Limits...
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 specific interpro domains across tissues.Venn diagrams showing the percentage of specific interpro domains across tissues (the different Venn sections are indicated in roman numbers). Analysis conducted excluding HK and CEG encoding genes (2,364 transcripts with Interpro annotation over 5,390). (A) Signal peptide domain. (B) Transmembrane domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4493671&req=5

fig-5: Distribution of specific interpro domains across tissues.Venn diagrams showing the percentage of specific interpro domains across tissues (the different Venn sections are indicated in roman numbers). Analysis conducted excluding HK and CEG encoding genes (2,364 transcripts with Interpro annotation over 5,390). (A) Signal peptide domain. (B) Transmembrane domain.

Mentions: As a starting point for the identification of chemosensory organs in M. calpeiana, we studied two features commonly present in the chemosensory-related proteins, the existence of a signal peptide (characteristic of soluble binding proteins such as insect and vertebrate OBP, and the NPC2, CSP, and CheA/B), and the presence of a transmembrane domain (characteristic of all chemosensory receptors, such as insect and vertebrate ORs, GRs and IRs). For that, we searched for a putative tissue-specific overrepresentation of such features in legs and palps (the candidate chemosensory structures in spiders) among the 3,353 transcripts with InterPro annotation. We found a significant over-representation of the signal peptide-encoding transcripts in legs-palps specific transcripts (Venn sections I, II and IV against the rest) (two tailed FET, P-value of 6.9 × 10−3), being especially evident for transcripts shared between palps and legs tissues (Venn section IV; two tailed FET, P-value of 9.7 × 10−7). Remarkably, the percentage of transcripts with signal peptide in section IV of the Venn diagram (transcripts expressed in both legs and palps, but not in ovary) is 27.8% (Fig. 5A), while the 40.6% of leg-specific transcripts have at least one transmembrane domain (Fig. 5B). Given that these features are not completely exclusive of chemosensory genes it is difficult to clearly assess whether these differences may reflect true differences in the chemosensory role of these tissues (see also Fig. S5).


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 specific interpro domains across tissues.Venn diagrams showing the percentage of specific interpro domains across tissues (the different Venn sections are indicated in roman numbers). Analysis conducted excluding HK and CEG encoding genes (2,364 transcripts with Interpro annotation over 5,390). (A) Signal peptide domain. (B) Transmembrane domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig-5: Distribution of specific interpro domains across tissues.Venn diagrams showing the percentage of specific interpro domains across tissues (the different Venn sections are indicated in roman numbers). Analysis conducted excluding HK and CEG encoding genes (2,364 transcripts with Interpro annotation over 5,390). (A) Signal peptide domain. (B) Transmembrane domain.
Mentions: As a starting point for the identification of chemosensory organs in M. calpeiana, we studied two features commonly present in the chemosensory-related proteins, the existence of a signal peptide (characteristic of soluble binding proteins such as insect and vertebrate OBP, and the NPC2, CSP, and CheA/B), and the presence of a transmembrane domain (characteristic of all chemosensory receptors, such as insect and vertebrate ORs, GRs and IRs). For that, we searched for a putative tissue-specific overrepresentation of such features in legs and palps (the candidate chemosensory structures in spiders) among the 3,353 transcripts with InterPro annotation. We found a significant over-representation of the signal peptide-encoding transcripts in legs-palps specific transcripts (Venn sections I, II and IV against the rest) (two tailed FET, P-value of 6.9 × 10−3), being especially evident for transcripts shared between palps and legs tissues (Venn section IV; two tailed FET, P-value of 9.7 × 10−7). Remarkably, the percentage of transcripts with signal peptide in section IV of the Venn diagram (transcripts expressed in both legs and palps, but not in ovary) is 27.8% (Fig. 5A), while the 40.6% of leg-specific transcripts have at least one transmembrane domain (Fig. 5B). Given that these features are not completely exclusive of chemosensory genes it is difficult to clearly assess whether these differences may reflect true differences in the chemosensory role of these tissues (see also Fig. S5).

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