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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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Related in: MedlinePlus

Contig size distribution.Transcriptome assembly contig size distribution of all contigs (left) and predicted full-length contigs (right).
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pone.0123887.g003: Contig size distribution.Transcriptome assembly contig size distribution of all contigs (left) and predicted full-length contigs (right).

Mentions: Full-length cDNAs are important resources for many applications, including reverse genetic and evolutionary studies. To search for potentially full-length cDNAs with complete open-reading frames (ORFs) in the assembled D. muscipula transcriptome, all contigs were analyzed by TargetIdentifier [22]. A total of 15,547 full-length sequences were identified from the assembly. The size distribution of full-length sequences compared to that of the total 80,806 cDNA contigs is shown in Fig 3. In contrast to the latter, full-length sequences are biased towards those > 1 kb in length. This indicates that short, full-length cDNA sequences may be underrepresented in our assembly and transcriptome data.


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)

Contig size distribution.Transcriptome assembly contig size distribution of all contigs (left) and predicted full-length contigs (right).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123887.g003: Contig size distribution.Transcriptome assembly contig size distribution of all contigs (left) and predicted full-length contigs (right).
Mentions: Full-length cDNAs are important resources for many applications, including reverse genetic and evolutionary studies. To search for potentially full-length cDNAs with complete open-reading frames (ORFs) in the assembled D. muscipula transcriptome, all contigs were analyzed by TargetIdentifier [22]. A total of 15,547 full-length sequences were identified from the assembly. The size distribution of full-length sequences compared to that of the total 80,806 cDNA contigs is shown in Fig 3. In contrast to the latter, full-length sequences are biased towards those > 1 kb in length. This indicates that short, full-length cDNA sequences may be underrepresented in our assembly and transcriptome data.

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