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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

Transcript distribution across tissues.Venn diagrams showing the number of sequences expressed specifically in each tissue or in their intersections (blue, ochre and yellow indicate leg, palp and ovary, respectively). (A) All transcripts (n = 6,696). (B) Transcripts excluding putative housekeeping or CEG genes (n = 5,390). (C) Number and percentage of transcripts encoded by housekeeping genes (n = 1,005). (D) Number and percentage of transcripts with homologs included in the CEG database (n = 789). The area of each Venn diagram section is approximately proportional to the number of transcripts (A and B), or to the particular fraction value (C and D). (E) Roman numerals used to designate the different sections.
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fig-3: Transcript distribution across tissues.Venn diagrams showing the number of sequences expressed specifically in each tissue or in their intersections (blue, ochre and yellow indicate leg, palp and ovary, respectively). (A) All transcripts (n = 6,696). (B) Transcripts excluding putative housekeeping or CEG genes (n = 5,390). (C) Number and percentage of transcripts encoded by housekeeping genes (n = 1,005). (D) Number and percentage of transcripts with homologs included in the CEG database (n = 789). The area of each Venn diagram section is approximately proportional to the number of transcripts (A and B), or to the particular fraction value (C and D). (E) Roman numerals used to designate the different sections.

Mentions: With our subtractive approach we aimed to enrich a number of tissue-specific transcripts. We detected 1,005 transcripts annotated as housekeeping genes (Table 2) and 789 transcripts with putative homology to 290 of 458 CEG members of the CEGs dataset. Out of the 789 transcripts with CEG homologs, 488 are also annotated as HK genes (Fig. S2 and Tables S3–S5). Despite the finding of about 15% of HK and CEG genes, the largest proportion of them are located at the intersection of the Venn diagram (Figs. 3C and 3D), indicating that tissue-specific transcripts should reliably represent tissue-specific functions. After excluding these likely ubiquitously expressed genes, the remaining sample (n = 5, 390 transcripts; 1,523 with GO annotation) exhibits the desired tissue-specific expression profile. In fact, the distributions of GO terms including (2,619 transcripts) or not (1,523 transcripts) HK/CEG genes are significantly different from each other (two tailed P-value < 0.018 for the most frequent GO categories within BP and MP) (Fig. 2).


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)

Transcript distribution across tissues.Venn diagrams showing the number of sequences expressed specifically in each tissue or in their intersections (blue, ochre and yellow indicate leg, palp and ovary, respectively). (A) All transcripts (n = 6,696). (B) Transcripts excluding putative housekeeping or CEG genes (n = 5,390). (C) Number and percentage of transcripts encoded by housekeeping genes (n = 1,005). (D) Number and percentage of transcripts with homologs included in the CEG database (n = 789). The area of each Venn diagram section is approximately proportional to the number of transcripts (A and B), or to the particular fraction value (C and D). (E) Roman numerals used to designate the different sections.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig-3: Transcript distribution across tissues.Venn diagrams showing the number of sequences expressed specifically in each tissue or in their intersections (blue, ochre and yellow indicate leg, palp and ovary, respectively). (A) All transcripts (n = 6,696). (B) Transcripts excluding putative housekeeping or CEG genes (n = 5,390). (C) Number and percentage of transcripts encoded by housekeeping genes (n = 1,005). (D) Number and percentage of transcripts with homologs included in the CEG database (n = 789). The area of each Venn diagram section is approximately proportional to the number of transcripts (A and B), or to the particular fraction value (C and D). (E) Roman numerals used to designate the different sections.
Mentions: With our subtractive approach we aimed to enrich a number of tissue-specific transcripts. We detected 1,005 transcripts annotated as housekeeping genes (Table 2) and 789 transcripts with putative homology to 290 of 458 CEG members of the CEGs dataset. Out of the 789 transcripts with CEG homologs, 488 are also annotated as HK genes (Fig. S2 and Tables S3–S5). Despite the finding of about 15% of HK and CEG genes, the largest proportion of them are located at the intersection of the Venn diagram (Figs. 3C and 3D), indicating that tissue-specific transcripts should reliably represent tissue-specific functions. After excluding these likely ubiquitously expressed genes, the remaining sample (n = 5, 390 transcripts; 1,523 with GO annotation) exhibits the desired tissue-specific expression profile. In fact, the distributions of GO terms including (2,619 transcripts) or not (1,523 transcripts) HK/CEG genes are significantly different from each other (two tailed P-value < 0.018 for the most frequent GO categories within BP and MP) (Fig. 2).

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