Plastid Genome Evolution in the Subtribe Calypsoinae (Epidendroideae, Orchidaceae)

Genome Biology and Evolution, Journal Year: 2020, Volume and Issue: 12(6), P. 867 - 870

Published: May 2, 2020

Abstract Calypsoinae is a small subtribe in Orchidaceae (Epidendroideae) characterized by diverse trophic strategies and morphological characters. includes 13 genera, four of which are leafless mycoheterotrophic. Mycoheterotrophic species the genus Corallorhiza well suited to studies plastome evolution. However, lack sequences for other genera limits scope comparative phylogenetic analyses, particular our understanding To understand plastid genome evolution Calypsoinae, we newly sequenced plastomes 12 subtribe, including representatives three mycoheterotrophic as five autotrophic genera. We detected two parallel photosynthetic losses Corallorhiza. Evolutionary analyses indicated that transition obligate mycoheterotrophy leads relaxation selection highly gene-specific pattern.

Language: Английский

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Genomic reconfiguration in parasitic plants involves considerable gene losses alongside global genome size inflation and gene births

PLANT PHYSIOLOGY, Journal Year: 2021, Volume and Issue: 186(3), P. 1412 - 1423

Published: April 26, 2021

Parasitic plant genomes and transcriptomes reveal numerous genetic innovations, the functional-evolutionary relevance roles of which open unprecedented research avenues.

Language: Английский

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Evolutionary Patterns of the Chloroplast Genome in Vanilloid Orchids (Vanilloideae, Orchidaceae)

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3808 - 3808

Published: Feb. 14, 2023

The Vanilloideae (vanilloids) is one of five subfamilies Orchidaceae and composed fourteen genera approximately 245 species. In this study, the six new chloroplast genomes (plastomes) vanilloids (two Lecanorchis, two Pogonia, Vanilla species) were decoded, then evolutionary patterns plastomes compared to all available vanilloid plastomes. Pogonia japonica has longest plastome, with 158,200 bp in genome size. contrast, Lecanorchis shortest plastome 70,498 have regular quadripartite structures, but small single copy (SSC) region was drastically reduced. Two different tribes (Pogonieae Vanilleae) showed levels SSC reductions. addition, various gene losses observed among photosynthetic (Pogonia Vanilla) signs stage 1 degradation had lost most their ndh genes. other three species (one Cyrotsia Lecanorchis), however, 3 or 4 almost genes plastomes, except for some housekeeping located between Apostasioideae Cypripedioideae maximum likelihood tree. A total ten rearrangements found when basal four sub-regions (SC) shifted into an inverted repeat (IR) region, IR SC regions. Both synonymous (dS) nonsynonymous (dN) substitution rates in-cooperated decelerated, while accelerated. 20 protein-coding remained mycoheterotrophic vanilloids. Almost these protein show accelerated base twenty faced strong "relaxed selection" pressure (p-value < 0.05).

Language: Английский

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Comparative and phylogenetic analysis of Chiloschista (Orchidaceae) species and DNA barcoding investigation based on plastid genomes

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Dec. 6, 2023

Chiloschista (Orchidaceae, Aeridinae) is an epiphytic leafless orchid that mainly distributed in tropical or subtropical forest canopies. This rare and threatened lacks molecular resources for phylogenetic barcoding analysis. Therefore, we sequenced assembled seven complete plastomes of to analyse the plastome characteristics relationships conduct a investigation.We are first publish plastomes, which possessed typical quadripartite structure ranged from 143,233 bp 145,463 size. The all contained 120 genes, consisting 74 protein-coding 38 tRNA genes eight rRNA genes. ndh were pseudogenes lost genus, petG psbF under positive selection. displayed stable structures with no large inversions rearrangements. A total 14 small (SIs) identified but similar within genus. Six noncoding mutational hotspots (trnNGUU-rpl32 > rpoB-trnCGCA psbK-psbI psaC-rps15 trnEUUC-trnTGGU accD-psaI) five coding sequences (ycf1 rps15 matK psbK ccsA) selected as potential barcodes based on nucleotide diversity species discrimination analysis, suggested barcode ycf1 was most suitable discrimination. 47-56 SSRs 11-14 long repeats (> 20 bp) they mostly located single copy intergenic region. Phylogenetic analysis indicated monophyletic. It clustered Phalaenopsis formed basic clade subtribe Aeridinae moderate support value. results also showed divided into three major clades full support.This study genus Orchidaceae, have conserved structures. Based diversity, several regions population studies. may provide ideal system investigate dynamics evolution DNA investigation

Language: Английский

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Convergent Plastome Evolution and Gene Loss in Holoparasitic Lennoaceae

Genome Biology and Evolution, Journal Year: 2018, Volume and Issue: 10(10), P. 2663 - 2670

Published: Aug. 29, 2018

The Lennoaceae, a small monophyletic plant family of root parasites endemic to the Americas, are one last remaining independently evolved lineages parasitic angiosperms lacking published plastome. In this study, we present assembled and annotated plastomes two species spanning crown node Lennoa madreporoides Pholisma arenarium, as well their close autotrophic relative from sister Ehretiaceae, Tiquilia plicata. We find that L. P. arenarium similar in size gene content, substantially reduced compared T. plicata, consistent with trends seen other holoparasitic lineages. particular, most plastid genes involved photosynthesis function have been lost, whereas housekeeping (ribosomal protein-coding genes, rRNAs, tRNAs) retained. One notable exception is persistence rbcL open reading frame but not suggesting nonphotosynthetic for gene. Of retained coding dN/dS ratios indicate some remain under purifying selection, others show relaxed selection. Overall, study supports mounting evidence convergent plastome evolution flowering plants following shift heterotrophy.

Language: Английский

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