Paul H. Dear

Medical Research Council (UKRI) | mrc · MRC Laboratory of Molecular Biology

For large genomes, such as most eukaryotes, it is difficult or impossible to produce a complete, gap‐free genome sequence. Genome mapping entails finding the relative positions of different deoxyribonucleic acid (DNA) sequences in such an incompletely sequenced genome, often across large distances (kb or Mb). An accurate genome map arranges sequenc...

Aims An assay based on 16S rDNA PCR technology has been designed to detect a single intact bacterium whilst eliminating free DNA from dead bacteria, thus offering unprecedented sensitivity and scope to the analysis of bacterial carriage in clinical specimens. We hypothesised that application of such an assay to neonatal CSF will enable accurate, fa...

Neonatal bacterial meningitis, 16SrDNA PCR.

Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to addre...

List of transcription factor annotation for Rafflesia cantleyi flower transcripts. (XLSX)

Functional annotation of the 52 transcripts that showed very high abundance in the Rafflesia cantleyi flower transcriptome. (XLSX)

K-mer distribution plot. (TIF)

List of annotation for Rafflesia cantleyi flower transcripts. (XLSX)

Top enriched KEGG pathways represented in the Rafflesia cantleyi flower transcripts. (XLSX)

Genes differentially expressed between flower and floral bud of Rafflesia cantleyi. (XLSX)

Annotation of genes that showed higher expression in the perigone tissue of the flower compared to the floral bud of Rafflesia cantleyi. (XLSX)

List of Rafflesia cantleyi genes selected for RT-qPCR analysis. (XLSX)

List of enzyme code annotation for Rafflesia cantleyi flower transcripts. (XLSX)

MIC DNA sequences surrounding Cbs sites.DOI: http://dx.doi.org/10.7554/eLife.19090.011

Putative TE annotation of high-confidence 7551 IESs.Raw RepeatMasker output of the high confidence set of 7551 IESs, with two additional columns: the IES identifier (as in Supplementary file 3A) and the total putative TE content of each IES.DOI: http://dx.doi.org/10.7554/eLife.19090.020

Genome assembly and centromere structure. (A) Genome assembly statistics. (B) T. thermophila superscaffolds assembled by HAPPY physical mapping. (C) Chromosome super-assemblies. (D) Suspected Chimeric MIC Supercontigs. (E) Most centric MAC chromosomes are among the ten longest MAC chromosomes. DOI: http://dx.doi.org/10.7554/eLife.19090.025

Chromosome breakage and NMCs. (A) The 225 Cbs identified in the T. thermophila MIC genome. (B) The 181 T. thermophila MAC chromosomes: Lengths and flanking Cbs's. (C) Conservation of chromosome breakage sites 3L-15 to 26 relative to flanking genes in all four examined Tetrahymena species. (D) Identity and lengths of Tetrahymena species scaffolds an...

Tetrahymena putative TE library.Consensus sequences of putative TEs of the Tetrahymena germline genome (fasta format): combination of de novo repeat library and TEs from the literature. See 'Materials and methods', 'Repeat Analysis'.DOI: http://dx.doi.org/10.7554/eLife.19090.018

Details of putative TEs contribution to the MIC chromosome super-assemblies.Detailed metrics for each putative TE contribution to Tetrahymena MIC chromosomes super-assemblies, such as numbers of fragments, total amount, average divergence to consensus (proxy for age), etc. Obtained by parsing the RepeatMasker output (.out file), using https://githu...

Internally eliminated sequences. (A) 7551 High Confidence IESs. (B) Summary of the putative TE content in IESs. (C) Interspersed repeat (putative TEs) content. (D) Characteristics of IESs within protein-coding regions. DOI: http://dx.doi.org/10.7554/eLife.19090.027

Cbs segment sequences and alignments. DOI: http://dx.doi.org/10.7554/eLife.19090.028

Meningitis in newborn babies is difficult to rule out either clinically or microbiologically, which leads to uncertainty with regards to the initiation and the length of antimicrobial treatment, with risks of either under- or over-treating. A different diagnostic approach that will offer high negative predictive value (NPV) is needed to overcome th...

Study objective Meningitis in newborn babies is difficult to rule out either clinically or microbiologically, which leads to uncertainty with regards to the initiation and the length of antimicro-bial treatment, with risks of either under-or over-treating. A different diagnostic approach that will offer high negative pre-dictive value (NPV) is need...

The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on...

The C-value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350-fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus Genlisea, displaying a 25-fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomi...

This was rejected by Archives of Disease of Childhood and will be used as a basis for a subsequent review paper.

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry dis...

Copy number alterations are frequently found in colorectal cancer (CRC), and recurrent gains or losses are likely to correspond to regions harbouring genes that promote or impede carcinogenesis respectively. Gain of chromosome 13q is common in CRC but, because the region of gain is frequently large, identification of the driver gene(s) has hitherto...

Chromosomal translocations and other abnormalities are central to the initiation of cancer in all cell types. Understanding the mechanism is therefore important to evaluate the evolution of cancer from the cancer initiating events to overt disease. Recent work has concentrated on model systems to develop an understanding of the molecular mechanisms...

Background Eimeria is a genus of parasites in the same phylum (Apicomplexa) as human parasites such as Toxoplasma, Cryptosporidium and the malaria parasite Plasmodium. As an apicomplexan whose life-cycle involves a single host, Eimeria is a convenient model for understanding this group of organisms. Although the genomes of the Apicomplexa are diver...

Details of Eimeria tenella HAPPY map markers. List of Eimeria tenella HAPPY map markers together with relevant details including mapping information, and primers and amplicon sequences.

Analysis of BAC-end sequences. Summary of results of BAC-end sequence analysis.

Alignment of the integrated HAPPY map with WGS assemblies of the E. tenellagenome. Graphical representation of the alignment of the HAPPY map and sequence of the Eimeria tenella draft genome assembly contigs. For each map segment, labels “Cxxxxxxxx” are contig numbers in the 2007 assembly; labels “SCxx.y” indicate the supercontig (xx) and contig (y...

Marker typing results according to stages. Summary of marker typing results for the initial (“First”) set of HAPPY markers, for redesigned markers (“Second” and “Third”), for markers designed against chromosomally-assigned genes (“Chr”), and for all markers combined ("Overall"). Based on the average DNA content of each aliquot in the mapping panel,...

The comparison of the HAPPY map and sequence of (A) contig _00031646 and (B) contig_00031359. Graphical representation of the alignment of the HAPPY map and sequence of the two largest Eimeria tenella draft genome assembly contigs.

In northwestern Iberia, two largely allopatric Lacerta lepida mitochondrial lineages occur, L5 occurring to the south of Douro River and L3 to the north, with a zone of putative secondary contact in the region of the Douro River valley. Cytochrome b sequence chromatograms with polymorphisms at nucleotide sites diagnostic for the two lineages were d...

The term 'field cancerization' is used to describe an epithelial surface that has a propensity to develop cancerous lesions, and in the case of the aerodigestive tract this is often as a result of chronic exposure to carcinogens in cigarette smoke 1, 2. The clinical endpoint is the development of multiple tumours, either simultaneously or sequentia...

Rearrangements of the genome can be detected by microarray methods and massively parallel sequencing, which identify copy-number alterations and breakpoint junctions, but these techniques are poorly suited to reconstructing the long-range organization of rearranged chromosomes, for example, to distinguish between translocations and insertions. The...

DNA not only transmits genetic information but can also serve as a versatile supramolecular scaffold. Here we describe a strategy for the synthesis and replication of DNA displaying hundreds of substituents using directed evolution of polymerase function by short-patch compartmentalized self-replication (spCSR) and the widely used fluorescent dye l...

Amplification of distal 3q is the most common genomic aberration in squamous lung cancer (SQC). SQC develops in a multistage progression from normal bronchial epithelium through dysplasia to invasive disease. Identifying the key driver events in the early pathogenesis of SQC will facilitate the search for predictive molecular biomarkers and the ide...

Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical "contig" maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes...

The term 'single-molecule genomics' (SMG) describes a group of molecular methods in which single molecules are detected or sequenced. The focus on the analysis of individual molecules distinguishes these techniques from more traditional methods, in which template DNA is cloned or PCR-amplified prior to analysis. Although technically challenging, th...

Copy-number variation (CNV)--the presence of additional or missing segments of chromosomes in some individuals--has been found to be abundant in humans and adds another dimension of variation to the genome. Copy-number variants have already been associated with some diseases and disease susceptibilities and are likely to prove as significant as seq...

Supplementary materials.

Most cancer genomes are characterized by the gain or loss of copies of some sequences through deletion, amplification or unbalanced translocations. Delineating and quantifying these changes is important in understanding the initiation and progression of cancer, in identifying novel therapeutic targets, and in the diagnosis and prognosis of individu...

Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. We present a fully resolved phylogeny for ursids based on ten complete mitochondrial ge...

Salmonella Genomic Island-1 (SGI-1) harbors a cluster of genes encoding multidrug resistance (MDR). SGI-1 is horizontally transmissible and is therefore of significant public health concern. This study presents two novel realtime PCRs detecting three SGI-1 protein-coding genes and a SGI-1 fingerprinting assay. These assays were applied to 445 Europ...

Eimeria tenella is an intracellular protozoan parasite that infects the intestinal tracts of domestic fowl and causes coccidiosis, a serious and sometimes lethal enteritis. Eimeria falls in the same phylum (Apicomplexa) as several human and animal parasites such as Cryptosporidium, Toxoplasma, and the malaria parasite, Plasmodium. Here we report th...

Many methods exist for genotyping—revealing which alleles an individual carries at different genetic loci. A harder problem is haplotyping—determining which alleles lie on each of the two homologous chromosomes in a diploid individual. Conventional approaches to haplotyping require the use of several generations to reconstruct haplotypes within a p...

Tetrahymena thermophila is the best studied of the ciliates, a diversified and successful lineage of eukaryotic protists. Mirroring the way in which many metazoans partition their germ line and soma into distinct cell types, ciliates separate germ line and soma into two distinct nuclei in a single cell. The diploid, transcriptionally silent micronu...

Human cancers and some congenital traits are characterized by cytogenetic aberrations including translocations, amplifications, duplications or deletions that can involve gain or loss of genetic material. We have developed a simple method to precisely delineate such regions with known or cryptic genomic alterations. Molecular copy-number counting (...

In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole...

This method is designed to assemble long, continuous DNA sequences using minimal amounts of fragmented ancient DNA as template. This is achieved by a two-step approach. In the first step, multiple fragments are simultaneously amplified in a single multiplex reaction. Subsequently, each of the generated fragments is amplified individually using a si...

A megabase pair (Mbp) is a unit of length of nucleic acids, equal to one million base pairs or to one thousand kilobase pairs.

A high-resolution metric HAPPY map of human chromosome 14 Dear, P.H., Bankier, A.T. and Piper, M.B. Genomics 48, 232–241

This article has no abstract.

In complex diseases, genome linkage analysis, fine mapping and association studies are used to identify disease-causing genes. With the completion of the human genome sequence and its annotation, positional candidate gene studies have become an attractive method to identify genes involved in complex disorders by screening for selected chromosomal i...

This article has no abstract.

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive ami...

Genome maps give the location of defined sequence features in the genome and serve as a framework around which to assemble the complete genome sequence. Without them, the complete assembly of complex genomes purely from the shotgun sequence data is effectively impossible. Here, I summarize the principle methods that are used to make detailed genome...

Cryptosporidium species cause acute gastroenteritis and diarrhoea worldwide. They are members of the Apicomplexa--protozoan pathogens that invade host cells by using a specialized apical complex and are usually transmitted by an invertebrate vector or intermediate host. In contrast to other Apicomplexans, Cryptosporidium is transmitted by ingestion...

An international consortium is the driving force behind several new genome-related projects, mainly focused on Eimeria tenella, the cause of avian, caecal coccidiosis. The largest project is a whole genome shotgun project, which is at 8.3-fold coverage, and is complemented by complete sequencing of the two smallest E. tenella chromosomes and the pr...

The apicomplexan Cryptosporidium parvum is an intestinal parasite that affects healthy humans and animals, and causes an unrelenting infection in immunocompromised individuals such as AIDS patients. We report the complete genome sequence of C. parvum, type II isolate. Genome analysis identifies extremely streamlined metabolic pathways and a relianc...

To detect a wide range of Cryptosporidium species from human faeces by analysis of the Cryptosporidium oocyst wall protein gene by PCR. The nested-assay comprised an initial amplification using a conventional thermocycler followed by real time PCR using a LightCycler with SYBR Green I for the characterization of the amplicons. The technique uses fo...

A nested PCR assay (TPILC-PCR) was developed to detect and distinguish between Giardia duodenalis assemblages A and B from human faeces by analysis of the triose phosphate isomerase gene (tpi). The assay comprised an initial multiplexed block-based amplification. This was followed by two separate real-time PCR assays specific for assemblages A and...

The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical map, we devised a novel and gene...

HAPPY mapping is an in vitro approach for defining the order and spacing of DNA markers directly on native genomic DNA. This cloning-free technique is based on analysing the segregation of markers amplified from high molecular weight genomic DNA which has been broken randomly and 'segregated' by limiting dilution into subhaploid samples. It is a un...

Much of the effort in any genomics programme arises from the need to generate and purify large numbers of identical molecules, since most analytical tools rely on the analysis of bulk DNA. Biological steps such as bacterial cloning--commonly used to prepare bulk samples of defined DNA fragments--are capricious and introduce their own restrictions a...

Locating DNA sequences to specific chromosomal segments is essential for associating genes with phenotypes. It is routinely achieved by segregation analysis using meiotic mapping populations that have also been used to collect phenotypic information. However, meiotic mapping is struggling to cope with the shear volume of sequences emerging from hig...

Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We...

The genome of the lower eukaryote Dictyostelium discoideum comprises six chromosomes. Here we report the sequence of the largest, chromosome 2, which at 8 megabases (Mb) represents about 25% of the genome. Despite an A + T content of nearly 80%, the chromosome codes for 2,799 predicted protein coding genes and 73 transfer RNA genes. This gene densi...

The genome of the lower eukaryote

An assay that uses heminested PCR-restriction fragment length polymorphism analysis for the detection and genotyping of Giardia duodenalis on the basis of polymorphism in the triose phosphate isomerase (tpi) gene was developed. This assay was evaluated with DNA extracted from purified parasite material, bacterial cultures, whole human feces contain...

The genome maps of a small number of prokaryotes have been completed. In recent years, efforts have been made to map the entire mouse and human genomes; indeed the human-genome project-a global effort to clone, sequence, and map the human genome-represents the most ambitious and challenging task of modem human biology.