Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae

Eugeny V Gruzdev; Vitaly V Kadnikov; Alexey V Beletsky; Andrey V Mardanov; Nikolai V Ravin

doi:10.7717/peerj.7830

Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae

PeerJ. 2019 Oct 2:7:e7830. doi: 10.7717/peerj.7830. eCollection 2019.

Authors

Eugeny V Gruzdev^{1

2}, Vitaly V Kadnikov¹, Alexey V Beletsky¹, Andrey V Mardanov¹, Nikolai V Ravin^{1

2}

Affiliations

¹ Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
² Moscow State University, Moscow, Russia.

Abstract

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.

Keywords: Diphelypaea; Orobanchaceae; Parasitic plant; Plastid genome.

Grants and funding

This work was supported by the Ministry of Science and Higher Education of the Russian Foundation and Russian Foundation for Basic Research (grant 14-04-00749). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.