Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

<p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p< Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Wincker Patrick [verfasserIn] Da Silva Corinne [verfasserIn] Casavant Thomas [verfasserIn] Scheetz Todd [verfasserIn] Bafna Vineet [verfasserIn] Soares Marcelo B [verfasserIn] Edsall Lee [verfasserIn] Gaasterland Terry [verfasserIn] Macagno Eduardo R [verfasserIn] Tasiemski Aurélie [verfasserIn] Salzet Michel [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2010

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 11(2010), 1, p 407
Übergeordnetes Werk:	volume:11 ; year:2010 ; number:1, p 407

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2164-11-407

Katalog-ID:	DOAJ058753788

Internformat


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allfields	10.1186/1471-2164-11-407 doi (DE-627)DOAJ058753788 (DE-599)DOAJ3b06eaf906854fe8976c5bbf7defebfb DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Wincker Patrick verfasserin aut Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p< Biotechnology Genetics Da Silva Corinne verfasserin aut Casavant Thomas verfasserin aut Scheetz Todd verfasserin aut Bafna Vineet verfasserin aut Soares Marcelo B verfasserin aut Edsall Lee verfasserin aut Gaasterland Terry verfasserin aut Macagno Eduardo R verfasserin aut Tasiemski Aurélie verfasserin aut Salzet Michel verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 407 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 407 https://doi.org/10.1186/1471-2164-11-407 kostenfrei https://doaj.org/article/3b06eaf906854fe8976c5bbf7defebfb kostenfrei http://www.biomedcentral.com/1471-2164/11/407 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 407
spelling	10.1186/1471-2164-11-407 doi (DE-627)DOAJ058753788 (DE-599)DOAJ3b06eaf906854fe8976c5bbf7defebfb DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Wincker Patrick verfasserin aut Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p< Biotechnology Genetics Da Silva Corinne verfasserin aut Casavant Thomas verfasserin aut Scheetz Todd verfasserin aut Bafna Vineet verfasserin aut Soares Marcelo B verfasserin aut Edsall Lee verfasserin aut Gaasterland Terry verfasserin aut Macagno Eduardo R verfasserin aut Tasiemski Aurélie verfasserin aut Salzet Michel verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 407 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 407 https://doi.org/10.1186/1471-2164-11-407 kostenfrei https://doaj.org/article/3b06eaf906854fe8976c5bbf7defebfb kostenfrei http://www.biomedcentral.com/1471-2164/11/407 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 407
allfields_unstemmed	10.1186/1471-2164-11-407 doi (DE-627)DOAJ058753788 (DE-599)DOAJ3b06eaf906854fe8976c5bbf7defebfb DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Wincker Patrick verfasserin aut Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p< Biotechnology Genetics Da Silva Corinne verfasserin aut Casavant Thomas verfasserin aut Scheetz Todd verfasserin aut Bafna Vineet verfasserin aut Soares Marcelo B verfasserin aut Edsall Lee verfasserin aut Gaasterland Terry verfasserin aut Macagno Eduardo R verfasserin aut Tasiemski Aurélie verfasserin aut Salzet Michel verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 407 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 407 https://doi.org/10.1186/1471-2164-11-407 kostenfrei https://doaj.org/article/3b06eaf906854fe8976c5bbf7defebfb kostenfrei http://www.biomedcentral.com/1471-2164/11/407 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 407
allfieldsGer	10.1186/1471-2164-11-407 doi (DE-627)DOAJ058753788 (DE-599)DOAJ3b06eaf906854fe8976c5bbf7defebfb DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Wincker Patrick verfasserin aut Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p< Biotechnology Genetics Da Silva Corinne verfasserin aut Casavant Thomas verfasserin aut Scheetz Todd verfasserin aut Bafna Vineet verfasserin aut Soares Marcelo B verfasserin aut Edsall Lee verfasserin aut Gaasterland Terry verfasserin aut Macagno Eduardo R verfasserin aut Tasiemski Aurélie verfasserin aut Salzet Michel verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 407 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 407 https://doi.org/10.1186/1471-2164-11-407 kostenfrei https://doaj.org/article/3b06eaf906854fe8976c5bbf7defebfb kostenfrei http://www.biomedcentral.com/1471-2164/11/407 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 407
allfieldsSound	10.1186/1471-2164-11-407 doi (DE-627)DOAJ058753788 (DE-599)DOAJ3b06eaf906854fe8976c5bbf7defebfb DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Wincker Patrick verfasserin aut Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p< Biotechnology Genetics Da Silva Corinne verfasserin aut Casavant Thomas verfasserin aut Scheetz Todd verfasserin aut Bafna Vineet verfasserin aut Soares Marcelo B verfasserin aut Edsall Lee verfasserin aut Gaasterland Terry verfasserin aut Macagno Eduardo R verfasserin aut Tasiemski Aurélie verfasserin aut Salzet Michel verfasserin aut In BMC Genomics BMC, 2003 11(2010), 1, p 407 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:11 year:2010 number:1, p 407 https://doi.org/10.1186/1471-2164-11-407 kostenfrei https://doaj.org/article/3b06eaf906854fe8976c5bbf7defebfb kostenfrei http://www.biomedcentral.com/1471-2164/11/407 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1, p 407
language	English
source	In BMC Genomics 11(2010), 1, p 407 volume:11 year:2010 number:1, p 407
sourceStr	In BMC Genomics 11(2010), 1, p 407 volume:11 year:2010 number:1, p 407
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Biotechnology Genetics
isfreeaccess_bool	true
container_title	BMC Genomics
authorswithroles_txt_mv	Wincker Patrick @@aut@@ Da Silva Corinne @@aut@@ Casavant Thomas @@aut@@ Scheetz Todd @@aut@@ Bafna Vineet @@aut@@ Soares Marcelo B @@aut@@ Edsall Lee @@aut@@ Gaasterland Terry @@aut@@ Macagno Eduardo R @@aut@@ Tasiemski Aurélie @@aut@@ Salzet Michel @@aut@@
publishDateDaySort_date	2010-01-01T00:00:00Z
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To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p<</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Biotechnology</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Genetics</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Da Silva Corinne</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Casavant Thomas</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Scheetz Todd</subfield><subfield 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author	Wincker Patrick
spellingShingle	Wincker Patrick misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
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topic_title	TP248.13-248.65 QH426-470 Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
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title	Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
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title_full	Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
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author_browse	Wincker Patrick Da Silva Corinne Casavant Thomas Scheetz Todd Bafna Vineet Soares Marcelo B Edsall Lee Gaasterland Terry Macagno Eduardo R Tasiemski Aurélie Salzet Michel
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title_sort	construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
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title_auth	Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
abstract	<p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<The medicinal leech, <it<Hirudo medicinalis</it<, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the <it<Hirudo </it<transcriptome that is available to the scientific community.</p< <p<Results</p< <p<A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p<
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title_short	Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
url	https://doi.org/10.1186/1471-2164-11-407 https://doaj.org/article/3b06eaf906854fe8976c5bbf7defebfb http://www.biomedcentral.com/1471-2164/11/407 https://doaj.org/toc/1471-2164
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The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.</p< <p<Conclusions</p< <p<The sequences obtained for <it<Hirudo </it<transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of <it<Helobdella robusta</it<, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with <it<Capitella capitata </it<(a polychaete) and 56% with <it<Aplysia californica </it<(a mollusk), as well as 58% with <it<Schistosoma mansoni </it<(a platyhelminth). Phylogenetic comparisons of putative <it<Hirudo </it<innate immune response genes present within the <it<Hirudo </it<transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.</p<</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Biotechnology</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Genetics</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Da Silva Corinne</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Casavant Thomas</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Scheetz Todd</subfield><subfield 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Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes

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