Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

BACKGROUND

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

RESULTS

As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.

CONCLUSIONS

Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

In Vivo Validation of Alternative FDXR Transcripts in Human Blood in Response to Ionizing Radiation

Following cell stress such as ionising radiation (IR) exposure, multiple cellular pathways are activated. We recently demonstrated that ferredoxin reductase (FDXR) has a remarkable IR-induced transcriptional responsiveness in blood. Here, we provided a first comprehensive FDXR variant profile following DNA damage. First, specific quantitative real-time polymerase chain reaction (qPCR) primers were designed to establish dose-responses for eight curated FDXR variants, all up-regulated after IR in a dose-dependent manner. The potential role of gender on the expression of these variants was tested, and neither the variants response to IR nor the background level of expression was profoundly affected; moreover, in vitro induction of inflammation temporarily counteracted IR response early after exposure. Importantly, transcriptional up-regulation of these variants was further confirmed in vivo in blood of radiotherapy patients. Full-length nanopore sequencing was performed to identify other FDXR variants and revealed the high responsiveness of FDXR-201 and FDXR-208. Moreover, FDXR-218 and FDXR-219 showed no detectable endogenous expression, but a clear detection after IR. Overall, we characterised 14 FDXR transcript variants and identified for the first time their response to DNA damage in vivo. Future studies are required to unravel the function of these splicing variants, but they already represent a new class of radiation exposure biomarkers.

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 highly contiguous human genomes de novo in 9 d. We achieved roughly 63× coverage, 42-kb read N50 values and 6.5× coverage in reads >100 kb using three flow cells per sample. Shasta produced a complete haploid human genome assembly in under 6 h on a single commercial compute node. MarginPolish and HELEN polished haploid assemblies to more than 99.9% identity (Phred quality score QV = 30) with nanopore reads alone. Addition of proximity-ligation sequencing enabled near chromosome-level scaffolds for all 11 genomes. We compare our assembly performance to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Generation of a Transcriptional Radiation Exposure Signature in Human Blood Using Long-Read Nanopore Sequencing

In the event of a large-scale event leading to acute ionizing radiation exposure, high-throughput methods would be required to assess individual dose estimates for triage purposes. Blood-based gene expression is a broad source of biomarkers of radiation exposure which have great potential for providing rapid dose estimates for a large population. Time is a crucial component in radiological emergencies and the shipment of blood samples to relevant laboratories presents a concern. In this study, we performed nanopore sequencing analysis to determine if the technology can be used to detect radiation-inducible genes in human peripheral blood mononuclear cells (PBMCs). The technology offers not only long-read sequencing but also a portable device which can overcome issues involving sample shipment, and provide faster results. For this goal, blood from nine healthy volunteers was 2 Gy ex vivo X irradiated. After PBMC isolation, irradiated samples were incubated along with the controls for 24 h at 37°C. RNA was extracted, poly(A)+ enriched and reverse-transcribed before sequencing. The data generated was analyzed using a Snakemake pipeline modified to handle paired samples. The sequencing analysis identified a radiation signature consisting of 46 differentially expressed genes (DEGs) which included 41 protein-coding genes, a long non-coding RNA and four pseudogenes, five of which have been identified as radiation-responsive transcripts for the first time. The genes in which transcriptional expression is most significantly modified after radiation exposure were APOBEC3H and FDXR, presenting a 25- and 28-fold change on average, respectively. These levels of transcriptional response were comparable to results we obtained by quantitative polymerase chain reaction (qPCR) analysis. In vivo exposure analyses showed a transcriptional radioresponse at 24 h postirradiation for both genes together with a strong dose-dependent response in blood irradiated ex vivo. Finally, extrapolating from the data we obtained, the minimum sequencing time required to detect an irradiated sample using APOBEC3H transcripts would be less than 3 min for a total of 50,000 reads. Future improvements, in sample processing and bioinformatic pipeline for specific radiation-responsive transcript identification, will allow the provision of a portable, rapid, real-time biodosimetry platform based on this new sequencing technology. In summary, our data show that nanopore sequencing can identify radiation-responsive genes and can also be used for identification of new transcripts.

Construction of a RFLP genetic linkage map for oil palm (Elaeis guineensis Jacq.)

We have developed a restriction fragment length polymorphism (RFLP) genetic map in oil palm (Elaeis guineensis Jacq.) for use in breeding programmes. A segregating population of 98 individuals was probed with 84 informative low copy clones (mainly PstI genomics). This yielded 103 scorable loci, of which 97 could be linked into 24 groups of two or more markers (n = 16 for oil palm), encompassing a total of 860 cM. The high level of linkage between markers (95%) suggests good genome coverage and very little segregation distortion of markers was observed. The mapping population, which was generated by the selfing of an important breeding palm (A 137/30), also segregated for the shell thickness character (Sh), enabling mapping of the gene conferring this major commercial trait. The nearest RFLP marker (pOPgSP1282) was located 9.8 cM from Sh in the mapping population and 6.6 cM away in a related (A137/30 x E80/29) smaller population (45 palms). Strategies for conversion of RFLP markers to a PCR format were explored and two important markers were shown to generate allelic variants following PCR amplification and restriction digestion of PCR products. The application of this map to oil palm breeding programmes is discussed.

The potential for underutilized crops to improve security of food production

Staple crops face major challenges in the near future and a diversification away from over-reliance on staples will be important as part of the progress towards the goal of achieving security of food production. Underutilized or neglected crops species are often indigenous ancient crop species which are still used at some level within the local, national or even international communities, but have the potential to contribute further to the mix of food sources than they currently do. The most cost-effective and easily disseminated changes that can be made to a crop are changes to the genetics, as these are contained within the seed itself and, for many species, the seed is a pure breeding, self-replicating, resource. This article focuses on the potential of underutilized crops to contribute to food security and, in particular, whether genetics and breeding can overcome some of the constraints to the enhanced uptake of these species in the future. The focus here is on overview rather than detail and subsequent articles will examine the current evidence base.

Using principle component analysis to compare genetic diversity across polyploidy levels within plant complexes: an example from British Restharrows (Ononis spinosa and Ononis repens)

The investigation of genetic diversity between related plant populations which differ in ploidy levels is problematic, with common statistical methods developed for diploids being inappropriate for polyploid species. Studies into gene flow in such complexes are critical and can shed light on the mechanisms that generate and maintain populations of different polyploidy levels. We have investigated the use of principle component (PCO) analysis as one approach to elucidate population structure within British Restharrows (Leguminsoae, Ononis spp). Restharrows were common agricultural weed species until the advent of mechanical ploughing and both diploid (2n=2x=30; O. spinosa and O. intermedia) and tetraploid (2n=4x=60; O. repens and O. maritima) taxa exist. Patterns of genetic diversity were investigated among British Restharrows using 10 microsatellite loci with 21 Restharrow populations analysed (411 individual plants) from Central and Eastern Britain. PCO analysis revealed clear genetic differentiation of the sampled plants into two groups, corresponding to O. spinosa/O. intermedia (diploid) and O. repens/O. maritima (tetraploid) plants. Evidence of genetic differentiation by distance was also revealed for O. repens/O. maritima, but not for O. spinosa/O. intermedia. The data suggest the presence of strong reproductive barriers between diploid and tetraploid Restharrows in Britain, but not within ploidy levels. This genetic isolation between ploidy levels is confirmed by a detailed analysis of a sympatric site (Harton Down Hill). These results demonstrate that PCA analysis is a suitable general tool for comparing related species of different ploidy levels.

Characterisation of copia-like retrotransposons in oil palm ( Elaeis guineensis Jacq.)

The work aimed to isolate and characterise copia-like sequences from Elaeis guineensis. Thirty-two different RT (reverse transcriptase) sequences were isolated from a single oil palm genome using degenerate primers. Extreme sequence heterogeneity was observed. The DNA and protein sequences were assigned to three different classes (A, B, C) on the basis of bootstrapping. We estimated the copy number of the three different classes by using a dot-blot analysis. The comparative results suggest that class-B RT sequences occur at a higher copy number in Cocos nucifera than in Elaeis guineensis and E. oleifera. Class-C RT sequences, which comprise the bulk of isolated sequences, occur in much higher copy number in Elaeis guineensis than in Cocos nucifera, and E. oleifera. Class-A sequences, which have low copy number in Elaeis guineensis and Cocos nucifera, are not present in E. oleifera. Our preliminary results suggest that class-C sequences represent about 5% of the E. guineensis genome, class B, 1% and class A, 0.1%. The methylation status of genomic domains specified by the RT probes was analysed using two pairs of restriction enzymes, each pair having the same recognition sites but different methylation sensitivities ( MspI, HpaII and Sau3AI, MboI). Results from these experiments showed clearly that the genomic domains specified by the RT probes are methylated. These also suggest that a higher copy number appears to correlate to a higher degree of methylation. Our preliminary results suggest that copia-like retrotransposons, because of their ubiquity and diversity, have great potential as genetic markers for plant genome and biodiversity analysis in E. guineensis.

The use of molecular markers to investigate the genetic structure of an oil palm breeding programme

RFLP markers (40 probes covering 60% of the oil palm genome) have been used to assess genetic diversity within 54 palms of a specific oil palm breeding programme. A further 10 palms encompassing a broader range of origins were also included to provide a wider framework for comparative analysis. These palms represent a majority of the parents in a crossing programme which aims to combine the best features of African tenera germplasm with South-east Asian Deli dura material. Progeny from these crosses are planted in up to six sites on three continents, where the palms are being assessed in detail for yield components. A total of 157 RFLP bands were scored and the data analysed by calculating genetic distances according to Nei & Li, and by correspondence and cluster analysis. The relationships that emerge through this molecular analysis correspond well with known pedigree and provenance. For example, south-east Asian Deli dura material forms a cluster clearly distinct from AVROS pisifera gene pools, and a selection of African breeding material forms a further and broader grouping. The potential ability of markers to assist in oil palm breeding through examination of the genetic structure of crossing programmes is discussed, as is their value in parental selection to maintain residual diversity within specific breeding pools and use in evaluating the fidelity of breeding lineages.

Hip and ankle range of motion in elite classical ballet dancers and controls

OBJECTIVE

To report range of motion at the hip and ankle in male and female ballet dancers compared with controls.

DESIGN

Cross-sectional cohort study with convenience control sample.

SETTING

National classical ballet school in Australia.

PARTICIPANTS

Thirty-three female and 30 male full-time ballet students of mean (SD) age 16.9 (0.8) and 18.0 (1.4) years, respectively. Controls were 31 female and 16 male nondancing, normally active university students of average ages 18.8 +/- 0.6 and 18.8 +/- 0.9 years, respectively.

MAIN OUTCOME MEASURES

Degrees of range of motion of left and right sides for the following four movements: standing plié in parallel-passive ankle dorsiflexion (DF), standing turnout in the balletic first position-lower limb external rotation (LLER), supine hip external rotation (ER), supine hip internal rotation (IR). Two additional ranges of motion were calculated. External rotation below the hip joint (BHER) was derived by subtracting hip ER from LLER, and total supine hip rotation (Hip IR + ER) was derived by summing hip ER and hip IR.

MAIN RESULTS

On both left and right sides, dancers had greater LLER (p < 0.0001) and hip ER (p < 0.0001) but lesser hip IR than the controls (p < 0.0001). Female but not male dancers had greater total supine hip rotation (hip ER+IR) than controls (p < 0.05). There was no difference in either BHER or ankle DF between dancers and controls. Within dancers, females had greater range in both left and right hip IR, LLER, and hip IR + ER. There was no difference in hip ER. Regression analysis revealed that LLER related to hip ER in both males and females.

CONCLUSIONS

Elite classical dance students had greater hip external rotation (both ER and LLER) and less hip internal rotation than controls but similar BHER and ankle DF. Since ER below the hip joint and ankle DF do not differ between dancers and controls, despite repeated training of these movements in ballet, there may be anatomical (bony/ligamentous) limitations to these movements.

Assessment of nuclear, mitochondrial and chloroplast RFLP markers in oil palm (Elaeis guineensis Jacq.)

A variety of DNA probes was used to screen a diverse set of oil palm accessions in order to identify markers with a utility in genotype discrimination. This survey included samples of the commercial oil palm native to Africa (Elaeis guineensis Jacq.), the closely-related South American species [E.oleifera (HBK) Cortes] and inter-specific hybrids of the two. Of 106 major chloroplast bands none showed differences between E. guineensis and E. Oleifera. Mitochondrial and ribosomal probes were more informative inter-specifically (the former allowing identification of the maternal inheritance of mitochondria) and may be useful in hybrid breeding programmes; however, they were unable to identify polymorphism within E. guineensis. In contrast, low-copy nuclear genomic clones were able to identify intra-specific variation, though in most cases they revealed a relatively small number of allelic variants. One DNA probe showed a much larger number of band variants, revealing ten patterns amongst 13 E. guineensis accessions, and should prove useful in genetic fingerprinting and evaluation of oil-palm germplasm collections.

Factors affecting glucose turnover and utilization in the neonatal subhuman primate (Macaca mulatta)

The rate of glucose turnover (RT) has been studied in 33 subhuman primate newborn (Macaca mulatta). There appears to be a linear relationship between RT and plasma glucose (G) such that RT = 1.053 G + 0.242. Liver enzymes show a change in specificity such that hexokinase is predominant in the preterm animals and glucokinase has little activity, while in the term animal these enzymes of of equal activity. In the 1-year-old animal glucokinase predominates. Hexokinase activity in the brain remains constant throughout development. These results imply that low blood glucose in the neonate is not associated with increased glucose utilization.

Factors affecting gluconeogenesis in the neonatal subhuman primate (Macaca mulatta)

The capacity for gluconeogenesis has been studied in 33 subhuman primate newborn (Macaca mulatta) in the basal steady state. Basal blood glucose levels were seen to rise with increasing postnatal age. Availability of the major gluconeogenic substrates, alanine and lactate, was adequate at times when blood glucose and the rate of gluconeogenesis were low. Hepatic and renal cortical content of the four key gluconeogenic enzymes was low during the 1st week of life compared to adult levels. Diminished induction of the gluconeogenic enzymes did not appear to be the cause of low blood glucose levels. The serum-free fatty levels were directly correlated to both the basal glucose levels and to the rate of gluconeogenesis.

Hypothalamic regulation of insulin release in rhesus monkeys

Evidence of a neurohumoral factor capable of stimulating insulin and glucagon secretion was found in perfusates from ventrolateral hypothalamus (VLH) of rhesus monkeys. The perfusates from the VLH were collected via push-pull cannulas and injected into the peripheral circulation. Increase in portal insulin and glucagon was observed following the injection of six different perfusates. The amount of insulin released from isolated rat islets incubated with perfusates was significantly increased at glucose concentrations greater than 5 mM. The perfusates from the VLH appear to have effects on insulin and glucagon secretion that are opposite those of somatostatin.