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Transcriptome and genome size analysis of the Venus flytrap.

Jensen MK, Vogt JK, Bressendorff S, Seguin-Orlando A, Petersen M, Sicheritz-Pontén T, Mundy J - PLoS ONE (2015)

Bottom Line: Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities.Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb.Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT
The insectivorous Venus flytrap (Dionaea muscipula) is renowned from Darwin's studies of plant carnivory and the origins of species. To provide tools to analyze the evolution and functional genomics of D. muscipula, we sequenced a normalized cDNA library synthesized from mRNA isolated from D. muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified into functional categories. A total of 15,547 full-length cDNA sequences were identified, from which open reading frames were detected in 10,941. Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities. Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.

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PCR assembly validation.Contigs assembled from 93 bp single-end reads were validated using standard PCR. A: genomic DNA, B: First-strand cDNA synthesis with reverse transcriptase, C: First-strand cDNA synthesis without reverse transcriptase. M: 100 bp O’GeneRuler. For primer and contig sequences, see S1 Table.
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pone.0123887.g001: PCR assembly validation.Contigs assembled from 93 bp single-end reads were validated using standard PCR. A: genomic DNA, B: First-strand cDNA synthesis with reverse transcriptase, C: First-strand cDNA synthesis without reverse transcriptase. M: 100 bp O’GeneRuler. For primer and contig sequences, see S1 Table.

Mentions: To quality assess contig assemblies and validate our normalization procedure, we selected 10 contigs for PCR-based validation. These contigs were selected based on alignment annotation to putative low- and high-abundant transcript genes. Actin and ubiquitin sequences were included as high-abundant mRNA transcripts, while transcription factor sequences were included as putative low-abundant mRNA transcripts. Also, primers for validation of assembly were designed to target a range of contig sizes. Using an independent biological replicate cDNA template of D. muscipula traps and flowers, we then validated transcript assemblies of putative low- and high- abundant transcripts ranging from 247–1,366 bp (Fig 1 and S3 Table), including both. Expected amplicon sizes were obtained from all ten contigs, although no genomic amplicon was obtained for DmUCH-like (S3 Table). This confirmed that assembly using Oases was reliable, and that our normalization procedure identified transcripts with varying abundances.


Transcriptome and genome size analysis of the Venus flytrap.

Jensen MK, Vogt JK, Bressendorff S, Seguin-Orlando A, Petersen M, Sicheritz-Pontén T, Mundy J - PLoS ONE (2015)

PCR assembly validation.Contigs assembled from 93 bp single-end reads were validated using standard PCR. A: genomic DNA, B: First-strand cDNA synthesis with reverse transcriptase, C: First-strand cDNA synthesis without reverse transcriptase. M: 100 bp O’GeneRuler. For primer and contig sequences, see S1 Table.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401711&req=5

pone.0123887.g001: PCR assembly validation.Contigs assembled from 93 bp single-end reads were validated using standard PCR. A: genomic DNA, B: First-strand cDNA synthesis with reverse transcriptase, C: First-strand cDNA synthesis without reverse transcriptase. M: 100 bp O’GeneRuler. For primer and contig sequences, see S1 Table.
Mentions: To quality assess contig assemblies and validate our normalization procedure, we selected 10 contigs for PCR-based validation. These contigs were selected based on alignment annotation to putative low- and high-abundant transcript genes. Actin and ubiquitin sequences were included as high-abundant mRNA transcripts, while transcription factor sequences were included as putative low-abundant mRNA transcripts. Also, primers for validation of assembly were designed to target a range of contig sizes. Using an independent biological replicate cDNA template of D. muscipula traps and flowers, we then validated transcript assemblies of putative low- and high- abundant transcripts ranging from 247–1,366 bp (Fig 1 and S3 Table), including both. Expected amplicon sizes were obtained from all ten contigs, although no genomic amplicon was obtained for DmUCH-like (S3 Table). This confirmed that assembly using Oases was reliable, and that our normalization procedure identified transcripts with varying abundances.

Bottom Line: Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities.Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb.Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT
The insectivorous Venus flytrap (Dionaea muscipula) is renowned from Darwin's studies of plant carnivory and the origins of species. To provide tools to analyze the evolution and functional genomics of D. muscipula, we sequenced a normalized cDNA library synthesized from mRNA isolated from D. muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified into functional categories. A total of 15,547 full-length cDNA sequences were identified, from which open reading frames were detected in 10,941. Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities. Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.

Show MeSH
Related in: MedlinePlus