Genome relationships in polyploid Poa pratensis and other Poa species inferred from phylogenetic analysis of nuclear and chloroplast DNA sequences

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 76-87 ◽  
Author(s):  
Jason T Patterson ◽  
Steven R Larson ◽  
Paul G Johnson
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Dna Sequences ◽  
Poa Pratensis ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Kentucky Bluegrass ◽  
Limited Information ◽  
The World ◽  
Chloroplast Dna Sequences

The genus Poa comprises approximately 500 species that occur throughout the world, including the widely grown Kentucky bluegrass (P. pratensis L.). Hybridization and polyploidization have played a prominent role in the evolution of this complex genus, but limited information is available regarding genome relationships in Poa. Thus, we amplified, cloned, and compared the DNA sequences of 2 nuclear genes (CDO504 and thioredoxin-like protein) and 2 chloroplast genome loci (ndhF and trnT–trnF) from 22 Poa species. Four distinct classes of sequences corresponding to 4 putative homoeologous loci from each nuclear gene were found within polyploid P. pratensis. Nuclear sequences from 15 other Poa species were found to group with at least 1 P. pratensis homoeolog, whereas 6 species displayed sequences not present in P. pratensis. The nuclear genome phylogenies presented here show the first evidence of diverse and related genomes in the genus Poa.Key words: phylogeny, polyploidy, chloroplast genome, nuclear genome, Kentucky bluegrass.

scholarly journals Risk of cardiac manifestations in adult mitochondrial disease caused by nuclear genetic defects

Open Heart ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. e001510
Author(s):  
Albert Zishen Lim ◽  
Daniel M Jones ◽  
Matthew G D Bates ◽  
Andrew M Schaefer ◽  
John O'Sullivan ◽  
...  
Keyword(s):  
Mitochondrial Disease ◽  
Nuclear Dna ◽  
Laboratory Data ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Left Ventricular ◽  
Adult Patients ◽  
Limited Information ◽  
Cardiac Abnormalities ◽  
Cardiac Manifestations

ObjectiveRegular cardiac surveillance is advocated for patients with primary mitochondrial DNA disease. However, there is limited information to guide clinical practice in mitochondrial conditions caused by nuclear DNA defects. We sought to determine the frequency and spectrum of cardiac abnormalities identified in adult mitochondrial disease originated from the nuclear genome.MethodsAdult patients with a genetically confirmed mitochondrial disease were identified and followed up at the national clinical service for mitochondrial disease in Newcastle upon Tyne, UK (January 2009 to December 2018). Case notes, molecular genetics reports, laboratory data and cardiac investigations, including serial electrocardiograms and echocardiograms, were reviewed.ResultsIn this cohort-based observational study, we included 146 adult patients (92 women) (mean age 53.6±18.7 years, 95% CI 50.6 to 56.7) with a mean follow-up duration of 7.9±5.1 years (95% CI 7.0 to 8.8). Eleven different nuclear genotypes were identified: TWNK, POLG, RRM2B, OPA1, GFER, YARS2, TYMP, ETFDH, SDHA, TRIT1 and AGK. Cardiac abnormalities were detected in 14 patients (9.6%). Seven of these patients (4.8%) had early-onset cardiac manifestations: hypertrophic cardiomyopathy required cardiac transplantation (AGK; n=2/2), left ventricular (LV) hypertrophy and bifascicular heart block (GFER; n=2/3) and mild LV dysfunction (GFER; n=1/3, YARS2; n=1/2, TWNK; n=1/41). The remaining seven patients had acquired heart disease most likely related to conventional cardiovascular risk factors and presented later in life (14.6±12.8 vs 55.1±8.9 years, p<0.0001).ConclusionsOur findings demonstrate that the risk of cardiac involvement is genotype specific, suggesting that routine cardiac screening is not indicated for most adult patients with nuclear gene-related mitochondrial disease.

scholarly journals A project for analyzing the ecology and phylogeny of western Pacific echinoids

Zoosymposia ◽  
2019 ◽  
Vol 15 (1) ◽  
pp. 83-87
Author(s):  
K. KANAZAWA ◽  
M. SAITOH ◽  
N. WAKAYAMA ◽  
M. OBUCHI ◽  
S. NAKACHI ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sea Urchins ◽  
Molecular Data ◽  
Western Pacific ◽  
The West ◽  
The World ◽  
The Western Pacific ◽  
Gathering Data ◽  
Northern Japan

In 2017 we started a project to analyze the ecology and phylogeny of western Pacific echinoids. As the first step, we are establishing methods to infer their phylogenetic relationships using molecular data; we developed effective methods to obtain complete mitochondrial DNA sequences, and determined their effectiveness in phylogenetic analysis. We have also been gathering data concerning the ecology and systematics of Japanese extant echinoids, which arguably has among the highest genus-level diversities in the West Pacific or perhaps even in the world. We have collected 58 species from middle and southern Japan representing 48 genera. In the next year, we will collect sea urchins from northern Japan, and within 2 years we will finish collecting data on ecology and systematics of Japanese echinoids, and provide a set of standardized data that will be useful for many researchers studying western Pacific echinoids. At that time, we will start comparative analyses of echinoid faunas distributed in the western Pacific.

A reassessment of tribal affinities of the enigmatic genera Printzia and Isoetopsis (Asteraceae), based on three chloroplast sequences

2002 ◽  
Vol 50 (6) ◽  
pp. 677 ◽  
Author(s):  
Randall J. Bayer ◽  
Edward W. Cross
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Trnl Intron ◽  
Coding Region ◽  
Strong Affinity ◽  
Taxonomic History ◽  
Chloroplast Dna Sequences ◽  
Chemical Characters

The tribal affinities of two dubiously placed genera of the Asteraceae, Printzia and Isoetopsis, were assessed by using three chloroplast DNA sequences, the trnL/F spacer, the trnL intron and the matK coding region. The outgroup was represented by two species of the tribe Barnadesieae, whereas one to six genera (43 species including Printzia and Isoetopsis) of the tribes of the Asteroideae [Anthemideae (six genera), Astereae (five) Calenduleae (two), Gnaphalieae (six), Heliantheae s.l. (five), Inuleae s.str. (three), Plucheeae (two), Senecioneae (four)] and Cichorioideae [Arctotideae (one), Cardueae (two), Lactuceae (two), Liabeae (one), Mutisieae (one), Vernonieae (one)] were chosen as the ingroup. Phylogenetic analysis indicates that both Printzia and Isoetopsis have a strong affinity with members of the tribe Astereae. At some point in their taxonomic history, both genera had been placed in this tribe and there are good morphological and chemical characters that justify this placement.

scholarly journals Hundreds of nuclear and plastid loci yield insights into orchid relationships

2020 ◽  
Author(s):  
Oscar Alejandro Pérez-Escobar ◽  
Steven Dodsworth ◽  
Diego Bogarín ◽  
Sidonie Bellot ◽  
Juan A. Balbuena ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Gene Trees ◽  
Deep Time ◽  
Plastid Genomes ◽  
Phylogenetic Informativeness ◽  
History Of ◽  
Phylogenetic Framework

ABSTRACTPremise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

scholarly journals Morphological Characteristics and Phylogenetic Analysis of Polygonatum Species Based on Chloroplast DNA Sequences

2014 ◽  
Vol 22 (6) ◽  
pp. 489-496 ◽  
Author(s):  
Jeong Hun Kim ◽  
Jae Wan Seo ◽  
Ji Hui Byeon ◽  
Young Sup Ahn ◽  
Seon Woo Cha ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Morphological Characteristics ◽  
Chloroplast Dna Sequences

scholarly journals Gene Loss and Evolution of the Plastome

2019 ◽  
Author(s):  
Tapan Kumar Mohanta ◽  
Awdhesh Kumar Mishra ◽  
Adil Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Dna Sequences ◽  
Nuclear Genome ◽  
Evolutionary Process ◽  
Life Forms ◽  
Evolutionary Analysis ◽  
Origin And Evolution ◽  
The Earth ◽  
Chloroplast Genomes ◽  
Duplication Events

AbstractChloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203–156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.

Ottelia guanyangensis (Hydrocharitaceae), a new species from southwestern China

Phytotaxa ◽  
2018 ◽  
Vol 361 (3) ◽  
pp. 294 ◽  
Author(s):  
ZHI-ZHONG LI ◽  
KUO LIAO ◽  
CHUN-YU ZOU ◽  
YAN LIU ◽  
GUANG-WAN HU ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Aquatic Plant ◽  
Nuclear Dna ◽  
Southwestern China ◽  
Molecular Phylogenetic ◽  
Chloroplast Dna Sequences ◽  
A New Species

Ottelia guanyangensis (Hydrocharitaceae), a new species from southwestern China, is described and illustrated. This aquatic plant is a perennial, submersed herb with bisexual flowers and a hexagonal-cylindric fruit. It is related to O. acuminata var. songmingensis and O. balansae but differs from these two taxa by its bisexual flowers, spathe with 2–5 flowers, trinerved leaf with obvious cross veins, and a winged, hexagonal-cylindric fruit. Molecular phylogenetic analysis based on nuclear DNA internal transcribed spacer (ITS) sequences and three chloroplast DNA sequences (rbcL, trnK5’ intron and trnS-trnG) resolves O. guanyangensis as a distinct clade, which further justifies its recognition as a new species.

Species delimitation in trematodes using DNA sequences: Middle-American Clinostomum as a case study

Parasitology ◽  
2016 ◽  
Vol 143 (13) ◽  
pp. 1773-1789 ◽  
Author(s):  
GERARDO PÉREZ-PONCE DE LEÓN ◽  
MARTÍN GARCÍA-VARELA ◽  
CARLOS D. PINACHO-PINACHO ◽  
ANA L. SERENO-URIBE ◽  
ROBERT POULIN
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Species Delimitation ◽  
Nuclear Gene ◽  
Species Tree ◽  
Coi Gene ◽  
Complex Life Cycle ◽  
Species Boundaries ◽  
Intermediate Hosts ◽  
Putative Species

SUMMARYThe recent development of genetic methods allows the delineation of species boundaries, especially in organisms where morphological characters are not reliable to differentiate species. However, few empirical studies have used these tools to delineate species among parasitic metazoans. Here we investigate the species boundaries of Clinostomum, a cosmopolitan trematode genus with complex life cycle. We sequenced a mitochondrial [cytochrome c oxidase subunit I (COI)] gene for multiple individuals (adults and metacercariae) from Middle-America. Bayesian phylogenetic analysis of the COI uncovered five reciprocally monophyletic clades. COI sequences were then explored using the Automatic Barcode Gap Discovery to identify putative species; this species delimitation method recognized six species. A subsample was sequenced for a nuclear gene (ITS1, 5·8S, ITS2), and a concatenated phylogenetic analysis was performed through Bayesian inference. The species delimitation of Middle-American Clinostomum was finally validated using a multispecies coalescent analysis (species tree). In total, five putative species are recognized among our samples. Mapping the second intermediate hosts (fish) onto the species tree suggests that metacercariae of these five species exhibit some level of host specificity towards their fish intermediate host (at the family level), irrespective of geographical distribution.

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