The evolution of the plastid genomes in the holoparasitic Balanophoraceae

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2043)

Published: March 1, 2025

The independent transition to a heterotrophic lifestyle in plants drove remarkably convergent evolutionary trajectories, characterized by morphological modifications and reductions their plastomes. characteristics of the minimum plastome required for survival, if they exist, remain topic debate. holoparasitic family Balanophoraceae was initially presumed have entirely lost plastids, however, recent reports revealed presence reduced aberrant plastids with odd genomes. Among outstanding features these genomes are highest nucleotide composition bias across tree life only two genetic code changes ever recorded among plants. In this study, we assembled plastomes from five genera, four which had never been studied. Major common include extremely high AT content, lack typical quadripartite structure extensive size reduction due gene elimination genome compaction. exhibits multiple intron losses, broad range scenarios regarding evolution plastid trnE , considered essential because its dual function tetrapyrrole biosynthesis translation within plastid. addition, phylogenetic analyses suggest that genus Scybalium is not monophyletic. An model proposed.

Language: Английский

---

Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites

Annals of Botany, Journal Year: 2023, Volume and Issue: 132(5), P. 909 - 928

Published: July 27, 2023

The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism emerged 12 times independently angiosperm evolution. Holoparasitism is the most severe form parasitism, and found ~10 % angiosperms. Although a few holoparasitic species have examined at level, reports involve plastomes instead mitogenomes. Parasitic plants establish vascular connections their hosts through haustoria to obtain water nutrients, which facilitates exchange genetic information, making them more susceptible horizontal gene transfer (HGT). HGT prevalent mitochondria than chloroplast or nuclear compartments.

Language: Английский

---

Evolution of Whirly1 in the angiosperms: sequence, splicing, and expression in a clade of early transitional mycoheterotrophic orchids

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: June 28, 2024

The plastid-targeted transcription factor Whirly1 ( WHY1 ) has been implicated in chloroplast biogenesis, plastid genome stability, and fungal defense response, which together represent characteristics of interest for the study autotrophic losses across angiosperms. While gene loss nuclear genomes well studied mycoheterotrophic plants, evolution molecular mechanisms impacting stability is completely unknown. Here, we characterize four early transitional orchid species genus Corallorhiza by synthesizing results phylogenetic, transcriptomic, comparative genomic analyses with sequences sampled from 21 orders We found an increased number non-canonical isoforms assembled all but greenest species, including intron retention some isoforms. Within , phylotranscriptomic revealed presence tissue-specific differential expression only most photosynthetically capable a coincident increase fully species. Gene- codon-level tests selective regimes did not infer significant signal either relaxed selection or episodic diversifying so late-stage full orchids Epipogium aphyllum Gastrodia elata . Additionally, nucleotide substitutions that likely impact function such as nonsense mutations, were observed mycoheterotrophs. propose our findings suggest splicing changes may precede shifts inferred therefore does support primary role transition to mycoheterotrophy Orchidaceae. Taken together, this provides comprehensive view angiosperms date.

Language: Английский

---

Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia

Annals of Botany, Journal Year: 2024, Volume and Issue: unknown

Published: May 28, 2024

Abstract Background and Aims Heterotrophic plants have long been a challenge for systematists, exemplified by the base of orchid subfamily Epidendroideae, which contains numerous mycoheterotrophic species. Methods Here we address utility organellar genomes in resolving relationships at epidendroid base, specifically employing models heterotachy, or lineage-specific rate variation over time. We further conduct comparative analyses plastid genome evolution heterotrophs structural matK. Key Results present first complete (plastomes) Wullschlaegelia, sole genus tribe Wullschlaegelieae, revealing highly reduced 37 kb, retains fraction genes related autotrophs. Plastid phylogenomic recovered strongly supported clade composed exclusively species with branches. analysed mitochondrial gene sets, similar to those other studies using nuclear data, but placement Wullschlaegelia remains uncertain. conducted plastome among heterotrophic orchids, suite correlated substitutional changes relative autotrophic Lastly, investigated evolutionary matK, is retained few ‘late stage’ found evidence conservation despite rapid substitution rates both leafless Gastrodia. Conclusions Our reveal limits what can tell us on this part tree, even when applying parameter-rich heterotachy models. study underscores need increased taxon sampling across all three illustrates research addressing analyses.

Language: Английский

---

Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(7)

Published: July 1, 2024

Abstract Premise Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences which have received considerable interest. In particular, plastid genomes (plastomes) being sequenced at a high rate, allowing continual refinement conceptual models reductive evolution in heterotrophs. However, numerous sampling gaps exist, hindering ability to conduct comprehensive phylogenomic analyses these plants. Methods Using floral tissue from an herbarium specimen, we and analyzed plastome Degranvillea dermaptera , rarely collected, leafless orchid species South America about little is known, including its phylogenetic affinities. Results The most reduced those among subfamily Orchidoideae. it has lost majority genes found leafy autotrophic species, structurally rearranged, similar gene content plastomes orchids. We strong evidence for placement within subtribe Spiranthinae using that explicitly account heterotachy, or lineage‐specific evolutionary rate variation over time. further relaxed selection on several correlations substitution rates other “traits” members Conclusions Our findings advance knowledge relationships paths genome orchids, experienced more independent transitions heterotrophy than any plant family. This study demonstrates importance collections comparative genomics poorly known conservation concern.

Language: Английский

---

Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 16, 2025

The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance host-derived nutrients and loss photosynthesis in holoparasites have led to highly degraded absent plastid genomes, but its impact mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions holoparasitism key evolutionary intermediates, we identified measurable predictable alterations genomic shuffling, RNA editing, intracellular (IGT) horizontal gene transfer (HGT) en route nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination repair processes, especially RNA-mediated retroprocessing, as significant drivers for structure evolution. particular, novel IGT HGT mechanism, which not been demonstrated cross-species inter-organelle transfers. Based this, propose generalized dosage effect mechanism explain biased transferability mitochondria across green lineages like parasites mycoheterotrophs. Evolutionary rates scaled with these changes, direction strength selection varied substantially among genes clades, resulting high contingency Finally, describe universal roadmap plants where increased activities, rather than relaxed alone, lead differentiated compared free-living species.

Language: Английский

---

The Impact of Parasites on the Physiological Function of Animals and the Host-Parasite Relationship

European Journal of Theoretical and Applied Sciences, Journal Year: 2025, Volume and Issue: 3(3), P. 3 - 15

Published: April 15, 2025

The presence of parasites in host animals can lead to changes various functions the animal, such as disorders haematopoiesis, immunosuppression, digestive gastrointestinal tract, effects on food intake and enzymatic degradation related digestion. modification animal's physiological subsequent fractal behaviour becomes a complex system that plays an important role this area. This work is based model, which was mainly used screen main modulations their inherent intrinsic properties space using histological criteria. Ultimately, spatial conformation tissues plastically adapted maximise efficient distribution resources within animal. many attractive statistics have facilitated developments field. To characterise these more specifically, shape model has generally been derived from relationship hypervolume surface high-dimensional Euclidean space. paper discusses two advanced biophysical models offers inductive equation constraints between samples amoebic infective amoebiasis with mode. results reflect growth patterns variations series.

Language: Английский

---

Cytonuclear evolution in fully heterotrophic plants: lifestyles and gene function determine scenarios

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 21, 2024

Evidence shows that full mycoheterotrophs and holoparasites often have reduced plastid genomes with rampant gene loss, elevated substitution rates, deeply altered to conventional evolution in mitochondrial genomes, but mechanisms of cytonuclear is unknown. Endoparasitic Sapria himalayana mycoheterotrophic Gastrodia Platanthera guangdongensis represent different heterotrophic types, providing a basis illustrate evolution. Here, we focused on nuclear-encoded / (N-pt mt) -targeting protein complexes, including caseinolytic protease (ClpP), ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo), oxidative phosphorylation system (OXPHOS), DNA recombination, replication, repair (DNA-RRR) system, pentatricopeptide repeat (PPR) proteins, identify evolutionary drivers for interaction. The severity loss N-pt PPR pt-RRR genes was positively associated increased degree heterotrophy S. himalayana, while N-mt mt-RRR were retained. Substitution rates organellar nuclear encoding N-pt/mt subunits complexes evaluated, coevolution identified whereas disproportionate observed the OXPHOS complex mycoheterotrophs, only slight accelerations mycoheterotrophs. Nuclear compensatory encoded by genes. Selection shaping codon preferences, functional constraint, regulation, post-transcriptional regulation all facilitate mito-nuclear Our study enriches our understanding genomic scenarios fully plants.

Language: Английский

---

The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in placing Rafflesiaceae

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 9, 2024

Abstract Two key factors have been implicated as major impediments to phylogenomic inference: incomplete lineage sorting (ILS)—especially in cases where clades are the anomaly zone—and erroneous gene tree estimation—commonly manifested by long-branch attraction Felsenstein zone. Seldom these analyzed when they occur simultaneously involving ancient adaptive radiations. Rafflesiaceae (Malpighiales) is an iconic holoparasitic plant clade growing west of Wallace’s line tropical Southeast Asia. This has notoriously difficult place phylogenetically and nested within explosive radiation Malpighiales. To complicate matters, parasitic plants like well-known exhibit accelerated rates nucleotide substitution. Here, using 2,141 genes we identify for first time that substitution a genome-wide phenomenon holoparasites. We demonstrate two orders magnitude increase compared its free-living relatives, rendering nearly every prone attraction. Our analyses rejected monophyletic (Rafflesiaceae, Euphorbiaceae) proposed previous studies but favored earlier divergence close affinity with Euphorbiaceae, Peraceae, Putranjivaceae, Pandaceae. therefore prey joint trap zones. Moreover, owing massive loss Rafflesiaceae, our simulation suggests this represents intractable phylogenetic problem will never achieve single resolution. case study highlights seemingly insurmountable confluence factors—a danger zone—that hinders resolution demonstrates need be flexible multiple placements equally likely.

Language: Английский

---

Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants

Plant and Cell Physiology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 11, 2024

Abstract Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal organelle gene expression. Splicing, editing processing of transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) the many group II introns present plant critical function since splicing defect or deficiency can severely impact growth development. This study investigates SEf free-living holoparasitic plants, focusing on 25 from 15 angiosperm species. Our comparative analyses reveal distinctive patterns holoparasites exhibiting significantly lower SEf, potentially linked to unique evolutionary trajectory. Given preponderance horizontal transfer (HGT) parasitic we investigated effect HGT such as presence foreign Contrary expectations, reductions do not correlate events, suggesting that other factors at play, loss photosynthesis transition lifestyle. The findings this broaden our understanding molecular evolution plants shed light multifaceted influencing

Language: Английский

---