scholarly journals Evidence for Persistent Heteroplasmy and Ancient Recombination in the Mitochondrial Genomes of the Edible Yellow Chanterelles From Southwestern China and Europe

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhang ◽  
Shaojuan Wang ◽  
Haixia Li ◽  
Chunli Liu ◽  
Fei Mi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Related Species ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Southwestern China ◽  
Mitochondrial Genomes ◽  
Mitochondrial Recombination ◽  
Geographic Locations ◽  
Mitochondrial Atp Synthase

Mitochondrial genes and genomes have patterns of inheritance that are distinctly different from those of nuclear genes and genomes. In nature, the mitochondrial genomes in eukaryotes are generally considered non-recombining and homoplasmic. If heteroplasmy and recombination exist, they are typically very limited in both space and time. Here we show that mitochondrial heteroplasmy and recombination may not be limited to a specific population nor exit only transiently in the basidiomycete Cantharellus cibarius and related species. These edible yellow chanterelles are an ecologically very important group of fungi and among the most prominent wild edible mushrooms in the Northern Hemisphere. At present, very little is known about the genetics and population biology of these fungia cross large geographical distances. Our study here analyzed a total of 363 specimens of edible yellow chanterelles from 24 geographic locations in Yunnan in southwestern China and six geographic locations in five countries in Europe. For each mushroom sample, we obtained the DNA sequences at two genes, one in the nuclear genome and one in the mitochondrial genome. Our analyses of the nuclear gene, translation elongation factor 1-alpha (tef-1) and the DNA barcode of C. cibarius and related species, suggested these samples belong to four known species and five potential new species. Interestingly, analyses of the mitochondrial ATP synthase subunit 6 (atp6) gene fragment revealed evidence of heteroplasmy in two geographic samples in Yunnan and recombination within the two new putative species in Yunnan. Specifically, all four possible haplotypes at two polymorphic nucleotide sites within the mitochondrial atp6 gene were found distributed across several geographic locations in Yunnan. Furthermore, these four haplotypes were broadly distributed across multiple phylogenetic clades constructed based on nuclear tef-1 sequences. Our results suggest that heteroplasmy and mitochondrial recombination might have happened repeatedly during the evolution of the yellow chanterelles. Together, our results suggest that the edible yellow chanterelles represent an excellent system from which to study the evolution of mitochondrial-nuclear genome relationships.

scholarly journals Discordant evolution of organellar genomes in peas (Pisum L.)

2020 ◽  
Author(s):  
Vera S. Bogdanova ◽  
Natalia V. Shatskaya ◽  
Anatoliy V. Mglinets ◽  
Oleg E. Kosterin ◽  
Gennadiy V. Vasiliev
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Plant Evolution ◽  
Hybrid Origin ◽  
Mitochondrial Genomes ◽  
North East ◽  
Plastid Genomes ◽  
First Time ◽  
Evolutionary Fate

AbstractPlastids and mitochondria have their own small genomes which do not undergo meiotic recombination and may have evolutionary fate different from each other and nuclear genome, thus highlighting interesting phenomena in plant evolution. We for the first time sequenced mitochondrial genomes of pea (Pisum L.), in 38 accessions mostly representing diverse wild germplasm from all over pea geographical range. Six structural types of pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Bayesian phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant implying not less than six events of hybridisation of diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles is supposed to have been driven by plastid-nuclear incompatibility, known to be widespread in pea wide crosses and apparently shaping the organellar phylogenies. The topology of a phylogenetic tree based on the nucleotide sequence of a nuclear gene His5 coding for a histone H1 subtype corresponds to the current taxonomy and resembles that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin resulting from crosses of peas similar to those presently inhabiting south-east and north-east Mediterranean in broad sense.

The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species

Planta Medica ◽  
2021 ◽  
Author(s):  
Iffat Parveen ◽  
Natascha Techen ◽  
Sara M. Handy ◽  
Jing Li ◽  
Charles Wu ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Starch Synthase ◽  
Species Discrimination ◽  
Success Rates ◽  
Discrimination Ability ◽  
Internal Transcribed Spacer 2 ◽  
Granule Bound Starch Synthase

AbstractMorphological similarity within species makes the identification and authentication of Salvia species challenging, especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of 2 potential DNA barcode regions from the nuclear genome was evaluated in 7 medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer 2 and the exon 9 – 14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase 1 were tested for their species discrimination ability using distance, phylogenetic, and BLAST-based methods. A novel 2-step PCR method with 2 different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The granule-bound starch synthase 1 region showed higher amplification and sequencing success rates, higher interspecific distances, and a perfect barcode gap for the tested species compared to the nuclear internal transcribed spacer 2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions (granule-bound starch synthase) that were proven to be effective barcodes for identifying 7 Salvia species have potential for identification and authentication of other Salvia species.

Typification for reliable application of subspecific names within Peridinium cinctum (Peridiniales, Dinophyceae)

Phytotaxa ◽  
2019 ◽  
Vol 424 (3) ◽  
pp. 147-157 ◽  
Author(s):  
CORINNA ROMEIKAT ◽  
ALEJANDRO IZQUIERDO LÓPEZ ◽  
CHRISTINE TIETZE ◽  
JULIANE KRETSCHMANN ◽  
MARC GOTTSCHLING
Keyword(s):  
Morphological Variation ◽  
Dna Sequences ◽  
Related Species ◽  
Original Material ◽  
Full Spectrum ◽  
Closely Related Species ◽  
Geographic Locations ◽  
Future Studies ◽  
Unicellular Organisms ◽  
Peridinium Cinctum

The application of scientific names is determined by means of nomenclatural types, and every name has to be typified properly. The concept has limitations for unicellular organisms, because original material frequently consists of drawings and/or inadequately preserved physical material. Peridinium cinctum is an abundant freshwater microalga and variable in both morphology and genotype. Morphological variation is mainly expressed in its epithecal conformation: shape deviations of plates, plate rearrangements, plate fusion and plate additions. Different epithecal conformations were traditionally described as either varieties of P. cinctum or were established as closely related species. Despite this, relations between varieties, ribotypes and geographic locations were oversighted, and the full spectrum of plate variation in P. cinctum is still not well represented. For this reason, we sampled localities in Germany and Poland, from which varieties of P. cinctum were described a century ago. We cultivated monoclonal strains, exhibiting two distinct ITS ribotypes, and assessed their epithecal variation of morphology. Based on ca 2,500 observations of individual cells we report a plethora of both plate and suture deviations from the archetypical epithecal conformation of P. cinctum. Morphologies corresponding to previously described varieties were rare, even at their type localities. Nevertheless, we found morphologies consistent with protologues in four cases and use this material for epitypification. These varieties are now linked to specific DNA sequences, allowing reliable application of scientific names for future studies.

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 Diatom Centromeres Suggest a Novel Mechanism for Nuclear Gene Acquisition

2016 ◽  
Author(s):  
Rachel E. Diner ◽  
Chari M. Noddings ◽  
Nathan C. Lian ◽  
Anthony K. Kang ◽  
Jeffrey B. McQuaid ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Gc Content ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Artificial Chromosomes ◽  
Conserved Sequence ◽  
Gene Acquisition ◽  
Eukaryotic Dna ◽  
Sequence Requirements ◽  
Dna Acquisition

AbstractCentromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. Diatom centromere sequences contain low GC content regions and an abundance of long contiguous AT windows, but lack repeats or other conserved sequence features. Native and foreign sequences of similar GC content can maintain episomes and recruit the diatom centromeric histone protein CENP-A, suggesting non-native sequences can also function as diatom centromeres. Thus, simple sequence requirements enable DNA from foreign sources to incorporate into the nuclear genome repertoire as stable extra-chromosomal episomes, revealing a potential mechanism for bacterial and foreign eukaryotic DNA acquisition.

The evolution of species-type specificity in the global DNA sequence organization of mitochondrial genomes

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 342-356 ◽  
Author(s):  
Kathleen A. Hill ◽  
Shiva M. Singh
Keyword(s):  
Dna Sequence ◽  
Related Species ◽  
Nuclear Genome ◽  
Sequence Length ◽  
Mitochondrial Genomes ◽  
Evolutionary Time ◽  
Closely Related Species ◽  
Sequence Organization ◽  
Dna Sequence Organization ◽  
Species Type

Prokaryote genomes and nuclear genomes of eukaryotes have a global DNA sequence organization that is species type specific, determined primarily by nearest-neighbor nucleotide associations, and independent of gene function and sequence length. The determinants of such a global structure have remained largely uncharacterized. The monophyletic and endosymbiotic origin of mitochondria permit examination of the influence of evolutionary time and host species type. Different global structures were seen among (i) protozoan and plant, (ii) fungal, (iii) algal (iv) nematode, (v) echinoderm, (vi) insect, and (vii) vertebrate species following examination of 28 complete mitochondrial genomes using chaos representation and measures of short-sequence representation. The mitochondrial genomes have biases in single-nucleotide and dinucleotide representation, specifically, an overrepresentation of A and T nucleotides and CC/GG and AG/CT dinucleotides and a deficiency of CG dinucleotides, in all but one genome. Dinucleotide representation is similar among (i) mitochondrial genomes of more closely related species; (ii) mitochondrial genomes and the Mycoplasma capricolum genome, a proposed progenitor of mitochondrial genomes; and (iii) mitochondrial genomes of diverse species, more so than between the mitochondrial and the nuclear genome of the same or a closely related species. It is hypothesized that sufficient evolutionary time has permitted host-specific constraints to affect nuclear and mitochondrial genomes and that different species type specific constraints influence nuclear and mitochondrial genome global structure.Key words: chaos representation, mitochondrial genomes, primary sequence organization, oligonucleotide frequencies.

scholarly journals Mitochondrial COI Sequence Variations within and among Geographic Samples of the Hemp Pest Psylliodes attenuata from China

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 370
Author(s):  
Litao Guo ◽  
Feng Gao ◽  
Yi Cheng ◽  
Chunsheng Gao ◽  
Jia Chen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Cannabis Sativa ◽  
Flea Beetle ◽  
Dna Barcode ◽  
Coi Gene ◽  
Long Distance ◽  
Mitochondrial Recombination ◽  
Mitochondrial Coi ◽  
Network Analyses ◽  
Industrial Hemp

The hemp flea beetle Psylliodes attenuata (Coleoptera: Chrysomelidae: Psylliodes) is a common pest of Cannabis sativa, including cultivars of both industrial hemp and medicinal marijuana. Both the larval and adult stages of this beetle can cause significant damages to C. sativa, resulting in substantial crop losses. At present, little is known about the populations of this pest, including its genetic diversity. In this study, we obtained 281 P. attenuata samples from nine field sites representing broad industrial hemp productions in China and analyzed their DNA sequences at the mitochondrial COI gene, the insect DNA barcode. Our analyses revealed a total of 48 haplotypes, with 28 being found only in one specimen each while the remaining 20 were shared by two or more specimens each. Of the 20 shared haplotypes, eight were shared among local populations often from far away locations, consistent with recent long-distance dispersals. However, the observed putative long-distance dispersals have not obscured the significant genetic differentiations among the regional populations from northeastern, eastern, central and southwestern China. Interestingly, haplotype network analyses suggest evidence for potential mitochondrial recombination in natural populations of this species. We briefly discuss the implications of our results on its evolution, center of diversity, route of spread, and pest management strategies in hemp fields.

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.

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