) |
title_full_unstemmed |
Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon ( Salmo salar ) |
title_sort |
characterization of full-length sequenced cdna inserts (flics) from atlantic salmon ( salmo salar ) |
publisher |
BMC |
publishDate |
2009 |
url |
https://doi.org/10.1186/1471-2164-10-502 https://doaj.org/article/40777f5516fa4ed79d61b71a52405553 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
BMC Genomics, Vol 10, Iss 1, p 502 (2009) |
op_relation |
http://www.biomedcentral.com/1471-2164/10/502 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-10-502 1471-2164 https://doaj.org/article/40777f5516fa4ed79d61b71a52405553 |
op_doi |
https://doi.org/10.1186/1471-2164-10-502 |
container_title |
BMC Genomics |
container_volume |
10 |
container_issue |
1 |
container_start_page |
502 |
_version_ |
1766361132247810048 |