Genome wide survey of the Toll-like receptor family in the Mediterranean seaurchin

Research output: Contribution to conferenceOther

Abstract

Toll-like receptors (TLRs) represent a conserved family of proteins widely expressed in eukaryotes. Theyplay crucial roles in the innate immune system recognizing different pathogen-associated molecular patterns.In mammals the TLR family comprises 10-13 members, while a huge number of TLR-like genes wererecovered in S.purpuratus[1-3]. The Paracentrotus lividus genome project recently generated a new highqualityassembly of the genome that represents a valuable resource also for clarifying the evolutionary originof immune system. In order to identify TLR genes in P.lividus, a genome wide survey was carried out andBLAT searches retrieved 119 TLR genes (PlivTLRs). Ab initio gene predictions and in silico analysesallowed us to compute gene structures and define TSS, start/stop codons and PolyA sites in the retrievedsequences. Remarkably, differently from other species, several PlivTLR genes possess one or two intronsinterrupting the coding region and two different predictions were often obtained, both compatible with TLRprotein structures. To support predictions and to get functional information, we examined the availableP.lividus transcriptomes. Based on transcriptomic analysis, more than 50% of PlivTLRs resulted expressedand ~30% of genes without matching sequences probably represent pseudogenes, due to defects in TSS,coding region or PolyA signal. A molecular phylogenetic analysis aiming to classify PlivTLRs and gaininsights into TLR evolution is in processing. Comparative genome analyses confirm the massive expansionof such family in sea urchins and suggests that TLRs are likely to function as part of a fundamentallydifferent immune mechanism.1-3. Rast group (2006, 2012, 2015)
Original languageEnglish
Pages68-68
Number of pages1
Publication statusPublished - 2018

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genome
genes
prediction
Paracentrotus lividus
start codon
pseudogenes
stop codon
Toll-like receptors
transcriptomics
Echinoidea
transcriptome
immune system
eukaryotic cells
mammals
pathogens
phylogeny
proteins

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Genome wide survey of the Toll-like receptor family in the Mediterranean seaurchin. / Ragusa, Maria Antonietta; Costa, Salvatore; Nicosia, Aldo.

2018. 68-68.

Research output: Contribution to conferenceOther

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title = "Genome wide survey of the Toll-like receptor family in the Mediterranean seaurchin",
abstract = "Toll-like receptors (TLRs) represent a conserved family of proteins widely expressed in eukaryotes. Theyplay crucial roles in the innate immune system recognizing different pathogen-associated molecular patterns.In mammals the TLR family comprises 10-13 members, while a huge number of TLR-like genes wererecovered in S.purpuratus[1-3]. The Paracentrotus lividus genome project recently generated a new highqualityassembly of the genome that represents a valuable resource also for clarifying the evolutionary originof immune system. In order to identify TLR genes in P.lividus, a genome wide survey was carried out andBLAT searches retrieved 119 TLR genes (PlivTLRs). Ab initio gene predictions and in silico analysesallowed us to compute gene structures and define TSS, start/stop codons and PolyA sites in the retrievedsequences. Remarkably, differently from other species, several PlivTLR genes possess one or two intronsinterrupting the coding region and two different predictions were often obtained, both compatible with TLRprotein structures. To support predictions and to get functional information, we examined the availableP.lividus transcriptomes. Based on transcriptomic analysis, more than 50{\%} of PlivTLRs resulted expressedand ~30{\%} of genes without matching sequences probably represent pseudogenes, due to defects in TSS,coding region or PolyA signal. A molecular phylogenetic analysis aiming to classify PlivTLRs and gaininsights into TLR evolution is in processing. Comparative genome analyses confirm the massive expansionof such family in sea urchins and suggests that TLRs are likely to function as part of a fundamentallydifferent immune mechanism.1-3. Rast group (2006, 2012, 2015)",
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AU - Costa, Salvatore

AU - Nicosia, Aldo

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N2 - Toll-like receptors (TLRs) represent a conserved family of proteins widely expressed in eukaryotes. Theyplay crucial roles in the innate immune system recognizing different pathogen-associated molecular patterns.In mammals the TLR family comprises 10-13 members, while a huge number of TLR-like genes wererecovered in S.purpuratus[1-3]. The Paracentrotus lividus genome project recently generated a new highqualityassembly of the genome that represents a valuable resource also for clarifying the evolutionary originof immune system. In order to identify TLR genes in P.lividus, a genome wide survey was carried out andBLAT searches retrieved 119 TLR genes (PlivTLRs). Ab initio gene predictions and in silico analysesallowed us to compute gene structures and define TSS, start/stop codons and PolyA sites in the retrievedsequences. Remarkably, differently from other species, several PlivTLR genes possess one or two intronsinterrupting the coding region and two different predictions were often obtained, both compatible with TLRprotein structures. To support predictions and to get functional information, we examined the availableP.lividus transcriptomes. Based on transcriptomic analysis, more than 50% of PlivTLRs resulted expressedand ~30% of genes without matching sequences probably represent pseudogenes, due to defects in TSS,coding region or PolyA signal. A molecular phylogenetic analysis aiming to classify PlivTLRs and gaininsights into TLR evolution is in processing. Comparative genome analyses confirm the massive expansionof such family in sea urchins and suggests that TLRs are likely to function as part of a fundamentallydifferent immune mechanism.1-3. Rast group (2006, 2012, 2015)

AB - Toll-like receptors (TLRs) represent a conserved family of proteins widely expressed in eukaryotes. Theyplay crucial roles in the innate immune system recognizing different pathogen-associated molecular patterns.In mammals the TLR family comprises 10-13 members, while a huge number of TLR-like genes wererecovered in S.purpuratus[1-3]. The Paracentrotus lividus genome project recently generated a new highqualityassembly of the genome that represents a valuable resource also for clarifying the evolutionary originof immune system. In order to identify TLR genes in P.lividus, a genome wide survey was carried out andBLAT searches retrieved 119 TLR genes (PlivTLRs). Ab initio gene predictions and in silico analysesallowed us to compute gene structures and define TSS, start/stop codons and PolyA sites in the retrievedsequences. Remarkably, differently from other species, several PlivTLR genes possess one or two intronsinterrupting the coding region and two different predictions were often obtained, both compatible with TLRprotein structures. To support predictions and to get functional information, we examined the availableP.lividus transcriptomes. Based on transcriptomic analysis, more than 50% of PlivTLRs resulted expressedand ~30% of genes without matching sequences probably represent pseudogenes, due to defects in TSS,coding region or PolyA signal. A molecular phylogenetic analysis aiming to classify PlivTLRs and gaininsights into TLR evolution is in processing. Comparative genome analyses confirm the massive expansionof such family in sea urchins and suggests that TLRs are likely to function as part of a fundamentallydifferent immune mechanism.1-3. Rast group (2006, 2012, 2015)

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