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Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae).

Frías-López C, Almeida FC, Guirao-Rico S, Vizueta J, Sánchez-Gracia A, Arnedo MA, Rozas J - PeerJ (2015)

Bottom Line: We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes.Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs.Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain ; Departament de Biologia Animal and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain.

ABSTRACT
The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.

No MeSH data available.


Related in: MedlinePlus

Distribution of the Gene Ontology (GO) terms associated with the complete set of M. calpeiana transcripts (2,619 transcripts with GO annotations over 6,696 sequences).(A) MF, molecular function. (B) BP, Biological process. Distribution GO terms excluding transcripts encoding HK or CEG genes (1,523 transcripts with GO annotations over 5,390 sequences). (C) MF, molecular function. (D) BP, Biological process.
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fig-2: Distribution of the Gene Ontology (GO) terms associated with the complete set of M. calpeiana transcripts (2,619 transcripts with GO annotations over 6,696 sequences).(A) MF, molecular function. (B) BP, Biological process. Distribution GO terms excluding transcripts encoding HK or CEG genes (1,523 transcripts with GO annotations over 5,390 sequences). (C) MF, molecular function. (D) BP, Biological process.

Mentions: Overall, 2,619, 3,353 and 776 out of the 6,696 identified transcripts have a GO, InterPro, or KEGG associated term, respectively (Table 2); in total 4,978 of them (74.3%) have some functional annotation information. We analysed the distribution of GO terms (at GO level 2) across the 2,619 M. calpeiana transcripts sequences with GO annotation. We found that the most frequent GO terms present in this sample are “metabolic” and “cellular processes” within the biological process domain (BP), and “binding” and “catalytic activities” within molecular function domain (MF). The distribution of GO terms in the complete data set (2,619 GO terms; Fig. 2) and in the data set excluding singleton sequences (1,734 GO terms; Fig. S1) is not significantly different (two tailed FET, P-value = 0.592 and 0.757 for BP and MF, respectively). Hence, we used the complete dataset for further functional annotation analyses.


Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae).

Frías-López C, Almeida FC, Guirao-Rico S, Vizueta J, Sánchez-Gracia A, Arnedo MA, Rozas J - PeerJ (2015)

Distribution of the Gene Ontology (GO) terms associated with the complete set of M. calpeiana transcripts (2,619 transcripts with GO annotations over 6,696 sequences).(A) MF, molecular function. (B) BP, Biological process. Distribution GO terms excluding transcripts encoding HK or CEG genes (1,523 transcripts with GO annotations over 5,390 sequences). (C) MF, molecular function. (D) BP, Biological process.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493671&req=5

fig-2: Distribution of the Gene Ontology (GO) terms associated with the complete set of M. calpeiana transcripts (2,619 transcripts with GO annotations over 6,696 sequences).(A) MF, molecular function. (B) BP, Biological process. Distribution GO terms excluding transcripts encoding HK or CEG genes (1,523 transcripts with GO annotations over 5,390 sequences). (C) MF, molecular function. (D) BP, Biological process.
Mentions: Overall, 2,619, 3,353 and 776 out of the 6,696 identified transcripts have a GO, InterPro, or KEGG associated term, respectively (Table 2); in total 4,978 of them (74.3%) have some functional annotation information. We analysed the distribution of GO terms (at GO level 2) across the 2,619 M. calpeiana transcripts sequences with GO annotation. We found that the most frequent GO terms present in this sample are “metabolic” and “cellular processes” within the biological process domain (BP), and “binding” and “catalytic activities” within molecular function domain (MF). The distribution of GO terms in the complete data set (2,619 GO terms; Fig. 2) and in the data set excluding singleton sequences (1,734 GO terms; Fig. S1) is not significantly different (two tailed FET, P-value = 0.592 and 0.757 for BP and MF, respectively). Hence, we used the complete dataset for further functional annotation analyses.

Bottom Line: We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes.Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs.Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain ; Departament de Biologia Animal and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain.

ABSTRACT
The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance.

No MeSH data available.


Related in: MedlinePlus