Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae
Background Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Pl...
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PeerJ Inc.
2019-10-01
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| author | Eugeny V. Gruzdev Vitaly V. Kadnikov Alexey V. Beletsky Andrey V. Mardanov Nikolai V. Ravin |
| author_facet | Eugeny V. Gruzdev Vitaly V. Kadnikov Alexey V. Beletsky Andrey V. Mardanov Nikolai V. Ravin |
| author_sort | Eugeny V. Gruzdev |
| collection | DOAJ |
| description | Background Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Plants from the family Orobanchaceae are used as models for studying plastid genome evolution in the transition from an autotrophic to parasitic lifestyle. Diphelypaea is a poorly studied genus of the Orobanchaceae, comprising two species of non-photosynthetic root holoparasites. In this study, we sequenced the plastid genome of Diphelypaea coccinea and compared it with other Orobanchaceae, to elucidate patterns of plastid genome evolution. In addition, we used plastid genome data to define the phylogenetic position of Diphelypaea spp. Methods The complete nucleotide sequence of the plastid genome of D. coccinea was obtained from total plant DNA, using pyrosequencing technology. Results The D. coccinea plastome is only 66,616 bp in length, and is highly rearranged; however, it retains a quadripartite structure. It contains only four rRNA genes, 25 tRNA genes and 25 protein-coding genes, being one of the most highly reduced plastomes among the parasitic Orobanchaceae. All genes related to photosynthesis, including the ATP synthase genes, had been lost, whereas most housekeeping genes remain intact. The plastome contains two divergent, but probably intact clpP genes. Intron loss had occurred in some protein-coding and tRNA genes. Phylogenetic analysis yielded a fully resolved tree for the Orobanchaceae, with Diphelypaea being a sister group to Orobanche sect. Orobanche. |
| first_indexed | 2024-03-09T07:28:16Z |
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| language | English |
| last_indexed | 2024-03-09T07:28:16Z |
| publishDate | 2019-10-01 |
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| spelling | doaj.art-727f6a6d33b448f49afd12678982ebdc2023-12-03T06:49:15ZengPeerJ Inc.PeerJ2167-83592019-10-017e783010.7717/peerj.7830Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family OrobanchaceaeEugeny V. Gruzdev0Vitaly V. Kadnikov1Alexey V. Beletsky2Andrey V. Mardanov3Nikolai V. Ravin4Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, RussiaInstitute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, RussiaInstitute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, RussiaInstitute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, RussiaInstitute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, RussiaBackground Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Plants from the family Orobanchaceae are used as models for studying plastid genome evolution in the transition from an autotrophic to parasitic lifestyle. Diphelypaea is a poorly studied genus of the Orobanchaceae, comprising two species of non-photosynthetic root holoparasites. In this study, we sequenced the plastid genome of Diphelypaea coccinea and compared it with other Orobanchaceae, to elucidate patterns of plastid genome evolution. In addition, we used plastid genome data to define the phylogenetic position of Diphelypaea spp. Methods The complete nucleotide sequence of the plastid genome of D. coccinea was obtained from total plant DNA, using pyrosequencing technology. Results The D. coccinea plastome is only 66,616 bp in length, and is highly rearranged; however, it retains a quadripartite structure. It contains only four rRNA genes, 25 tRNA genes and 25 protein-coding genes, being one of the most highly reduced plastomes among the parasitic Orobanchaceae. All genes related to photosynthesis, including the ATP synthase genes, had been lost, whereas most housekeeping genes remain intact. The plastome contains two divergent, but probably intact clpP genes. Intron loss had occurred in some protein-coding and tRNA genes. Phylogenetic analysis yielded a fully resolved tree for the Orobanchaceae, with Diphelypaea being a sister group to Orobanche sect. Orobanche.https://peerj.com/articles/7830.pdfParasitic plantPlastid genomeOrobanchaceaeDiphelypaea |
| spellingShingle | Eugeny V. Gruzdev Vitaly V. Kadnikov Alexey V. Beletsky Andrey V. Mardanov Nikolai V. Ravin Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae PeerJ Parasitic plant Plastid genome Orobanchaceae Diphelypaea |
| title | Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae |
| title_full | Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae |
| title_fullStr | Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae |
| title_full_unstemmed | Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae |
| title_short | Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae |
| title_sort | extensive plastome reduction and loss of photosynthesis genes in diphelypaea coccinea a holoparasitic plant of the family orobanchaceae |
| topic | Parasitic plant Plastid genome Orobanchaceae Diphelypaea |
| url | https://peerj.com/articles/7830.pdf |
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