scholarly journals First nuclear genome assembly of an extinct moa species, the little bush moa (Anomalopteryx didiformis)

2018 ◽  
Author(s):  
Alison Cloutier ◽  
Timothy B. Sackton ◽  
Phil Grayson ◽  
Scott V. Edwards ◽  
Allan J. Baker
Keyword(s):  
Ancient Dna ◽  
Genome Assembly ◽  
Limb Development ◽  
High Throughput Sequencing ◽  
Nuclear Dna ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Population Level ◽  
Single Copy ◽  
Vertebrate Limb Development

AbstractHigh throughput sequencing (HTS) has revolutionized the field of ancient DNA (aDNA) by facilitating recovery of nuclear DNA for greater inference of evolutionary processes in extinct species than is possible from mitochondrial DNA alone. We used HTS to obtain ancient DNA from the little bush moa (Anomalopteryx didiformis), one of the iconic species of large, flightless birds that became extinct following human settlement of New Zealand in the 13 th century. In addition to a complete mitochondrial genome at 249.9X depth of coverage, we recover almost 900 Mb of the moa nuclear genome by mapping reads to a high quality reference genome for the emu (Dromaius novaehollandiae). This first nuclear genome assembly for moa covers approximately 75% of the 1.2 Gb emu reference with sequence contiguity sufficient to identify more than 85% of bird universal single-copy orthologs. From this assembly, we isolate 40 polymorphic microsatellites to serve as a community resource for future population-level studies in moa. We also compile data for a suite of candidate genes associated with vertebrate limb development and show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization among this candidate set. We also identify potential function-altering coding sequence variants in moa for future experimental assays.

scholarly journals Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama

2020 ◽  
Author(s):  
Alexis P. Sullivan ◽  
Stephanie Marciniak ◽  
Aaron O’Dea ◽  
Thomas A. Wake ◽  
George H. Perry
Keyword(s):  
Mitochondrial Genome ◽  
Ancient Dna ◽  
Evolutionary Biology ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Nuclear Genome ◽  
Average Frequency ◽  
Land Snail ◽  
Marine Bivalve ◽  
Bocas Del Toro

ABSTRACTAlthough protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n=3), Late Holocene (984-1258 BP) archaeological midden (n=5), and a mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n=5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n=5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7x higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behavior on mollusc evolutionary biology.

DNA sequence components of the Pinusstrobus nuclear genome

1985 ◽  
Vol 15 (1) ◽  
pp. 1-4 ◽  
Author(s):  
Howard B. Kriebel
Keyword(s):  
Nuclear Dna ◽  
Nuclear Genome ◽  
Single Copy ◽  
White Pine ◽  
General Hypothesis ◽  
Reassociation Kinetics ◽  
Dna Reassociation ◽  
Sequence Components ◽  
Dna Reassociation Kinetics ◽  
Continuous Range

The nuclear DNA of Pinusstrobus L. was characterized by whole-genome hydroxyapatite reassociation kinetics. The genome, which is very large, is not well described by partition into three, four, or five major kinetic components. Instead, it consists of a large array of sequence components with kinetics suggesting a more or less continuous range of frequencies from very large to a single copy. The single-copy fraction, which is estimated to be about 24% of the total, appears to fit the general hypothesis for large genomes, i.e., most of it probably consists of ancient diverged repeated sequences. Under standard conditions of DNA reassociation kinetics, these sequences are not completely diverged but react with kinetics indicating that there is an average of about three repeats for the fraction. It is estimated that only about 0.1% of white pine nuclear DNA is expressed as mRNAs.

scholarly journals A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata

GigaScience ◽  
2019 ◽  
Vol 8 (8) ◽  
Author(s):  
Qin Liu ◽  
Yunhai Guo ◽  
Yi Zhang ◽  
Wei Hu ◽  
Yuanyuan Li ◽  
...  
Keyword(s):  
Chagas Disease ◽  
Genome Assembly ◽  
Nuclear Genome ◽  
Single Copy ◽  
Insect Vector ◽  
Female Individual ◽  
Base Level ◽  
Sexual Determination ◽  
High Level ◽  
Triatoma Rubrofasciata

AbstractBackgroundTriatoma rubrofasciata is a widespread pathogen vector for Chagas disease, an illness that affects approximately 7 million people worldwide. Despite its importance to human health, its evolutionary origin has not been conclusively determined. A reference genome for T. rubrofasciata is not yet available.FindingWe have sequenced the genome of a female individual with T. rubrofasciatausing a single molecular DNA sequencing technology (i.e., PacBio Sequel platform) and have successfully reconstructed a whole-genome (680-Mb) assembly that covers 90% of the nuclear genome (757 Mb). Through Hi-C analysis, we have reconstructed full-length chromosomes of this female individual that has 13 unique chromosomes (2n = 24 = 22 + X1 + X2) with a contig N50 of 2.72 Mb and a scaffold N50 of 50.7 Mb. This genome has achieved a high base-level accuracy of 99.99%. This platinum-grade genome assembly has 12,691 annotated protein-coding genes. More than 95.1% of BUSCO genes were single-copy completed, indicating a high level of completeness of the genome.ConclusionThe platinum-grade genome assembly and its annotation provide valuable information for future in-depth comparative genomics studies, including sexual determination analysis in T. rubrofasciata and the pathogenesis of Chagas disease.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals Next-generation sequencing yields complete mitochondrial genome assembly of peaceful betta fish, Betta imbellis (Teleostei: Osphronemidae)

2020 ◽  
Vol 5 (4) ◽  
pp. 3856-3858
Author(s):  
Syed Farhan Ahmad ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
Aorarat Suntronpong ◽  
Tavun Pongsanarm ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mitochondrial Genome ◽  
Genome Assembly ◽  
Complete Mitochondrial Genome ◽  
Next Generation ◽  
Generation Sequencing

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 INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. eabe5054
Author(s):  
Qianxin Wu ◽  
Chenqu Suo ◽  
Tom Brown ◽  
Tengyao Wang ◽  
Sarah A. Teichmann ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Limit Of Detection ◽  
Point Of Care ◽  
Population Level ◽  
Reaction Products ◽  
Testing Strategy ◽  
Asymptomatic Patients ◽  
Testing Stage ◽  
Population Scale

We present INSIGHT [isothermal NASBA (nucleic acid sequence–based amplification) sequencing–based high-throughput test], a two-stage coronavirus disease 2019 testing strategy, using a barcoded isothermal NASBA reaction. It combines point-of-care diagnosis with next-generation sequencing, aiming to achieve population-scale testing. Stage 1 allows a quick decentralized readout for early isolation of presymptomatic or asymptomatic patients. It gives results within 1 to 2 hours, using either fluorescence detection or a lateral flow readout, while simultaneously incorporating sample-specific barcodes. The same reaction products from potentially hundreds of thousands of samples can then be pooled and used in a highly multiplexed sequencing–based assay in stage 2. This second stage confirms the near-patient testing results and facilitates centralized data collection. The 95% limit of detection is <50 copies of viral RNA per reaction. INSIGHT is suitable for further development into a rapid home-based, point-of-care assay and is potentially scalable to the population level.

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