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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

Gene Ontology (GO) categories of the unigenes.Distribution of the GO categories assigned to the D. muscipula transcriptome. Unique transcripts (unigenes) were annotated in three categories: cellular components, molecular functions, and biological processes.
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pone.0123887.g002: Gene Ontology (GO) categories of the unigenes.Distribution of the GO categories assigned to the D. muscipula transcriptome. Unique transcripts (unigenes) were annotated in three categories: cellular components, molecular functions, and biological processes.

Mentions: Functional analysis was conducted on these 17,047 unique proteins using InterProScan (http://www.ebi.ac.uk/Tools/pfa/iprscan/) and integrated protein databases with default parameters. A total of 9,909 unique proteins were assigned to at least one gene ontology (GO) term for describing biological processes, molecular functions and cellular components. GO annotations were plotted with WEGO (http://wego.genomics.org.cn) (Fig 2). Briefly, in the cellular component division, genes related to cell parts and macromolecular complexes (2,588 (26.3%) GO:0044464 and 746 (7.6%), GO: 0032991, respectively) are highly represented. Interestingly, in contrast to other plants, D. muscipula also has genes related to a virion part (3 (0.1%), GO:0044423). For the molecular function division, a large abundance of genes are related to binding and catalytic activity (5348 (54.4%) GO:0005488 and 4847 (49.3%) GO:0003824, respectively). Also, antioxidant (56 (0.6%) GO:0016209) and electron carrier activities (184 (1.9%) GO:0009055) are represented. For the biological process division, genes involved in cellular (4,285 (43.6%), GO:0009987) and metabolic processes (5,136 (52.2%), GO: 0008152) are highly represented, including the child term of establishment of localization (733 (7.4%), GO:0051234). In contrast, genes associated with developmental and multicellular organismal processes were lowly represented (6 (0.1%), GO:0032502; and 14 (0.1%) GO:0032501, respectively) compared to full-genome annotations for Arabidopsis (15% and 15.5%, respectively). This may well reflect the limited tissues and developmental stages sampled here for D. muscipula. The complete GO annotation results are in S5 Table.


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)

Gene Ontology (GO) categories of the unigenes.Distribution of the GO categories assigned to the D. muscipula transcriptome. Unique transcripts (unigenes) were annotated in three categories: cellular components, molecular functions, and biological processes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123887.g002: Gene Ontology (GO) categories of the unigenes.Distribution of the GO categories assigned to the D. muscipula transcriptome. Unique transcripts (unigenes) were annotated in three categories: cellular components, molecular functions, and biological processes.
Mentions: Functional analysis was conducted on these 17,047 unique proteins using InterProScan (http://www.ebi.ac.uk/Tools/pfa/iprscan/) and integrated protein databases with default parameters. A total of 9,909 unique proteins were assigned to at least one gene ontology (GO) term for describing biological processes, molecular functions and cellular components. GO annotations were plotted with WEGO (http://wego.genomics.org.cn) (Fig 2). Briefly, in the cellular component division, genes related to cell parts and macromolecular complexes (2,588 (26.3%) GO:0044464 and 746 (7.6%), GO: 0032991, respectively) are highly represented. Interestingly, in contrast to other plants, D. muscipula also has genes related to a virion part (3 (0.1%), GO:0044423). For the molecular function division, a large abundance of genes are related to binding and catalytic activity (5348 (54.4%) GO:0005488 and 4847 (49.3%) GO:0003824, respectively). Also, antioxidant (56 (0.6%) GO:0016209) and electron carrier activities (184 (1.9%) GO:0009055) are represented. For the biological process division, genes involved in cellular (4,285 (43.6%), GO:0009987) and metabolic processes (5,136 (52.2%), GO: 0008152) are highly represented, including the child term of establishment of localization (733 (7.4%), GO:0051234). In contrast, genes associated with developmental and multicellular organismal processes were lowly represented (6 (0.1%), GO:0032502; and 14 (0.1%) GO:0032501, respectively) compared to full-genome annotations for Arabidopsis (15% and 15.5%, respectively). This may well reflect the limited tissues and developmental stages sampled here for D. muscipula. The complete GO annotation results are in S5 Table.

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