The Plastid Genome of Mycoheterotrophic Monocot Petrosavia stellaris Exhibits Both Gene Losses and Multiple Rearrangements

Logacheva, Maria D.; Schelkunov, Mikhail I.; Nuraliev, Maxim S.; Samigullin, Tahir H.; Penin, Aleksey A.

doi:10.1093/gbe/evu001

Cited by 79 publications

(95 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…clandest i ne 68 . Previous studies have demonstrated that positions of IR junction and SSC region are correlated with degeneration of ndhF and ycf1 genes 57,69 . Loss of ycf1 and all ndh genes (including ndhF ), as revealed by this study may explain why SSC chloroplast genome regions of the two considered species are shorter than those of others.…”

Section: Discussionmentioning

confidence: 97%

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Zhou

Chen

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively. Compared with the chloroplast genomes of Nicotiana tabacum and Osyris alba, all ndh genes as well as three ribosomal protein genes, seven tRNA genes, four ycf genes, and the infA gene of these two species have been lost. The results of the maximum likelihood and neighbor-joining phylogenetic trees strongly support the theory that Loranthaceae and Viscaceae are monophyletic clades. This research reveals the effect of a parasitic lifestyle on the chloroplast structure and genome content of T. chinensis and T. sutchuenensis, and enhances our understanding of the discrepancies in terms of assembly results between Illumina and PacBio.

show abstract

Section: Discussionmentioning

confidence: 97%

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Zhou

Chen

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…These organisms show extensive plastome reduction due to relaxed selective pressure on photosynthetic capacities because they are highly dependent on mycorrhizal fungi. Plastid genome rearrangements have been known to occur in heterotrophs, as observed in Petrosavia stellaris (Logacheva et al 2014); however, rearrangements were not observed in the sequenced section of C. dispar. The presence of rearrangements within the plastome remains tentative until it is completely sequenced.…”

Section: Plastid Reduction Within Mycoheterotrophsmentioning

confidence: 99%

“…2 0 1 3 ) and the mycoheterotrophic Petrosavia stellaris (Logacheva et al 2014). Previously, the only complete plastid genome data for mycoheterotrophic species were from the liverwort Aneura mirabilis (Wickett et al 2008) and three mycoheterotrophic orchids (Neottia nidus-avis, Logacheva et al 2011;Rhizanthella gardneri, Delannoy et al 2011; Corallorhiza striata var.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic Corsia dispar D.L Jones & B. Gray (Corsiaceae)

Bodin

Kim

2015

Plant Mol Biol Rep

View full text Add to dashboard Cite

The phylogenetic positions of the families Campynemataceae and Corsiaceae within the order Liliales remains unclear. To date, molecular data from the plastid genome of Corsiaceae has been obtained exclusively from Arachnitis, for which alignment and phylogenetic inference has proved difficult. The extent of gene conservation among mycoheterotrophic species within Corsiaceae remains unknown. To clarify the phylogenetic position of Campynemataceae and Corsiaceae within Liliales, functional plastid-coding genes of species representing both families have been analyzed. Examination of two phylogenetic data sets of plastid genes employing parsimony, maximum-likelihood, and Bayesian inference methods strongly supported both families forming a basal clade to the remaining taxa of Liliales. The first data set consists of five functional plastid-encoded genes (mat-K, rps7, rps2, rps19, and rpl2) sequenced from Corsia dispar (Corsiaceae). The data set included 31 species representing all families within Liliales, as well as selected orders that are related closely to Liliales (10 outgroup species from Asparagales, Dioscoreales, and Pandanales). The second phylogenetic analysis was based on 75 plastid genes. This data set included 18 species from Liliales, representing major clades within the order, and 10 outgroup species from Asparagales, Dioscoreales, and Pandanales. In this latter data set, Campynemataceae was represented by 60 plastid-encoded genes sequenced from herbarium material of Campynema lineare. A large proportion of the plastid genome of C. dispar was also sequenced and compared to the plastid genomes of photosynthetic plants within Liliales and mycoheterotrophic plants within Asparagales to explore plastid genome reduction. The plastid genome of C. dispar is in the advanced stages of reduction, which signifies its high dependency on mycorrhizal fungi and is suggestive of a loss in photosynthetic ability. Functional plastid genes found in C. dispar may be applicable to other species in Corsiaceae, which will provide a basis for in-depth molecular analyses of interspecies relationships within the family, once molecular data from other members become available.

show abstract

“…As we pointed out in a previous study (Logacheva et al, 2014), a quality of the plastome assembly from the low coverage genome sequence data depends on the relative coverage of plastid and mitochondrial genomes. The assembly was most successful for Leitneria, where we were able to completely reconstruct the plastome sequence (see below).…”

Section: Plastid Sequence Assembly and Annotationmentioning

confidence: 81%

Phylogenomic analysis of Picramnia, Alvaradoa, and Leitneria supports the independent Picramniales

Logacheva

Shipunov

2017

J of Sytematics Evolution

Self Cite

View full text Add to dashboard Cite

Picramniales is a recently established monotypic order that has not yet acquired a stable position on the phylogenetic tree of flowering plants. While Picramnia and Alvaradoa were transferred from Simaroubaceae (Sapindales) into Picramniaceae (Picramniales), Leitneria was transferred from the “hamamelids” into Simaroubaceae. Using next‐generation sequencing, we obtained plastome sequences of Picramnia and Alvaradoa (partial) and Leitneria (complete). Protein coding and rRNA genes common for flowering plant plastomes were used for phylogenetic analysis. The resulting phylogenetic trees demonstrate a robust placement of Picramniales among the rosids as a sister group to Sapindales + Brassicales + Malvales. Leitneria is placed as a sister to Citrus. We also found that the plastome of Leitneria carries ycf68 gene that is absent from most other rosids and infA pseudogene.

show abstract

The Plastid Genome of Mycoheterotrophic Monocot Petrosavia stellaris Exhibits Both Gene Losses and Multiple Rearrangements

Cited by 79 publications

References 48 publications

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic Corsia dispar D.L Jones & B. Gray (Corsiaceae)

Phylogenomic analysis of Picramnia, Alvaradoa, and Leitneria supports the independent Picramniales

Contact Info

Product

Resources

About