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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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Genomic DNA purification and genome size estimate of D. muscipula.(A) Agarose gel showing a purified fraction of D. muscipula genomic DNA (1) using a modified CTAB procedure. M1: DNA ladder D2000 (Tiangen), M2: DNA ladder λ-Hind3 digest (Takara). (B) Genome size estimate of D. muscipula using a single-copy qPCR method with DmACT7 as amplicon. A. thaliana serves as a control, using ACTIN1 as amplicon.
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pone.0123887.g004: Genomic DNA purification and genome size estimate of D. muscipula.(A) Agarose gel showing a purified fraction of D. muscipula genomic DNA (1) using a modified CTAB procedure. M1: DNA ladder D2000 (Tiangen), M2: DNA ladder λ-Hind3 digest (Takara). (B) Genome size estimate of D. muscipula using a single-copy qPCR method with DmACT7 as amplicon. A. thaliana serves as a control, using ACTIN1 as amplicon.

Mentions: An intriguing observation from genome studies of carnivorous plants is the extreme size differences observed among individual family members [11]. To expand the list of genome size estimates of members of the carnivorous orders, we estimated the genome size of D. muscipula. Using an improved protocol adapted from Bekesiova et al. [23], we routinely obtained approx. 25 and 50 μg high quality genomic DNA (gDNA) per g fresh weight from traps and flowers, respectively (Fig 4A).


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)

Genomic DNA purification and genome size estimate of D. muscipula.(A) Agarose gel showing a purified fraction of D. muscipula genomic DNA (1) using a modified CTAB procedure. M1: DNA ladder D2000 (Tiangen), M2: DNA ladder λ-Hind3 digest (Takara). (B) Genome size estimate of D. muscipula using a single-copy qPCR method with DmACT7 as amplicon. A. thaliana serves as a control, using ACTIN1 as amplicon.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123887.g004: Genomic DNA purification and genome size estimate of D. muscipula.(A) Agarose gel showing a purified fraction of D. muscipula genomic DNA (1) using a modified CTAB procedure. M1: DNA ladder D2000 (Tiangen), M2: DNA ladder λ-Hind3 digest (Takara). (B) Genome size estimate of D. muscipula using a single-copy qPCR method with DmACT7 as amplicon. A. thaliana serves as a control, using ACTIN1 as amplicon.
Mentions: An intriguing observation from genome studies of carnivorous plants is the extreme size differences observed among individual family members [11]. To expand the list of genome size estimates of members of the carnivorous orders, we estimated the genome size of D. muscipula. Using an improved protocol adapted from Bekesiova et al. [23], we routinely obtained approx. 25 and 50 μg high quality genomic DNA (gDNA) per g fresh weight from traps and flowers, respectively (Fig 4A).

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