Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 10

Published: April 30, 2019

The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding taxonomy evolution. However, phylogenetic relationships some sections (such as section Daghestanica) genetic bases adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species Daghestanica by combining these with another 35 allied species, performed a series analyses including genome structure, GC content, pairwise Ka/Ks ratios, SSR component, nucleotide diversity codon usage. Positively selected genes (PSGs) were detected lineage using branch-site model. Comparison analysis Bayesian ML phylogeny on CCG (complete genome), SCG (single copy genes) CDS (conding DNA sequences) produced well-resolved Allioideae plastid lineages, which illustrated several novel Daghestanica. In addition, showed highly conserved structures. content GC3s exhibited lower values than studied non-Allioideae along elevated ratios. rps2 gene was lost all examined ten significant posterior probabilities sites identified positive selection analysis, seven them associated photosynthesis. Our study uncovered new relationship suggested selective pressure has played an role adaptation results will facilitate further evolution Allium.

Language: Английский

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Backbone phylogeny and evolution of Apioideae (Apiaceae): New insights from phylogenomic analyses of plastome data

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 161, P. 107183 - 107183

Published: April 21, 2021

Language: Английский

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Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(4), P. 2193 - 2193

Published: Feb. 12, 2024

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains China, have high medicinal ornamental value. diversity of plant morphology this genus poses significant challenges for identification, given their propensity highland dwelling, which makes it a question worth exploring how they cope with harsh surroundings. In study, we recently generated chloroplast (cp) genomes two species, paniculata (M. paniculata) M. pinnatifolia, compared them those ten cp to comprehend genomic features, phylogenetic relationships, what part might play plateau adaptation. These shared great deal similarities terms genome size, structure, gene content, GC codon usage patterns. were between 151,864 bp 154,997 length, contain 133 predictive genes. Through sequence divergence analysis, identified three highly variable regions (trnD-psbD, ccsA-ndhD, ycf1 genes), could be used as potential markers or DNA barcodes analysis. Between 22 38 SSRs some long repeat sequences from 12 species. Our analysis confirmed that clustered into monophyletic clade Papaveraceae, corroborated intrageneric relationships. results indicated pinnatifolia sister tree. addition, atpA ycf2 genes positively selected high-altitude functions these involved adaptation extreme environment cold low CO2 concentration conditions at plateau.

Language: Английский

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Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships

BMC Plant Biology, Journal Year: 2020, Volume and Issue: 20(1)

Published: Nov. 13, 2020

Abstract Background The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one most taxonomically difficult taxa within Apiaceae, largely due to varied morphological characteristics. To investigate plastome evolution and phylogenetic relationships , we determined complete sequences eight using a de novo assembly approach. Results Through comprehensive comparative analysis, found that plastomes were similar terms repeat sequence, SSR, codon usage, RNA editing site. However, compared with other seven species, L. delavayi exhibited striking differences genome size, gene number, IR/SC borders, sequence identity. Most genes remained under purifying selection, whereas four showed relaxed namely ccsA rpoA ycf1 ycf2 . Non-monophyly was inferred from internal transcribed spacer (ITS) analyses. Conclusion tree ITS produced incongruent topologies, which may be attributed hybridization incomplete lineage sorting. Our study highlighted advantage mass informative sites resolving relationships. Moreover, combined previous studies, considered current taxonomy system needs improved revised. In summary, our provides new insights into evolution, phylogeny, species.

Language: Английский

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Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 163, P. 107229 - 107229

Published: June 13, 2021

Language: Английский

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Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 12

Published: Feb. 1, 2022

Tribe Lilieae, encompassing Lilium, Notholirion, Cardiocrinum, and Fritillaria, includes economically important crops with a horticultural medicinal value. It is considered to be core lineage of Liliaceae, but phylogenetic relationships within it, the timing origin individual clades, remain incompletely resolved. To address these issues, we reconstructed evolutionary history tribe. We sequenced 45 Liliaceae plastomes combined them publicly available data (for total 139 plastomes) explore systematics, origin, divergence, evolution Lilieae. Our taxon sampling covers all ten sections Cardiocrinum species, three Notholirion major clades Fritillaria. analysis confirms monophyly sections/subgenera Lilium Fritillaria strong support. dated Lilieae Eocene, genera species radiations inferred have occurred in Miocene. The reconstruction ancestral area implies that may originated from Qinghai-Tibet Plateau (QTP): Himalayas Hengduan Mountains uplifting QTP likely promoted divergence Ancestral-state reconstructions bulb component number (including bulblets scales) show correlation genus-level diversity They also predict most recent common ancestor had bulbs numerous bulblets. Based on observations, predicted climatic oscillations associated uplift played an role bulb. findings provide well-supported picture useful framework for understanding pathway contributing better lilies.

Language: Английский

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The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: Jan. 5, 2023

Abstract Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many possessing important medical value. previous studies provided more information for , but its infrageneric relationships are still confusing. In addition, genetic basis adaptive evolution remains poorly understood. Plastid genomes variable sites have potential to reconstruct robust phylogeny plants investigate plants. Although chloroplast been reported within genus, few conducted using genomes, especially endemic China. Results Comprehensively comparative analyses 22 newly sequenced assembled plastomes indicated that these had highly conserved genome structure, gene number, codon usage, repeats type distribution, varied size, GC content, SC/IR boundaries. Thirteen mutation hotspot regions were detected they would serve as promising DNA barcodes candidates identification related genera. Phylogenomic high supports resolutions showed Talassia transiliensis Soranthus meyeri nested thus should be transferred into genus. Our phylogenies also monophyly subgenera Sinoferula Narthex Twelve genes significant posterior probabilities identified positively selective analysis, their function may relate photosystem II, ATP subunit, NADH dehydrogenase. Most them might play an role help adapt high-temperatures, strong-light, drought habitats. Conclusion Plastome data powerful efficient improve support resolution complicated phylogeny. helpful harsh environment. Overall, our study supplies a new perspective comprehending .

Language: Английский

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Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae)

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: May 4, 2023

Abstract Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported size and gene contents plastomes, with little information on comparative analysis plastid genomes genus. Additionally, there are still some whose chloroplast genome has not been reported. In study, complete plastomes six were sequenced assembled, among them, P. campanulatum was for first time. Comparative phylogenetic analyses then conducted published three related species. Results indicated that whole plastome length ranged from 154,564 bp ( multiflorum ) 156,028 stenophyllum having a quadripartite structure LSC SSC separated by two IR regions. A total 113 unique genes detected each revealed content GC these highly identical. No significant contraction or expansion observed boundaries all except sibiricum 1, which rps19 pseudogenized owing incomplete duplication. Abundant long dispersed repeats SSRs genome. There five remarkably variable regions 14 positively selected identified Heteropolygonatum. Phylogenetic results based strongly supported placement alternate leaves sect. Verticillata , group characterized whorled leaves. Moreover, verticillatum cyrtonema displayed paraphyletic. This study characters Heteropolygonatum maintained high degree similarity. Five found be potential specific DNA barcodes . suggested leaf arrangement suitable basis delimitation subgeneric groups definitions require further study.

Language: Английский

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Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)

Scientific Reports, Journal Year: 2021, Volume and Issue: 11(1)

Published: Feb. 5, 2021

Abstract Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species Allioideae, five Amaryllidoideae, one Agapanthoideae. These cpDNA represent 80 protein-coding, 30 tRNA, four rRNA genes, range from 151,808 to 159,998 bp length. Loss pseudogenization multiple genes (i.e., rps2, infA , rpl22 ) appear have occurred times during evolution Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1 rps16-trnQ-UUG petG-trnW-CCA psbA upstream, rpl32-trnL-UAG ycf1 matK ndhF were identified studied Allium species. present first phylogenomic analysis among tribes based on 74 coding regions 21 Agapanthoideae, representing selected members Asparagales. Our molecular results strongly support monophyly which is sister Amaryllioideae. Within Tulbaghieae was Gilliesieae-Leucocoryneae whereas Allieae clade Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed crown age Eocene (40.1 mya) followed by differentiation early Miocene (21.3 mya). The split Gilliesieae Leucocoryneae estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for subsequent spread Eurasia middle Eocene. Cool arid conditions late led isolation between Eurasian may diverged South American taxa Oligocene. Rather than vicariance, long-distance dispersal most likely explanation intercontinental distribution

Language: Английский

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Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: July 8, 2021

Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus— Allium —is vast, comprising about thousand species. species (as well as other members of the ) are widespread and diversified, they adapted wide range habitats from shady forests open like meadows, steppes, deserts. genes present in chloroplast genomes (plastomes) play fundamental roles for photosynthetic plants. Plastome traits could thus be associated geophysical abiotic characteristics habitats. Most highly conserved used phylogenetic markers many families vascular Nevertheless, some studies revealed signatures positive selection plant including . We have sequenced plastomes following nine (tribe Allieae Allioideae species: A. zebdanense , moly victorialis macleanii nutans obliquum schoenoprasum pskemense platyspathum fistulosum semenovii Nothoscordum bivalve Leucocoryneae ). compared our data previously published provided interpretation plastome genes’ annotations because we found noteworthy inconsistencies reported. For estimated integral evolutionary rate, counted SNPs indels per nucleotide position pseudogenization events three main lines genus estimate whether potentially important physiology or just follow pattern. During examination 38 11 that rps16 rps2 infA ccsA lost their functionality multiple times different (regularly events), while was stochastic events. “normal” “pseudo” state correlates line belongs to. various NADH dehydrogenase ( ndh matK accD others were found. Taking into account known mechanisms coping excessive light by cyclic electron transport, can hypothesize adaptive evolution genes, coding subunits NADH-plastoquinone oxidoreductase driven factors alpine habitats, especially intensive UV radiation.

Language: Английский

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