Temperature affects the duration of embryonic and larval periods in amphibians. Plasticity in tim... more Temperature affects the duration of embryonic and larval periods in amphibians. Plasticity in time to metamorphosis is especially important in amphibian populations of Mediterranean semi-arid zones where temperatures are high and precipitation is low, increasing the rate of pond desiccation. In order to test the influence of water temperature on the larval development and growth of the natterjack toad (Bufo calamita), we collected two spawns in a semi¿arid zone at Balaguer (Lleida, NE Iberian peninsula). Approximately 50 (+/-10) eggs (stage 14-16) were raised in the lab at different temperature conditions: 10, 15, 20, 22.5 and 25ºC with 12:12 photoperiod. The results show a lengthening of development time with decreasing temperatures and a better survival performance of B. calamita to high temperatures. However, mean size at metamorphosis was not different across treatments, thus, suggesting that this population of B. calamita requires a minimum size to complete the metamorphosis. T...
This data set contains processed results of the f<b>unctional annotation </b>of Non-r... more This data set contains processed results of the f<b>unctional annotation </b>of Non-redundant ORF unigenes to Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Protein Family databases.GO term were simplified using a generic GOSlim vocabulary (GOslim annotation of non-redundant ORF unigene sequences.xlsx). Unigenes mapped to the reference canonical pathways in the KEGG database (KEGG pathway annotation of non-redundant ORF unigene sequences.xlsx). Protein motif were assigned by Pfam database (Protein family (Pfam) assignation to non-redundant ORF unigenes.xlsx).
This dataset consists of jpg files corresponding to:FigS1. Size distribution of full trinity asse... more This dataset consists of jpg files corresponding to:FigS1. Size distribution of full trinity assembled transcripts (A) and non-redundant ORF unigenes (B)FigS2. Gene Ontology level 2 annotation of non-redundant ORF unigenes. GO annotation was simplified using the generic GOSlim vocabulary. C: Cellular component, F: Molecular function, P: Biological process.FigS3. Expression profile of muscle (red) and brain (green) non-redundant ORF unigenes. Venn diagram of muscle and brain expressed unigenes (A). Histogram distribution and box plot of Log<sub>10</sub> units of FPKM values of muscle and brain expresed unigenes (B), unigenes expressed only in muscle and unigenes expressed only in brain (C) and unigenes that were common in both tissues (D).
This data set contains procesed results derived from the SAMtools pipeline of the SNP discovery a... more This data set contains procesed results derived from the SAMtools pipeline of the SNP discovery applied to non-redundant ORF unigenes.1) SNP prediction: Variant call format file "SNP prediction to non-redundant ORF unigene sequence.vcf"2) 150bp sequence surrounding each SNP: Spreadsheet "SNP context sequence.xlsx"<br>
This data set contains processed results of the f<b>unctional annotation </b>of Non-r... more This data set contains processed results of the f<b>unctional annotation </b>of Non-redundant ORF unigenes to Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Protein Family databases.GO term were simplified using a generic GOSlim vocabulary (GOslim annotation of non-redundant ORF unigene sequences.xlsx). Unigenes mapped to the reference canonical pathways in the KEGG database (KEGG pathway annotation of non-redundant ORF unigene sequences.xlsx). Protein motif were assigned by Pfam database (Protein family (Pfam) assignation to non-redundant ORF unigenes.xlsx).
This data set contains two document files:Supplementary file1:Methodology descriptionSupplementar... more This data set contains two document files:Supplementary file1:Methodology descriptionSupplementary file2:Descriptive statistics of assembly and sequencing
Trinity predicted denovo transcripts. The FASTQ sequence reads were assembled using Trinity which... more Trinity predicted denovo transcripts. The FASTQ sequence reads were assembled using Trinity which is specifically designed for <i>de novo </i>assembly of transcriptomes. Trinity was run on the paired end sequences with the fixed default k-mer size of 25 and minimum contig length of 200. Assembly algorithm runs on three steps, Inchworm, Chrysalis and Butterfly. Inchworm first assembles overlapping sequences using a greedy extension and reports the unique portions of alternatively spliced transcripts (contigs). Chrysalis then clusters related contigs into components (i.e., compXXXX_c0) and models complexity using de Bruijn graphs for each of the clusters. Finally, Butterfly processes the graphs and reports subcomponents (i.e., compXXXX_c0_seq1, compXXXX_c0_seq2, etc.), roughly corresponding to genes that are made up of individual transcripts.
Muscle and Brain derived reads were mapped to ORF unigenes by TopHat. Tissue specific transcripto... more Muscle and Brain derived reads were mapped to ORF unigenes by TopHat. Tissue specific transcriptome expression analysis was performed by normalization of raw reads (FPKM, fragments per kilobase of exon per million fragments) obtained from both tissues, brain and muscle. Tissue expression threshold was set at FPKM≥0.5. This data set contains raw output from raw Cufflinks transcript expression analysis of brain (Raw_Cufflinks_Brain_transcript_expression.txt) and muscle (Raw_Cufflinks_Muscle_transcript_expression.txt) tissues, raw Cuffdiff transcript differential expression testing (Raw_Cuffdiff_Brain_Muscle_transcript_differential_expression_testing.txt) and procesed results of transcript differential expression testing at FDR<0.01 (Differentialy expressed non-redundant ORF unigenes at FDR<0.01.xlsx).
Skeletochronology was used to estimate age and several life history traits of the Iberian spadefo... more Skeletochronology was used to estimate age and several life history traits of the Iberian spadefoot toad (Pelobates cultripes) from a semiarid zone of the Ebro Valley (in the northeastern Iberian Peninsula). The lines of arrested growth (LAGs) were clearly visible in all cross sections of the adult phalanges, showing fast growth in the first year of life, with large adult sizes. The growth, size (SVL) and age structure varied between sexes, suggesting that the larger size of females (mean±SE=76.14±0.95 mm; males: 71.76±0.90 mm) is related to a delay in age at maturity (3 years) compared to males (2 years). In addition, females were more long-lived (6 years) than males (5 years), resulting in a similar potential reproductive life span (PRLS=3 years). A data set including life history traits from several P. cultripes populations was used to analyse demographic variation. We suggest multiple factors such as altitude, latitude, predation, and soil characteristics can explain life histor...
Variations on embryonic and larval life history traits of ectotherm organisms are strongly affect... more Variations on embryonic and larval life history traits of ectotherm organisms are strongly affected by temperature conditions. However, these effects can vary between species and populations depending on the mechanisms that act in a determinate local habitat. In the present study, we analysed the effects of temperature on several embryonic and larval traits (survival, development and growth rate until the metamorphosis) of Rana temporaria in two populations living at different altitude (1540 and 2100 m) in the Pyrenees. Five spawns from each population were distributed in a common garden experiment at different temperature treatments according to the normal temperature range that tadpoles might experience in the field and also considering a high treatment (24 °C) to test a possible effect of global warming. Like in other studies of the same species in a latitudinal gradient, the temperature effects depended on the analysed trait. Our results support the general rule that the rate of...
Temperature affects the duration of embryonic and larval periods in amphibians. Plasticity in tim... more Temperature affects the duration of embryonic and larval periods in amphibians. Plasticity in time to metamorphosis is especially important in amphibian populations of Mediterranean semi-arid zones where temperatures are high and precipitation is low, increasing the rate of pond desiccation. In order to test the influence of water temperature on the larval development and growth of the natterjack toad (Bufo calamita), we collected two spawns in a semi¿arid zone at Balaguer (Lleida, NE Iberian peninsula). Approximately 50 (+/-10) eggs (stage 14-16) were raised in the lab at different temperature conditions: 10, 15, 20, 22.5 and 25ºC with 12:12 photoperiod. The results show a lengthening of development time with decreasing temperatures and a better survival performance of B. calamita to high temperatures. However, mean size at metamorphosis was not different across treatments, thus, suggesting that this population of B. calamita requires a minimum size to complete the metamorphosis. T...
This data set contains processed results of the f<b>unctional annotation </b>of Non-r... more This data set contains processed results of the f<b>unctional annotation </b>of Non-redundant ORF unigenes to Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Protein Family databases.GO term were simplified using a generic GOSlim vocabulary (GOslim annotation of non-redundant ORF unigene sequences.xlsx). Unigenes mapped to the reference canonical pathways in the KEGG database (KEGG pathway annotation of non-redundant ORF unigene sequences.xlsx). Protein motif were assigned by Pfam database (Protein family (Pfam) assignation to non-redundant ORF unigenes.xlsx).
This dataset consists of jpg files corresponding to:FigS1. Size distribution of full trinity asse... more This dataset consists of jpg files corresponding to:FigS1. Size distribution of full trinity assembled transcripts (A) and non-redundant ORF unigenes (B)FigS2. Gene Ontology level 2 annotation of non-redundant ORF unigenes. GO annotation was simplified using the generic GOSlim vocabulary. C: Cellular component, F: Molecular function, P: Biological process.FigS3. Expression profile of muscle (red) and brain (green) non-redundant ORF unigenes. Venn diagram of muscle and brain expressed unigenes (A). Histogram distribution and box plot of Log<sub>10</sub> units of FPKM values of muscle and brain expresed unigenes (B), unigenes expressed only in muscle and unigenes expressed only in brain (C) and unigenes that were common in both tissues (D).
This data set contains procesed results derived from the SAMtools pipeline of the SNP discovery a... more This data set contains procesed results derived from the SAMtools pipeline of the SNP discovery applied to non-redundant ORF unigenes.1) SNP prediction: Variant call format file "SNP prediction to non-redundant ORF unigene sequence.vcf"2) 150bp sequence surrounding each SNP: Spreadsheet "SNP context sequence.xlsx"<br>
This data set contains processed results of the f<b>unctional annotation </b>of Non-r... more This data set contains processed results of the f<b>unctional annotation </b>of Non-redundant ORF unigenes to Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Protein Family databases.GO term were simplified using a generic GOSlim vocabulary (GOslim annotation of non-redundant ORF unigene sequences.xlsx). Unigenes mapped to the reference canonical pathways in the KEGG database (KEGG pathway annotation of non-redundant ORF unigene sequences.xlsx). Protein motif were assigned by Pfam database (Protein family (Pfam) assignation to non-redundant ORF unigenes.xlsx).
This data set contains two document files:Supplementary file1:Methodology descriptionSupplementar... more This data set contains two document files:Supplementary file1:Methodology descriptionSupplementary file2:Descriptive statistics of assembly and sequencing
Trinity predicted denovo transcripts. The FASTQ sequence reads were assembled using Trinity which... more Trinity predicted denovo transcripts. The FASTQ sequence reads were assembled using Trinity which is specifically designed for <i>de novo </i>assembly of transcriptomes. Trinity was run on the paired end sequences with the fixed default k-mer size of 25 and minimum contig length of 200. Assembly algorithm runs on three steps, Inchworm, Chrysalis and Butterfly. Inchworm first assembles overlapping sequences using a greedy extension and reports the unique portions of alternatively spliced transcripts (contigs). Chrysalis then clusters related contigs into components (i.e., compXXXX_c0) and models complexity using de Bruijn graphs for each of the clusters. Finally, Butterfly processes the graphs and reports subcomponents (i.e., compXXXX_c0_seq1, compXXXX_c0_seq2, etc.), roughly corresponding to genes that are made up of individual transcripts.
Muscle and Brain derived reads were mapped to ORF unigenes by TopHat. Tissue specific transcripto... more Muscle and Brain derived reads were mapped to ORF unigenes by TopHat. Tissue specific transcriptome expression analysis was performed by normalization of raw reads (FPKM, fragments per kilobase of exon per million fragments) obtained from both tissues, brain and muscle. Tissue expression threshold was set at FPKM≥0.5. This data set contains raw output from raw Cufflinks transcript expression analysis of brain (Raw_Cufflinks_Brain_transcript_expression.txt) and muscle (Raw_Cufflinks_Muscle_transcript_expression.txt) tissues, raw Cuffdiff transcript differential expression testing (Raw_Cuffdiff_Brain_Muscle_transcript_differential_expression_testing.txt) and procesed results of transcript differential expression testing at FDR<0.01 (Differentialy expressed non-redundant ORF unigenes at FDR<0.01.xlsx).
Skeletochronology was used to estimate age and several life history traits of the Iberian spadefo... more Skeletochronology was used to estimate age and several life history traits of the Iberian spadefoot toad (Pelobates cultripes) from a semiarid zone of the Ebro Valley (in the northeastern Iberian Peninsula). The lines of arrested growth (LAGs) were clearly visible in all cross sections of the adult phalanges, showing fast growth in the first year of life, with large adult sizes. The growth, size (SVL) and age structure varied between sexes, suggesting that the larger size of females (mean±SE=76.14±0.95 mm; males: 71.76±0.90 mm) is related to a delay in age at maturity (3 years) compared to males (2 years). In addition, females were more long-lived (6 years) than males (5 years), resulting in a similar potential reproductive life span (PRLS=3 years). A data set including life history traits from several P. cultripes populations was used to analyse demographic variation. We suggest multiple factors such as altitude, latitude, predation, and soil characteristics can explain life histor...
Variations on embryonic and larval life history traits of ectotherm organisms are strongly affect... more Variations on embryonic and larval life history traits of ectotherm organisms are strongly affected by temperature conditions. However, these effects can vary between species and populations depending on the mechanisms that act in a determinate local habitat. In the present study, we analysed the effects of temperature on several embryonic and larval traits (survival, development and growth rate until the metamorphosis) of Rana temporaria in two populations living at different altitude (1540 and 2100 m) in the Pyrenees. Five spawns from each population were distributed in a common garden experiment at different temperature treatments according to the normal temperature range that tadpoles might experience in the field and also considering a high treatment (24 °C) to test a possible effect of global warming. Like in other studies of the same species in a latitudinal gradient, the temperature effects depended on the analysed trait. Our results support the general rule that the rate of...
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