DNA AS X: An Information-Coding-Based Model to Improve the Sensitivity in Comparative Gene Analysis

Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler.

Sex chromosomes have evolved multiple times in many taxa. The recent explosion in the availability of whole genome sequences from a variety of organisms makes it possible to investigate sex chromosome evolution within and across genomes. Comparative genomic studies have shown that quite distant species may share fundamental properties of sex chromosome evolution, while very similar species can evolve unique sex chromosome systems. Furthermore, within-species genomic analyses can illuminate chromosome-wide sequence and expression polymorphisms. Here, we explore recent advances in the study of vertebrate sex chromosomes achieved using genomic analyses.

BackgroundSweet potato (Ipomoea batatas (L.) Lam.) is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither a complete reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid crop are available, which in turn impedes progress in research studies in I. batatas functional genomics and molecular breeding.MethodsIn this study, we sequenced full-length transcriptomes in I. batatas and its diploid ancestor I. trifida by single-molecule real-time sequencing and Illumina second-generation sequencing technologies. With the generated datasets, we conducted comprehensive intraspecific and interspecific sequence analyses and experimental characterization.ResultsA total of 53,861/51,184 high-quality long-read transcripts were obtained, which covered about 10,439/10,452 loci in the I. batatas/I. trifida genome. These datasets enabled us to predict open reading frames successfully in 96.83%/96.82% of transcripts and identify 34,963/33,637 full-length cDNA sequences, 1,401/1,457 transcription factors, 25,315/27,090 simple sequence repeats, 1,656/1,389 long non-coding RNAs, and 5,251/8,901 alternative splicing events. Approximately, 32.34%/38.54% of transcripts and 46.22%/51.18% multi-exon transcripts underwent alternative splicing in I. batatas/I. trifida. Moreover, we validated one alternative splicing event in each of 10 genes and identified tuberous-root-specific expressed isoforms from a starch-branching enzyme, an alpha-glucan phosphorylase, a neutral invertase, and several ABC transporters. Overall, the collection and analysis of large-scale long-read transcripts generated in this study will serve as a valuable resource for the I. batatas research community, which may accelerate the progress in its structural, functional, and comparative genomics studies.

Comparative genomic studies in primates have the potential to reveal the genetic and mechanistic basis for human specific traits. These studies may also help us better understand inter-species phenotypic differences that are clinically relevant. Unfortunately, the obvious limitation on sample collection and experimentation in humans and non-human apes severely restrict our ability to perform dynamic comparative studies in primates. Induced pluripotent stem cells (iPSCs), and their corresponding differentiated cells, may provide a suitable alternative system for dynamic comparative studies. Yet, to effectively use iPSCs and differentiated cells for comparative studies, one must characterize the extent to which these systems faithfully represent biological processes in primary tissues. To do so, we compared gene expression data from primary adult heart tissue and iPSC-derived cardiomyocytes from multiple human and chimpanzee individuals. We determined that gene expression in cultured cardiomyocytes from both human and chimpanzee is most similar to that of adult hearts compared to other adult tissues. Using a comparative framework, we found that 50% of gene regulatory differences between human and chimpanzee hearts are also observed between species in cultured cardiomyocytes; conversely, inter-species regulatory differences seen in cardiomyocytes are found significantly more often in hearts than in other primary tissues. Our work provides a detailed description of the utility and limitation of differentiated cardiomyocytes as a system for comparative functional genomic studies in primates.

Genome sequencing of a virulent avian Pasteurella multocida strain GX-Pm reveals the candidate genes involved in the pathogenesis

Non-synonymous cSNPs that occurred in the protein-coding region could potentially alter the amino acid composition and thus the functionality of gene product. Protein variants generated by these non-synonymous cSNPs are thought to be responsible for the diversity of human population and the cause of human diseases associated with inheritance. It is essential to identify these non-synonymous cSNPs/functional variants for functional genomic studies. In addition to direct genome sequencing methods, dbEST has been used for SNP discovery due to its rich information of millions ESTs. Previous SNP discovery methods from dbEST needed to include many ESTs per cluster, which greatly reduce the effectiveness of dbEST. Such approaches would be useful in identifying SNPs for polymorphic markers. We would like to identify these sequence variations as either disease association mutations or functional variants. Therefore, it is necessary to use alternative bioinformatic tools to extract these low frequency functional variants. We have used our CGI bioinformatic tools to data-mining functional variants from ESTs, especially low frequency non-synonymous cSNPs. We have established the CGI tools for comparative genomic studies in identifying novel human genes. With 9848 human reference protein as starting alignment scaffolds and 2.2 million human ESTs, we have now identified more than 50,000 potential functional variants. In addition, our approach can be used to validate and correct amino acid sequences of human reference proteins.

Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. Here, we generated germline and somatic reference genome sequences of the DNA eliminating pig parasitic nematode Ascaris suum and the horse parasite Parascaris univalens. In addition, we carried out in-depth analyses of DNA elimination in the parasitic nematode of humans, Ascaris lumbricoides, and the parasitic nematode of dogs, Toxocara canis. Our analysis of nematode DNA elimination reveals that in all species, repetitive sequences (that differ among the genera) and germline-expressed genes (approximately 1000–2000 or 5%–10% of the genes) are eliminated. Thirty-five percent of these eliminated genes are conserved among these nematodes, defining a core set of eliminated genes that are preferentially expressed during spermatogenesis. Our analysis supports the view that DNA elimination in nematodes silences germline-expressed genes. Over half of the chromosome break sites are conserved between Ascaris and Parascaris, whereas only 10% are conserved in the more divergent T. canis. Analysis of the chromosomal breakage regions suggests a sequence-independent mechanism for DNA breakage followed by telomere healing, with the formation of more accessible chromatin in the break regions prior to DNA elimination. Our genome assemblies and annotations also provide comprehensive resources for analysis of DNA elimination, parasitology research, and comparative nematode genome and epigenome studies.

Genomic characterisation of a clinical Acinetobacter baumannii ST1928 isolate carrying a new ampC allelic variant blaADC-196 gene from China.

On May 31 this year, James Watson received the DNA sequence of his full genome in a ceremony at the Baylor College of Medicine in Houston (TX, USA). It marked the end of a two‐month project by 454 Life Sciences, a biotech company in Branford (CT, USA) specializing in DNA sequencing, which generated the raw data from a blood sample given by Watson. Baylor College then verified whether the sequence encompassed the entire genome and, on July 6, Watson posted his genome—excluding a portion including the ApoE gene, which he had asked to be redacted—online at the GenBank database maintained by the US National Center for Biology Information (Bethesda, MD, USA). Watson, the co‐discoverer of the double helical structure of DNA and the father of the Human Genome Project, must have expected to be the first person to make his genome publicly available. He was not. Nine days earlier, on June 27, J. Craig Venter, the inventor of the ‘shot‐gun’ sequencing strategy, who once acknowledged a love–hate relationship with his former boss Watson, had posted his own complete genome online prior to a publication (Levy et al , 2007). There was no official race between Venter and Watson to be the first. The timing of the publications of their genomes was the result of two unrelated projects. But what is the rationale for making the genome data of noted geneticists publicly available in the first place? Is it pure scientific research or genetic exhibitionism? Or has science finally embraced celebrity culture? The media hoopla surrounding the sequencing of Watson's genome has already had some commentators worrying that genome sequencing could become the next must‐have for the rich and privileged (Check, 2007). However, beyond the publicity, it is only a matter of time until genome sequencing will be affordable for most …

Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced fungal genomes. Several important plant pathogenic fungi are among those that have been sequenced or are being sequenced. Additional fungal pathogens are likely to be sequenced in the near future. Analysis of the available genomes has provided useful information about genes that may be important for plant infection and colonization. Genome features, such as repetitive sequences, telomeres, conserved syntenic blocks, and expansion of pathogenicity-related genes, are discussed in detail with Magnaporthe oryzae (M. grisea) and Fusarium graminearum as examples. Functional and comparative genomic studies in plant pathogenic fungi, although still in the early stages and limited to a few pathogens, have enormous potential to improve our understanding of the molecular mechanisms involved in host-pathogen interactions. Development of advanced genomics tools and infrastructure is critical for efficient utilization of the vast wealth of available genome sequence information and will form a solid foundation for systems biology studies of plant pathogenic fungi.

Background: Tumor heterogeneity poses a significant challenge to the success of treatment; tumors with similar histological features may have substantially different underlying biological drivers. Applying personal genomic information prospectively to assist in chemotherapy decision-making could result in more effective and efficient cancer treatment. Methods: Eligible subjects with incurable cancers for whom there are limited or no standard chemotherapy options, have a tumor biopsy and when possible a tissue matched normal sample plus “normal” blood samples taken specifically for genomic analysis. Archival specimens are concurrently analyzed to look for changes over time and with chemo and/or radiation. Samples are subject to both an Ampliseq amplicon cancer panel analysis and whole genome DNA and RNA sequencing. State-of-the-art bioinformatics approaches are used to identity genes with somatic variants, copy number variants, and expression changes. All variants are integrated into a pathway analysis to identify tumor specific biological processes that may be driving the tumor. These pathways are matched to the known drug databases and to manual literature reviews to identify drugs that may be useful or drugs that may be counter-indicated and a report is generated and discussed. Results: Between July 2012 and January 2013, 10 subjects (of 30 planned) have been enrolled; 3 cases of colorectal and 2 of breast, 1 each of squamous skin, squamous ethmoid sinus cancer, nasopharynx, lung, and one CLL-peripheral mantle cell cancer. The Ampliseq panel results have generally correlated well with whole genome and RNA sequencing results, although the panel, providing less comprehensive information albeit more rapidly, has not been as informative a modality for identifying candidate druggable driver events. And the case of ethmoid cancer was discovered to be a rare pediatric tumor, this was not identified by the panel. Each case had extensive pathway mapping and uncovered potential drug targets that would not have necessarily been considered without this analyses. To date, 3 subjects have initiated treatment based on the reports generated; the analyses are in process for the remaining cases. We also note that we observe significant genomic differences between the archival and fresh tumor materials. Conclusions: Initial results suggest that the information garnered from detailed genomic analysis can inform chemotherapy decision-making. The panel is adept at profiling the common abnormalities that are the target of many of the current generation of molecular targeted drugs; however the whole genome approach provides a comprehensive view of the genomic landscape providing more information on particular aberrant pathways affected and ideas for drug repositioning. For now we have elected to employ whole genome and transcriptome analysis in addition to an “oncogene panel” to both compare the relative utility of these two approaches and provide as comprehensive a view of candidate druggable driver events across patients to inform on the next generation of rapid panel designs. Citation Format: Janessa J. Laskin, Karen Gelmon, Howard Lim, Daniel Renouf, Stephen Yip, David Huntsman, Anna Tinker, Cheryl Ho, Erin D. Pleasance, Yvonne Li, Yaoqing Shen, Katayoon Kasaian, Richard Corbett, Karen Mungall, Yongjun Zhao, Andy Mungall, Jacquie Schein, Robyn Roscoe, Steven Jones, Marco Marra. Genome analysis informs chemotherapy decision-making in patients with advanced malignancies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-173. doi:10.1158/1538-7445.AM2013-LB-173

Two-Component Systems and Their Co-Option for Eukaryotic Signal Transduction

Post-sequencing genomic data analysis becomes a major challenge while next-generation sequencing technologies evolve by leaps and bounds. The data-intensive and compute-intensive nature of genome analysis makes cluster computing an attractive choice for building efficient solutions. This paper presents HiGene, a high-performance genome analysis platform that exploits big data technology to revolutionize genomics data crunching power. HiGene reconstructs the genome analysis pipeline by exploiting both multi-core and multi-node parallelization using Apache Spark, and employs two key techniques to further boost the performance. First, a dynamic computing resource re-allocator is implemented, which allows flexible on-demand resource allocation for operations inside tasks. Second, an efficient skew mitigation approach is proposed, which automatically identifies and resolves data skew and computation skew through task repartitioning and resource reallocating respectively. HiGene has been evaluated with a whole human genome dataset on a 10-node Huawei 5885 cluster. Experimental results show that HiGene achieves remarkable high performance that reduces the total running time on a whole genome sequence dataset from days to nearly one hour. Furthermore, it is two times faster than state-of-the-art cluster based approaches.

Snake gourd (Trichosanthes anguina L.), which belongs to the Cucurbitaceae family, is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world. Although progress has been made in its genetic improvement, the organization, composition, and evolution of the snake gourd genome remain largely unknown. Here, we report a high-quality genome assembly for snake gourd, comprising 202 contigs, with a total size of 919.8 Mb and an N50 size of 20.1 Mb. These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date. The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0% of the genome consists of repetitive sequences. Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor ~33–47 million years ago. The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species. In addition, fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.

Genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis.