Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

<p>Abstract</p> <p>Background</p> <p>Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined.</p> <p>Results</p> <p>To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, <it>Macropus eugenii</it>, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements.</p> <p>Conclusion</p> <p>Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials and eutherians that may have predisposed these genomic regions to large-scale chromosomal instability.</p

Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages

The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential expansion and contraction of individual classes

Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)

Dataset: Salp genome and transcriptomeA preliminary genome sequence and complete reference transcriptome have been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). The reference transcriptome contains 216,931 sequences; 41,210 (18%) were associated with predicted, hypothetical, or known proteins; 13,058 (6%) were mapped and annotated. Whole-transcriptome (RNA-seq) analysis of 39 samples collected during austral spring and summer 2011 in the WAP, and in summer 2009 in the Indian Sector revealed clustering of samples by regions, seasons, and areas (Bray-Curtis similarity). Spring versus summer samples showed significant differential expression of 77 genes associated with environmental stress response and 51 genes associated with sexual reproduction (paired t-tests, p&lt;0.05). Gene Ontology (GO) term enrichment analysis identified 41 GO terms responsible for spring versus summer differences, including 156 genes associated with translation (i.e., protein synthesis). The genome sequence of 318,767,936 bp covers &gt;50% of the estimated 602 MB (±173 MB) genome size for S. thompsoni, with &gt;50% (16,823) of sequences showing significant homology to known proteins and ~38% (12,151) of the total protein predictions associated with Gene Ontology functional information. A total of 109,958 SNP variants and 9,782 indel predictions were generated, serving as a resource for future phylogenomic and population genomic studies. Salpa thompsoni exhibits rapid rates of evolution (&gt;1.5 times that observed for vertebrates) typical of other urochordates examined. An initial survey of small RNAs revealed the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/675040NSF Antarctic Sciences (NSF ANT) ANT-104498

Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)

Dataset: Salp sample logThis dataset is a sample log of the Salpa thompsoni specimens used for genomic and transcriptomic analysis. Collections were from three cruises in the Southern Ocean. Collections were made in Summer of 2009 during a cruise of the Umitaka-Maru (UM-08-09) from off-shelf sites in the Indian Sector. During cruises of the ARSV Laurence M. Gould (LMG-1110) and R/V Polarstern (ANT-XXVII-2) samples were collected from on- and off-shelf regions of the Western Antarctic Peninsula Region and in Bransfield Strait during Spring and Summer 2011, respectively. Reported parameters include cruise id, region, season and area, location, number of samples collected, temperature, salinity, sampled depth range, and the depth of the water at the collection site. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/672600NSF Antarctic Sciences (NSF ANT) ANT-104498

Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)

<p>Abstract</p> <p>Background</p> <p>Deer mice (<it>Peromyscus maniculatus</it>) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of <it>Peromyscus </it>from laboratory mice (<it>Mus</it>) and rats (<it>Rattus</it>) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest <it>Peromyscus </it>to be exhibit greater similarities with <it>Rattus </it>than with <it>Mus</it>.</p> <p>Results</p> <p>Comparative linkage mapping of an estimated 35% of the deer mouse genome was done with respect to the Rattus and Mus genomes. We particularly focused on regions that span synteny breakpoint regions between the rat and mouse genomes. The linkage analysis revealed the Peromyscus genome to have a higher degree of synteny and gene order conservation with the Rattus genome.</p> <p>Conclusion</p> <p>These data suggest that: 1. the <it>Rattus </it>and <it>Peromyscus </it>genomes more closely represent ancestral Muroid and rodent genomes than that of <it>Mus</it>. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in <it>Mus</it>. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency).</p

The Chlamydia muridarum plasmid revisited : new insights into growth kinetics.

Background: Research in chlamydial genetics is challenging because of its obligate intracellular developmental cycle. In vivo systems exist that allow studies of different aspects of basic biology of chlamydiae, the murine Chlamydia muridarum model is one of great importance and thus an essential research tool. C. muridarum carries a plasmid that has a role in virulence.  Our aim was to compare and contrast the C. muridarum plasmid-free phenotype with that of a chromosomally isogenic plasmid-bearing strain, through the inclusion phase of the developmental cycle. Methods: We measured infectivity for plasmid bearing and plasmid-cured C. muridarum by inclusion forming assays in McCoy cells and in parallel bacterial chromosome replication by quantitative PCR, throughout the developmental cycle. In addition to these studies, we have carefully monitored chlamydial inclusion formation by confocal microscopy and transmission electron microscopy. A new E.coli/chlamydial shuttle vector (pNigg::GFP) was constructed using standard cloning technology and used to transform C. muridarum for further phenotypic studies. Results: We have advanced the definition of the chlamydial phenotype away from the simple static observation of mature inclusions and redefined the C. muridarum plasmid-based phenotype on growth profile and inclusion morphology. Our observations on the growth properties of plasmid-cured C. muridarum challenge the established interpretations, especially with regard to inclusion growth kinetics. Introduction of the shuttle plasmid pNigg::GFP into plasmid-cured C. muridarum restored the wild-type plasmid-bearing phenotype and confirmed that loss of the plasmid was the sole cause for the changes in growth and chromosomal replication. Conclusions: Accurate growth curves and sampling at multiple time points throughout the developmental cycle is necessary to define plasmid phenotypes.  There are subtle but important (previously unnoticed) differences in the overall growth profile of plasmid-bearing and plasmid-free C. muridarum.  We have proven that the differences described are solely due to the plasmid pNigg

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

During routine screens of the NCBI databases using human repetitive elements we discovered an unlikely level of nucleotide identity across a broad range of phyla. To ascertain whether databases containing DNA sequences, genome assemblies and trace archive reads were contaminated with human sequences, we performed an in depth search for sequences of human origin in non-human species. Using a primate specific SINE, AluY, we screened 2,749 non-primate public databases from NCBI, Ensembl, JGI, and UCSC and have found 492 to be contaminated with human sequence. These represent species ranging from bacteria (B. cereus) to plants (Z. mays) to fish (D. rerio) with examples found from most phyla. The identification of such extensive contamination of human sequence across databases and sequence types warrants caution among the sequencing community in future sequencing efforts, such as human re-sequencing. We discuss issues this may raise as well as present data that gives insight as to how this may be occurring