Diatom Centromeres Suggest a Novel Mechanism for Nuclear Gene 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.

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Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1700764114 ◽

2017 ◽

Vol 114 (29) ◽

pp. E6015-E6024 ◽

Cited By ~ 26

Author(s):

Rachel E. Diner ◽

Chari M. Noddings ◽

Nathan C. Lian ◽

Anthony K. Kang ◽

Jeffrey B. McQuaid ◽

...

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Gc Content ◽

Nuclear Genome ◽

Artificial Chromosomes ◽

Conserved Sequence ◽

Foreign Dna ◽

Sequence Requirements ◽

Simple Sequence ◽

Dna Acquisition

Centromeres 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. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequence features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.

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Hundreds of nuclear and plastid loci yield insights into orchid relationships

10.1101/2020.11.17.386508 ◽

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.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2021.699598 ◽

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.

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

Genome ◽

10.1139/g04-102 ◽

2005 ◽

Vol 48 (1) ◽

pp. 76-87 ◽

Cited By ~ 32

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.

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DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Bioinformatics ◽

10.1093/bioinformatics/btab083 ◽

2021 ◽

Author(s):

Yanrong Ji ◽

Zhihan Zhou ◽

Han Liu ◽

Ramana V Davuluri

Keyword(s):

Dna Sequences ◽

Regulatory Elements ◽

Ease Of Use ◽

Fine Tuning ◽

Supplementary Information ◽

Sequence Motifs ◽

Semantic Relationship ◽

Accurate Identification ◽

Conserved Sequence ◽

Genome Wide

Abstract Motivation Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios. Results To address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widely used programs for genome-wide regulatory elements prediction and demonstrate its ease of use, accuracy and efficiency. We show that the single pre-trained transformers model can simultaneously achieve state-of-the-art performance on prediction of promoters, splice sites and transcription factor binding sites, after easy fine-tuning using small task-specific labeled data. Further, DNABERT enables direct visualization of nucleotide-level importance and semantic relationship within input sequences for better interpretability and accurate identification of conserved sequence motifs and functional genetic variant candidates. Finally, we demonstrate that pre-trained DNABERT with human genome can even be readily applied to other organisms with exceptional performance. We anticipate that the pre-trained DNABERT model can be fined tuned to many other sequence analyses tasks. Availability and implementation The source code, pretrained and finetuned model for DNABERT are available at GitHub (https://github.com/jerryji1993/DNABERT). Supplementary information Supplementary data are available at Bioinformatics online.

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

Open Heart ◽

10.1136/openhrt-2020-001510 ◽

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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Coupling of Bacterial Endosymbiont and Host Mitochondrial Genomes in the Hydrothermal Vent Clam Calyptogena magnifica

Applied and Environmental Microbiology ◽

10.1128/aem.69.4.2058-2064.2003 ◽

2003 ◽

Vol 69 (4) ◽

pp. 2058-2064 ◽

Cited By ~ 48

Author(s):

Luis A. Hurtado ◽

Mariana Mateos ◽

Richard A. Lutz ◽

Robert C. Vrijenhoek

Keyword(s):

Dna Sequences ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Nuclear Gene ◽

Sexual Population ◽

Origin And Evolution ◽

Bacterial Endosymbionts ◽

Sulfur Oxidizing ◽

Tight Association ◽

Clam Population

ABSTRACT The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. This symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. If symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if coupled to the host's maternally inherited mitochondrial DNA. This coupling would be obscured, however, with low rates of horizontal or environmental transfers, the equivalent of recombination between host lineages. Population genetic analyses of C. magnifica clams and associated symbionts from eastern Pacific hydrothermal vents clearly supported the hypothesis of strictly maternal cotransmission. Host mitochondrial and symbiont DNA sequences were coupled in a clam population that was polymorphic for both genetic markers. These markers were not similarly coupled with sequence variation at a nuclear gene locus, as expected for a randomly mating sexual population. Phylogenetic analysis of the two cytoplasmic genes also revealed no evidence for recombination. The tight association between vesicomyid clams and their vertically transmitted bacterial endosymbionts is phylogenetically very young (<50 million years) and may serve as a model for the origin and evolution of eukaryotic organelles.

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First Complete Genome Sequence of Brucella abortus 2308 isolated from an abortion storm in a dairy farm in India

10.21203/rs.3.rs-420448/v1 ◽

2021 ◽

Author(s):

Amit Kumar ◽

Malyaj R Prajapati ◽

Surendra Upadhyay ◽

Anamika Bhordia ◽

Vinod Kumar Singh ◽

...

Keyword(s):

Genome Sequence ◽

Dna Sequences ◽

Brucella Abortus ◽

Complete Genome Sequence ◽

Complete Genome ◽

Messenger Rna ◽

Gc Content ◽

Dairy Farm ◽

Rrna Genes ◽

Sequence Length

Abstract The present report communicates the first complete genome sequence of Brucella abortus 2308 strain isolated from a an abortion storm in a dairy farm located at Kanpur, Uttar Pradesh in India. It caused the last trimester abortions of 32 animals out of 100 cows in a dairy over a period of 60 days. The bacteria were isolated in pure culture from the placenta of aborted cows. The genome sequence length of isolated bacteria is 3,285,606 bp with a 57.25 % GC content, an N50 value of 296,426, L50 value of 4 containing 3,119 coding DNA sequences (CDSs), 49 tRNAs, 1 transfer messenger RNA (mRNA), and 3 rRNA genes. It is the first report of Brucella abortus 2308 isolation and complete genome sequence from Indian subcontinent.

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

10.1101/2020.05.19.104224 ◽

2020 ◽

Cited By ~ 1

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.

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Evolutionary dynamics of neutral phenotypes under DNA substitution models

10.1101/2020.10.26.355438 ◽

2020 ◽

Author(s):

Shadi Zabad ◽

Alan M Moses

Keyword(s):

Dna Sequences ◽

Evolutionary Dynamics ◽

Gc Content ◽

Stabilizing Selection ◽

Restoring Force ◽

Dna Substitution ◽

Long Term Trends ◽

The Mean ◽

Molecular Phenotypes

AbstractWe study the evolution of quantitative molecular traits in the absence of selection. Using a simple theory based on Felsenstein’s 1981 DNA substitution model, we predict a linear restoring force on the mean of an additive phenotype. Remarkably, the mean dynamics are independent of the effect sizes and genotype and are similar to the widely-used OU model for stabilizing selection. We confirm the predictions empirically using additive molecular phenotypes calculated from ancestral reconstructions of putatively unconstrained DNA sequences in primate genomes. We show that the OU model is favoured by inference software even when applied to GC content of unconstrained sequences or simulations of DNA evolution. We predict and confirm empirically that the dynamics of the variance are more complicated than those predicted by the OU model, and show that our results for the restoring force of mutation hold even for non-additive phenotypes, such as number of transcription factor binding sites, longest encoded peptide and folding propensity of the encoded peptide. Our results have implications for efforts to infer selection based on quantitative phenotype dynamics as well as to understand long-term trends in evolution of quantitative molecular traits.

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