The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks.
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperm...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5516982?pdf=render |
| _version_ | 1818566583239311360 |
|---|---|
| author | Saura R Silva Danillo O Alvarenga Yani Aranguren Helen A Penha Camila C Fernandes Daniel G Pinheiro Marcos T Oliveira Todd P Michael Vitor F O Miranda Alessandro M Varani |
| author_facet | Saura R Silva Danillo O Alvarenga Yani Aranguren Helen A Penha Camila C Fernandes Daniel G Pinheiro Marcos T Oliveira Todd P Michael Vitor F O Miranda Alessandro M Varani |
| author_sort | Saura R Silva |
| collection | DOAJ |
| description | The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome. Here we report the sequencing and assembly of the complete mtDNA from the endemic terrestrial Brazilian species Utricularia reniformis. The 857,234bp master circle mitochondrial genome encodes 70 transcriptionaly active genes (42 protein-coding, 25 tRNAs and 3 rRNAs), covering up to 7% of the mtDNA. A ltrA-like protein related to splicing and mobility and a LAGLIDADG homing endonuclease have been identified in intronic regions, suggesting particular mechanisms of genome maintenance. RNA-seq analysis identified properties with putative diverse and important roles in genome regulation and evolution: 1) 672kbp (78%) of the mtDNA is covered by full-length reads; 2) most of the 243kbp intergenic regions exhibit transcripts; and 3) at least 69 novel RNA editing sites in the protein-coding genes. Additional genomic features are hypothetical ORFs (48%), chloroplast insertions, including truncated plastid genes that have been lost from the chloroplast DNA (5%), repeats (5%), relics of transposable elements mostly related to LTR retrotransposons (5%), and truncated mitovirus sequences (0.4%). Phylogenetic analysis based on 32 different Lamiales mitochondrial genomes corroborate that Lentibulariaceae is a monophyletic group. In summary, the U. reniformis mtDNA represents the eighth largest plant mtDNA described to date, shedding light on the genomic trends and evolutionary characteristics and phylogenetic history of the family Lentibulariaceae. |
| first_indexed | 2024-12-14T01:55:35Z |
| format | Article |
| id | doaj.art-4b6eb5debcc84fa2b52cbe4963215818 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T01:55:35Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-4b6eb5debcc84fa2b52cbe49632158182022-12-21T23:21:13ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01127e018048410.1371/journal.pone.0180484The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks.Saura R SilvaDanillo O AlvarengaYani ArangurenHelen A PenhaCamila C FernandesDaniel G PinheiroMarcos T OliveiraTodd P MichaelVitor F O MirandaAlessandro M VaraniThe carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome. Here we report the sequencing and assembly of the complete mtDNA from the endemic terrestrial Brazilian species Utricularia reniformis. The 857,234bp master circle mitochondrial genome encodes 70 transcriptionaly active genes (42 protein-coding, 25 tRNAs and 3 rRNAs), covering up to 7% of the mtDNA. A ltrA-like protein related to splicing and mobility and a LAGLIDADG homing endonuclease have been identified in intronic regions, suggesting particular mechanisms of genome maintenance. RNA-seq analysis identified properties with putative diverse and important roles in genome regulation and evolution: 1) 672kbp (78%) of the mtDNA is covered by full-length reads; 2) most of the 243kbp intergenic regions exhibit transcripts; and 3) at least 69 novel RNA editing sites in the protein-coding genes. Additional genomic features are hypothetical ORFs (48%), chloroplast insertions, including truncated plastid genes that have been lost from the chloroplast DNA (5%), repeats (5%), relics of transposable elements mostly related to LTR retrotransposons (5%), and truncated mitovirus sequences (0.4%). Phylogenetic analysis based on 32 different Lamiales mitochondrial genomes corroborate that Lentibulariaceae is a monophyletic group. In summary, the U. reniformis mtDNA represents the eighth largest plant mtDNA described to date, shedding light on the genomic trends and evolutionary characteristics and phylogenetic history of the family Lentibulariaceae.http://europepmc.org/articles/PMC5516982?pdf=render |
| spellingShingle | Saura R Silva Danillo O Alvarenga Yani Aranguren Helen A Penha Camila C Fernandes Daniel G Pinheiro Marcos T Oliveira Todd P Michael Vitor F O Miranda Alessandro M Varani The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. PLoS ONE |
| title | The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. |
| title_full | The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. |
| title_fullStr | The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. |
| title_full_unstemmed | The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. |
| title_short | The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. |
| title_sort | mitochondrial genome of the terrestrial carnivorous plant utricularia reniformis lentibulariaceae structure comparative analysis and evolutionary landmarks |
| url | http://europepmc.org/articles/PMC5516982?pdf=render |
| work_keys_str_mv | AT saurarsilva themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT danillooalvarenga themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT yaniaranguren themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT helenapenha themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT camilacfernandes themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT danielgpinheiro themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT marcostoliveira themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT toddpmichael themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT vitorfomiranda themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT alessandromvarani themitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT saurarsilva mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT danillooalvarenga mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT yaniaranguren mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT helenapenha mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT camilacfernandes mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT danielgpinheiro mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT marcostoliveira mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT toddpmichael mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT vitorfomiranda mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks AT alessandromvarani mitochondrialgenomeoftheterrestrialcarnivorousplantutriculariareniformislentibulariaceaestructurecomparativeanalysisandevolutionarylandmarks |