At #BoG14, Posters Are Far More Interesting than Talks
You can find the abstracts here. There are ~50 talks and 324 posters. In twitter, follow #BOG14 hashtag to learn what is going on.
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This is a conference run by the ENCODE gang, which means almost all talks are from their F&F;, whereas most good abstracts are hidden in the posters.
A few interesting titles -
**Meltz Steinberg, K.N. - A single haplotype platinum genome assembly **
Since Bog does not give out abstract, we will borrow the ASHG abstract from the same group (Eichler at UW).
The human genome reference sequence has provided a foundation for studies of genome structure, human variation, evolutionary biology and human disease. Many of these studies have also revealed, however, that there are regions of the human reference genome that are not represented optimally. At the time the reference genome was completed it was clear that there were some loci recalcitrant to closure with the technology and resources available at that time. It was not clear, however, the degree to which structural variation and diversity affected our ability to produce a truly representative genome sequence at these loci. Many of these regions in the genome, particularly the structural variant loci, are often associated with repetitive sequences. In order to discriminate between repeat copy and allelic copies, the sequence from a single haplotype across these regions is necessary. To this end, we have utilized a hydatidiform mole source, CHM1 to finish highly complex, repetitive regions to high quality. Our aim is to develop a single allelic representation of the entire human genome, the platinum reference. In order to achieve this, we have generated ~100X whole genome shotgun sequence as Illumina paired end data, as well as over 450 BAC sequences from the CHM1 libraries. The whole genome data has been assembled using a reference-guided assembly and the finished BAC sequences have been incorporated into this assembly. We have compared the CHM1 assembly to the current reference, GRCh37 to identify single nucleotide variants, structural variants, and missing sequence from the reference. In addition, we have aligned the CHM1 Illumina sequence to the CHM1 assembly to evaluate the efficacy of our assembly strategy.
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Bachtrog, D. - Numerous transitions of sex chromosome in diptera
Bachtrog, D. - The genomic landscape of incipient species reveals a candidate behavioral isolation gene in Drosophila athabasca
Reversal of an ancient sex chromosome to an autosome in Drosophila
Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes1, 2, 3, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome- specific adaptations such as dosage compensation or an accumulation of sex- specific mutations1, 4. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination5 or its targeting by a chromosome-specific regulatory mechanism6. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur.
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Bracht, J.R. - Chromosome fusions triggered by noncoding RNA
Genomes on the Edge: Programmed Genome Instability in Ciliates
Ciliates are an ancient and diverse group of microbial eukaryotes that have emerged as powerful models for RNA-mediated epigenetic inheritance. They possess extensive sets of both tiny and long noncoding RNAs that, together with a suite of proteins that includes transposases, orchestrate a broad cascade of genome rearrangements during somatic nuclear development. This Review emphasizes three important themes: the remarkable role of RNA in shaping genome structure, recent discoveries that unify many deeply diverged ciliate genetic systems, and a surprising evolutionary sign change in the role of small RNAs between major species groups.
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Brawand, D. - Genomes of 5 African cichlid fishGene duplication as a substrate for adaptive radiation
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Eckalbar, W.L. - Genomic characterization of the developing bat wing in the Natal long-fingered bat, Miniopterus natalensis
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Engel, S.R. - Transcriptional regulation and protein complexes in budding yeast
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Giacomello, S. - Spatial single-cell transcriptomics to study evolutionary differences between angiosperms and gymnosperms
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Hancock, A. - Arabidopsis in the Cape Verde IslandsA model for understanding complex trait evolution during adaptive range expansion
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Lamichhaney, S. - The evolutionary history of Darwins finches revealed by whole genome sequencing
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Schatz, M.C. - Near perfect de novo assemblies of eukaryotic genomes using PacBio long read sequencing
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Smith, J.J. - The sea lamprey meiotic map resolves ancient vertebrate genome duplications
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Venkatesh, B. - Sequencing and comparative analysis of the elephant shark genomeNew insights into gnathostome evolution
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Worley, K.C. - Better genomes using long reads and PBJelly 2
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Yue, J. - A genomic study of Asymmetron lucayanum offers insight into the evolution of cephalochordates
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What could we have learned, if some of those posters were turned into talks? We can give two examples.
1. J. J. Smith works on lamprey, which has a very interesting adaptive immune system. For example, check “Lamprey immunity is far from primitive - Rast”. By learning about genomic differences between lamprey and other vertebrates, we can learn about how the human immune system evolved.
2. Venkatesh, along with Sidney Brenner, works on elephant shark genome. Here is their project description, which is far better than ENCODE’s goal of finding function in 100% of human genome.
We are using a comparative genomics approach to better understand the structure, function and evolution of the human genome. Our group is one of the pioneers in the field of comparative genomics. We proposed the compact genome of the fugu (Takifugu rubripes) as a model vertebrate genome in 1993 (Nature 366: 265-268, 1993) and determined its whole genome sequence in 2002 (Science 297: 1301-1310, 2002). Fugu genome was the first vertebrate genome to be sequenced soon after the completion of the human genome. It is being widely used as a reference genome for comparative analysis of human and other vertebrate genomes. More recently, we identified elephant shark (Callorhinchus milii) as having the smallest genome among cartilaginous fishes and initiated the Elephant Shark Genome Project (PLoS Biol 5(4): e101, 2007). Cartilaginous fishes are the oldest living group of jawed vertebrates (gnathostomes) and serve as a critical reference for understanding the evolution of vertebrate genomes. We have also initiated a genome project for a model jawless vertebrate, the Japanese lamprey (Lethenteron japonicum), which has a smaller genome than the sea lamprey. Jawless vertebrates (cyclostomes), comprising lampreys and hagfishes, are the most basally branching lineage of vertebrates and hence an important reference for understanding the origin and evolution of vertebrates. In addition, we are exploring other model vertebrate genomes such as coelacanth, gar and cichlid fishes that can contribute to our understanding of human and other vertebrate genomes. Our group is also participating in Genome 10K, an international project which aims to sequence the genomes of 10,000 vertebrates.
