The promise of comparative genomics in mammals

Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an 'orphan crop legume'. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation's Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an 'orphan legume crop' to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.

Mus lepidoides (Muridae, Rodentia) of central Burma is a distinct species of potentially great evolutionary and biogeographic significance

Mus lepidoides of central Burma (Myanmar) was described 75 years ago but has since been dismissed as a regional variant of the Indian field mouse, M. booduga. DNA sequences of multiple mitochondrial and nuclear genes from recently collected specimens, combined with a fresh morphological reassessment, reaffirm the distinctiveness of M. lepidoides from M. booduga and from all other species of Mus. Mus lepidoides is so distinct in fact that it warrants placement in its own Species Group within subgenus Mus. Molecular and morphological assessments of phylogenetic affinities converge on the exciting possibility that M. lepidoides represents the previously elusive sibling taxon to the Mus musculus Species Group. If confirmed, this relationship would provide the previously missing connection between the main radiation of subgenus Mus in Southeast and South Asia, and the radiation of the M. musculus Species Group in western Asia and Europe. We speculate that a common ancestor of M. lepidoides and the M. musculus Species Group occupied a continuous but episodic tract of xeric habitat that linked central Burma with northern India at various times during the late Pliocene and Quaternary. Further molecular and cytogenetic studies on the phylogenetic position of M. lepidoides clearly represent a high priority in mouse research.

Gene, region and pathway level analyses in whole-genome studies

In the setting of genome-wide association studies, we propose a method for assigning a measure of significance to pre-defined sets of markers in the genome. The sets can be genes, conserved regions, or groups of genes such as pathways. Using the proposed methods and algorithms, evidence for association between a particular functional unit and a disease status can be obtained not just by the presence of a strong signal from a SNP within it, but also by the combination of several simultaneous weaker signals that are not strongly correlated. This approach has several advantages. First, moderately strong signals from different SNPs are combined to obtain a much stronger signal for the set, therefore increasing power. Second, in combination with methods that provide information on untyped markers, it leads to results that can be readily combined across studies and platforms that might use different SNPs. Third, the results are easy to interpret, since they refer to functional sets of markers that are likely to behave as a unit in their phenotypic effect. Finally, the availability of gene-level P-values for association is the first step in developing methods that integrate information from pathways and networks with genome-wide association data, and these can lead to a better understanding of the complex traits genetic architecture. The power of the approach is investigated in simulated and real datasets. Novel Crohn's disease associations are found using the WTCCC data.

Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map

Background

The prairie vole (Microtus ochrogaster) is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC) library from a single male prairie vole and a prairie vole-mouse (Mus musculus) comparative cytogenetic map.

Results

We constructed a prairie vole BAC library (CHORI-232) consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH) mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements.

Conclusions

The construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this species. The BAC library will support future genomic, genetic and molecular characterization of this genome and species, and the isolation of clones of high interest to the vole research community will allow for immediate characterization of the regulatory and coding sequences of genes known to play important roles in social behaviors. In addition, these resources provide an excellent platform for future higher resolution cytogenetic mapping and full genome sequencing.

Idiosyncratic nutrient requirements of cats appear to be diet-induced evolutionary adaptations

Cats have obligatory requirements for dietary nutrients that are not essential for other mammals. The present review relates these idiosyncratic nutritional requirements to activities of enzymes involved in the metabolic pathways of these nutrients. The high protein requirement of cats is a consequence of the lack of regulation of the aminotransferases of dispensable N metabolism and of the urea cycle enzymes. The dietary requirements for taurine and arginine are consequences of low activities of two enzymes in the pathways of synthesis that have a negative multiplicative effect on the rate of synthesis. Cats have obligatory dietary requirements for vitamin D and niacin which are the result of high activities of enzymes that catabolise precursors of these vitamins to other compounds. The dietary requirement for pre-formed vitamin A appears to result from deletion of enzymes required for cleavage and oxidation of carotenoids. The n-3 polyunsaturated fatty acids (PUFA) requirements have not been defined but low activities of desaturase enzymes indicate that cats may have a dietary need for pre-formed PUFA in addition to those needed by other animals to maintain normal plasma concentrations. The nutrient requirements of domestic cats support the thesis that their idiosyncratic requirements arose from evolutionary pressures arising from a rigorous diet of animal tissue. These pressures may have favoured energy conservation through deletion of redundant enzymes and modification of enzyme activities to result in metabolites more suited to the cat's metabolism. However, this retrospective viewpoint allows only recognition of association rather than cause and effect.

Quantitative TaqMan real-time PCR assays for gene expression normalisation in feline tissues

Background

Gene expression analysis is an important tool in contemporary research, with real-time PCR as the method of choice for quantifying transcription levels. Co-analysis of suitable reference genes is crucial for accurate expression normalisation. Reference gene expression may vary, e.g., among species or tissues; thus, candidate genes must be tested prior to use in expression studies. The domestic cat is an important study subject in both medical research and veterinary medicine. The aim of the present study was to develop TaqMan^® real-time PCR assays for eight potential reference genes and to test their applicability for feline samples, including blood, lymphoid, endocrine, and gastrointestinal tissues from healthy cats, and neoplastic tissues from FeLV-infected cats.

Results

RNA extraction from tissues was optimised for minimal genomic DNA (gDNA) contamination without use of a DNase treatment. Real-time PCR assays were established and optimised for v-abl Abelson murine leukaemia viral oncogene homolog (ABL), β-actin (ACTB), β-2-microglobulin (B2M), β-glucuronidase (GUSB), hydroxymethyl-bilane synthase (HMBS), hypoxanthine phosphoribosyltransferase (HPRT), ribosomal protein S7 (RPS7), and tryptophan 5-monooxygenase activation protein, zeta polypeptide (YWHAZ). The presence of pseudogenes was confirmed for four of the eight investigated genes (ACTB, HPRT, RPS7, and YWHAZ). The assays were tested together with previously developed TaqMan^® assays for feline glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the universal 18S rRNA gene. Significant differences were found among the expression levels of the ten candidate reference genes, with a ~10⁶-fold expression difference between the most abundant (18S rRNA) and the least abundant genes (ABL, GUSB, and HMBS). The expression stability determined by the geNorm and NormFinder programs differed significantly. Using the ANOVA-based NormFinder program, RPS7 was the most stable gene in the tissues studied, followed by ACTB and ABL; B2M, HPRT, and the 18S rRNA genes were the least stable ones.

Conclusion

The reference gene expression stability varied considerably among the feline tissues investigated. No tested gene was optimal for normalisation in all tissues. For the majority of the tissues, two to three reference genes were necessary for accurate normalisation. The present study yields essential information on the correct choice of feline reference genes depending on the tissues analysed.

An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe

Histone variant H2A.Z has a conserved role in genome stability, although it remains unclear how this is mediated. Here we demonstrate that the fission yeast Swr1 ATPase inserts H2A.Z (Pht1) into chromatin and Kat5 acetyltransferase (Mst1) acetylates it. Deletion or an unacetylatable mutation of Pht1 leads to genome instability, primarily caused by chromosome entanglement and breakage at anaphase. This leads to the loss of telomere-proximal markers, though telomere protection and repeat length are unaffected by the absence of Pht1. Strikingly, the chromosome entanglement in pht1Delta anaphase cells can be rescued by forcing chromosome condensation before anaphase onset. We show that the condensin complex, required for the maintenance of anaphase chromosome condensation, prematurely dissociates from chromatin in the absence of Pht1. This and other findings suggest an important role for H2A.Z in the architecture of anaphase chromosomes.

On the karyotypic origin and evolution of cancer cells

Cancers have clonal, aneuploid karyotypes that evolve ever more malignant phenotypes spontaneously. Because these facts are hard to explain by conventional mutation theory, we propose here a karyotypic cancer theory. According to this theory, carcinogens initiate carcinogenesis by inducing random aneuploidy. Aneuploidy then catalyzes karyotypic evolutions, because it destabilizes the karyotype by unbalancing teams of proteins that segregate, synthesize, and repair chromosomes. Sporadically, such evolutions generate new cancer-causing karyotypes, which are stabilized within narrow limits against the inherent instability of aneuploidy by selection for oncogenic function. Here we have tested this theory prospectively by analyzing the karyotypes of distinct tumorigenic clones, which arose from mass cultures of human cells within a few months after transfection with artificially activated oncogenes. All clones from the same parental cells had individual, "near-clonal" karyotypes and phenotypes, although the parental oncogenes were identical. The karyotypes of distinct tumors formed by a given clone in immunodeficient mice were variants of those of the input clones. The karyotypes of tumorigenic clones also evolved on passages in vitro, in which they acquired either enhanced tumorigenicity spontaneously or resistance against methotrexate upon selection. We conclude that activated oncogenes initiate carcinogenesis indirectly by inducing random aneuploidy, much like conventional carcinogens, but more effectively because the oncogenes are integrated into the genome. Since aneuploidy destabilizes the karyotype, such cells evolve new, cancer-specific karyotypes spontaneously, much like new species. Because individual karyotypes of tumorigenic clones correlate and coevolve with individual phenotypes, we conclude that specific karyotypes as a whole are the genomes of cancer cells. Owing to the flexibility of their aneuploid karyotypes, cancers evolve at rates that are roughly proportional to their degrees of aneuploidy. In sum, genomes consisting of individual and flexible karyotypes explain the characteristic individuality, stability, and flexibility of cancers.

ABT-510 is an effective chemopreventive agent in the mouse 4-nitroquinoline 1-oxide model of oral carcinogenesis

Despite numerous advances, the 5-year survival rate for head and neck squamous cell cancer (HNSCC) has remained largely unchanged. This poor outcome is due to several variables, including the development of multiple primary tumors. Therefore, it is essential to supplement early detection with preventive strategies. Using the 4-nitroquinoline 1-oxide (4-NQO) mouse model, we sought to define an appropriate dose and duration of administration that would predict the histologic timeline of HNSCC progression. Additionally, we sought to determine the timing of the onset of the angiogenic phenotype. Finally, using ABT-510 as a proof-of-principle drug, we tested the hypothesis that inhibitors of angiogenesis can slow/delay the development of HNSCC. We determined that 8 weeks of 100 microg/mL 4-NQO in the drinking water was the optimal dosage and duration to cause a sufficient incidence of hyperkeratoses, dysplasias, and HNSCC over a period of 32 weeks with minimal morbidity and mortality. Increased microvessel density and vascular endothelial growth factor expression in hyperkeratotic lesions provided evidence that the initiation of the angiogenic phenotype occurred before the development of dysplasia. Importantly, ABT-510 significantly decreased the overall incidence of HNSCC from 37.3% to 20.3% (P = 0.021) as well as the combined incidence of dysplasia and HNSCC from 82.7% to 50.6% (P < 0.001). These findings suggest that our refinement of the 4-NQO model allows for the investigation of the histologic, molecular, and biological alterations that occur during the premalignant phase of HNSCC. In addition, these data support the hypothesis that inhibitors of angiogenesis may be promising chemopreventive agents.

Identification of a novel common proviral integration site, flit-1, in feline leukemia virus induced thymic lymphoma

A new proviral integration site for feline leukemia virus (FeLV), termed flit-1, was identified from feline thymic lymphoma. Among 35 FeLV-related tumors examined, 5 of 25 thymic lymphomas demonstrated proviral insertion within flit-1 locus whereas none of four alimentary and five multicentric lymphomas and one T-lymphoid leukemia examined had rearrangement in this region. Extensive sequence analysis has shown that flit-1, which is noncoding, is conserved on human chromosome 12 and mouse chromosome 15. The human and murine homologs of flit-1 are positioned approximately 30-kb upstream to activin-A receptor type II-like 1 (ACVRL1/ALK1) gene. Expression of ACVRL1 mRNA was examined in two of five lymphomas with flit-1 rearrangement and detected in both of the two whereas normal thymuses and seven lymphoid tumors without flit-1 rearrangement had no detectable expression. Therefore, flit-1 appears to represent a novel FeLV proviral common integration domain that may influence lymphomagenesis as insertional mutagenesis.

Revisiting the missing protein-coding gene catalog of the domestic dog

Background

Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog.

Results

Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (d_N/d_S), we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates.

Conclusion

This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.

Cancer-causing karyotypes: chromosomal equilibria between destabilizing aneuploidy and stabilizing selection for oncogenic function

The chromosomes of cancer cells are unstable, because of aneuploidy. Despite chromosomal instability, however, cancer karyotypes are individual and quasi-stable, as is evident especially from clonal chromosome copy numbers and marker chromosomes. This paradox would be resolved if the karyotypes in cancers represent chromosomal equilibria between destabilizing aneuploidy and stabilizing selection for oncogenic function. To test this hypothesis, we analyzed the initial and long-term karyotypes of seven clones of newly transformed human epithelial, mammary, and muscle cells. Approximately 1 in 100,000 such cells generates transformed clones at 2-3 months after introduction of retrovirus-activated cellular genes or the tumor virus SV40. These frequencies are too low for direct transformation, so we postulated that virus-activated genes initiate transformation indirectly, via specific karyotypes. Using multicolor fluorescence in situ hybridization with chromosome-specific DNA probes, we found individual clonal karyotypes that were stable for at least 34 cell generations-within limits, as follows. Depending on the karyotype, average clonal chromosome numbers were stable within +/- 3%, and chromosome-specific copy numbers were stable in 70-100% cells. At any one time, however, relative to clonal means, per-cell chromosome numbers varied +/-18% and chromosome-specific copy numbers varied +/-1 in 0-30% of cells; unstable nonclonal markers were found within karyotype-specific quotas of <1% to 20% of the total chromosome number. For two clones, karyotypic ploidies also varied. With these rates of variation, the karyotypes of transformed clones would randomize in a few generations unless selection occurs. We conclude that individual aneuploid karyotypes initiate and maintain cancers, much like new species. These cancer-causing karyotypes are in flexible equilibrium between destabilizing aneuploidy and stabilizing selection for transforming function. Karyotypes as a whole, rather than specific mutations, explain the individuality, fluidity, and phenotypic complexity of cancers.

High levels of genetic variation at MHC class II DBB loci in the tammar wallaby (Macropus eugenii)

High levels of MHC diversity are crucial for immunological fitness of populations, with island populations particularly susceptible to loss of genetic diversity. In this study, the level of MHC class II DBB diversity was examined in tammar wallabies (Macropus eugenii) from Kangaroo Island by genotyping class II-linked microsatellite loci and sequencing of DBB genes. Here we show that the tammar wallaby has at least four expressed MHC class II DBB loci and extensive genetic variation in the peptide-binding region of the DBB genes. These results contradict early studies which suggested that wallabies lacked MHC class II diversity and demonstrate that, in spite of the long-term isolation on an offshore island, this population of wallabies has a high level of DBB diversity.

The evolution of epigenetic regulators CTCF and BORIS/CTCFL in amniotes

CTCF is an essential, ubiquitously expressed DNA-binding protein responsible for insulator function, nuclear architecture, and transcriptional control within vertebrates. The gene CTCF was proposed to have duplicated in early mammals, giving rise to a paralogue called "brother of regulator of imprinted sites" (BORIS or CTCFL) with DNA binding capabilities similar to CTCF, but testis-specific expression in humans and mice. CTCF and BORIS have opposite regulatory effects on human cancer-testis genes, the anti-apoptotic BAG1 gene, the insulin-like growth factor 2/H19 imprint control region (IGF2/H19 ICR), and show mutually exclusive expression in humans and mice, suggesting that they are antagonistic epigenetic regulators. We discovered orthologues of BORIS in at least two reptilian species and found traces of its sequence in the chicken genome, implying that the duplication giving rise to BORIS occurred much earlier than previously thought. We analysed the expression of CTCF and BORIS in a range of amniotes by conventional and quantitative PCR. BORIS, as well as CTCF, was found widely expressed in monotremes (platypus) and reptiles (bearded dragon), suggesting redundancy or cooperation between these genes in a common amniote ancestor. However, we discovered that BORIS expression was gonad-specific in marsupials (tammar wallaby) and eutherians (cattle), implying that a functional change occurred in BORIS during the early evolution of therian mammals. Since therians show imprinting of IGF2 but other vertebrate taxa do not, we speculate that CTCF and BORIS evolved specialised functions along with the evolution of imprinting at this and other loci, coinciding with the restriction of BORIS expression to the germline and potential antagonism with CTCF.

State of cat genomics

Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays

Background

Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions.

Results

Gene specific linear mixed models were fit to each of the log₂ transformed probe intensities on these arrays, using fixed effects for breed, probe, breed-by-probe interaction, and a random effect for array. After surveying the day 25 placental transcriptome, 857 probes with a q-value ≤ 0.05 and |fold change| ≥ 2 for the breed-by-probe interaction were identified as candidates containing SFP. To address the quality of the bioinformatics approach, universal pyrosequencing assays were designed from Affymetrix exemplar sequences to independently assess polymorphisms within a subset of probes for validation. Additionally probes were randomly selected for sequencing to determine an unbiased confirmation rate. In most cases, the 25-mer probe sequence printed on the microarray diverged from Meishan, not occidental crosses. This analysis was used to define a set of highly reliable predicted SFPs according to their probability scores.

Conclusion

By applying a SFP detection method to two mammalian breeds for the first time, we detected transition and transversion single nucleotide polymorphisms, as well as insertions/deletions which can be used to rapidly develop markers for genetic mapping and association analysis in species where high density genotyping platforms are otherwise unavailable.

SNPs and INDELS discovered by this approach have been publicly deposited in NCBI's SNP repository dbSNP. This method is an attractive bioinformatics tool for uncovering breed-by-probe interactions, for rapidly identifying expressed SNPs, for investigating potential functional correlations between gene expression and breed polymorphisms, and is robust enough to be used on any Affymetrix gene expression platform.

Flying lemurs--the 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background

Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous.

Results

To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome.

Conclusion

Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

Genetic linkage map of the house musk shrew, Suncus murinus, constructed with PCR-based and RFLP markers

A genetic linkage map for Suncus murinus was previously constructed with 11 marker loci. In this study, we developed 172 new microsatellite and three RFLP markers, and re-constructed a new framework map by combining all markers. The new map comprises 42 markers that are distributed into 12 linkage groups, two of which are assigned to chromosomes, and spans 403.5 cM with an average inter-marker distance of 13.5 cM.

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

BACKGROUND

Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds.

RESULTS

We present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs.

CONCLUSION

This is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents.

Molecular ecological approaches to studying the evolutionary impact of selective harvesting in wildlife

Harvesting of wildlife populations by humans is usually targeted by sex, age or phenotypic criteria, and is therefore selective. Selective harvesting has the potential to elicit a genetic response from the target populations in several ways. First, selective harvesting may affect population demographic structure (age structure, sex ratio), which in turn may have consequences for effective population size and hence genetic diversity. Second, wildlife-harvesting regimes that use selective criteria based on phenotypic characteristics (e.g. minimum body size, horn length or antler size) have the potential to impose artificial selection on harvested populations. If there is heritable genetic variation for the target characteristic and harvesting occurs before the age of maturity, then an evolutionary response over time may ensue. Molecular ecological techniques offer ways to predict and detect genetic change in harvested populations, and therefore have great utility for effective wildlife management. Molecular markers can be used to assess the genetic structure of wildlife populations, and thereby assist in the prediction of genetic impacts by delineating evolutionarily meaningful management units. Genetic markers can be used for monitoring genetic diversity and changes in effective population size and breeding systems. Tracking evolutionary change at the phenotypic level in the wild through quantitative genetic analysis can be made possible by genetically determined pedigrees. Finally, advances in genome sequencing and bioinformatics offer the opportunity to study the molecular basis of phenotypic variation through trait mapping and candidate gene approaches. With this understanding, it could be possible to monitor the selective impacts of harvesting at a molecular level in the future. Effective wildlife management practice needs to consider more than the direct impact of harvesting on population dynamics. Programs that utilize molecular genetic tools will be better positioned to assess the long-term evolutionary impact of artificial selection on the evolutionary trajectory and viability of harvested populations.

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

BACKGROUND

Deer mice (Peromyscus maniculatus) 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 Peromyscus from laboratory mice (Mus) and rats (Rattus) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus.

RESULTS

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.

CONCLUSION

These data suggest that: 1. the Rattus and Peromyscus genomes more closely represent ancestral Muroid and rodent genomes than that of Mus. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in Mus. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency).

Comparative genomics for detecting human disease genes

Originally, comparative genomics was geared toward defining the synteny of genes between species. As the human genome project accelerated, there was an increase in the number of tools and means to make comparisons culminating in having the genomic sequence for a large number of organisms spanning the evolutionary tree. With this level of resolution and a long history of comparative biology and comparative genetics, it is now possible to use comparative genomics to build or select better animal models and to facilitate gene discovery. Comparative genomics takes advantage of the functional genetic information from other organisms, (vertebrates and invertebrates), to apply it to the study of human physiology and disease. It allows for the identification of genes and regulatory regions, and for acquiring knowledge about gene function. In this chapter, the current state of comparative genomics and the available tools are discussed in the context of developing animal model systems that reflect the clinical picture.

Identification of cryptic sex chromosomes and isolation of X- and Y-borne genes

Comparative molecular cytogenetics provides a powerful tool for deciphering the evolutionary history of vertebrate sex chromosomes. We have adapted cell culture and molecular cytogenetic techniques to study the sex chromosomes of many exotic mammals, birds, and reptiles. Here we describe differential chromosome banding and staining techniques that distinguish sex chromosomes in species with no morphologically distinct XY or ZW chromosome pairs. We describe a method to isolate, identify, and map genomic BAC clones from the Y chromosome, and we also identify strategies for isolating candidate sex chromosome genes.

Initial sequence and comparative analysis of the cat genome

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing approximately 65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.

Genetic analysis of albuminuria in a cross between C57BL/6J and DBA/2J mice

Chronic kidney disease (CKD) is a growing medical problem and a significant risk factor for the development of end-stage renal disease, cardiovascular disease, and cardiovascular mortality. The genetic basis of CKD is recognized, but knowledge of the specific genes that contribute to the onset and progression of kidney disease is limited, mainly because of the difficulty and expense of identifying genes underlying CKD in humans. Results from genetic studies of CKD in rodents often correspond to findings in humans; therefore, we used quantitative trait locus (QTL) analysis to detect genomic regions affecting albuminuria in a cross between C57BL/6J and DBA/2J mice, strains resistant and susceptible to CKD, respectively. We identified several independent and interacting loci affecting albuminuria, including one QTL on mouse chromosome (Chr) 2 that is concordant with QTL influencing urinary albumin excretion on rat Chr 3 and diabetic nephropathy on human Chr 20p. Because this QTL was identified in multiple mouse crosses, as well as in rats and in humans, we used comparative genomics, haplotype analysis, and expression profiling to narrow the initial QTL interval from 386 genes to 10 genes with known coding sequence polymorphisms or expression differences between the strains. These results support the continued use of multiple cross-mapping and cross-species comparisons to further our understanding of the genetic basis of kidney disease.

A most distant intergeneric hybrid offspring (Larcon) of lesser apes, Nomascus leucogenys and Hylobates lar

Unlike humans, which are the sole remaining representatives of a once larger group of bipedal apes (hominins), the "lesser apes" (hylobatids) are a diverse radiation with numerous extant species. Consequently, the lesser apes can provide a valuable evolutionary window onto the possible interactions (e.g., interbreeding) of hominin lineages coexisting in the same time and place. In the present work, we employ chromosomal analyses to verify the hybrid ancestry of an individual (Larcon) produced by two of the most distant genera of lesser apes, Hylobates (lar-group gibbons) and Nomascus (concolor-group gibbons). In addition to a mixed pelage pattern, the hybrid animal carries a 48-chromosome karyotype that consists of the haploid complements of each parental species: Hylobates lar (n = 22) and Nomascus leucogenys leucogenys (n = 26). Studies of this animal's karyotype shed light onto the processes of speciation and genus-level divergence in the lesser apes and, by extension, across the Hominoidea.

Phylogenomics of the genus Mus (Rodentia; Muridae): extensive genome repatterning is not restricted to the house mouse

The house mouse (Mus musculus) is universally adopted as the mammalian laboratory model, and it is involved in most studies of large-scale comparative genomics. Paradoxically, this taxon is rarely the index species for evolutionary analyses of genome architecture owing to its highly rearranged karyotype. To unravel the origin and nature of this extensive repatterning genome, we performed a multidirectional chromosome painting study of representative species within the genus Mus. However, the latter includes four extant subgenera (Mus, Coelomys, Nannomys and Pyromys) between which the phylogenetic relationships remain elusive despite the numerous molecular studies. Comparative genomic maps were established using chromosome-specific painting probes of the laboratory mouse and Nannomys minutoides. Hence, by integrating closely related species within Mus, this study allowed us to: (i) unambiguously resolve for the first time the long-standing controversial phylogeny, (ii) trace the evolution of genome organization in the house mouse, (iii) track rearrangements that necessitated new centromere locations, i.e. formation of neocentromere or reactivation of latent centromeres, (iv) reveal an extremely high rate of karyotypic evolution, with a 10- to 30-fold acceleration which was coincidental with subgeneric cladogenesis and (v) highlight genomic areas of interest for high-resolution studies on neocentromere formation and synteny breakpoints.

Comparative genomic analysis of a mammalian beta-defensin gene cluster

Comparative genomic analyses have yielded valuable insights into conserved and divergent aspects of gene function, regulation, and evolution. Herein, we describe the characterization of a mouse beta-defensin gene cluster locus on chromosome 2F6. In addition, we present the evolutionary analysis of this cluster and its human, rhesus, and rat orthologs. Expression analysis in mouse revealed the occurrence of defensin cluster transcripts in multiple tissues, with the highest abundance in the urogenital tract. Molecular evolutionary analysis suggests that this cluster originated by a series of duplication events, and by positive selection occurring even after the rodent-primate split. In addition, the constraints analysis showed higher positive selection in rodents than in primates, especially distal to the six-cysteine array. Positive selection in the evolution of these defensins may relate not only to the evolving enhancement of ancestral host defense but also to functional innovations in reproduction. The multiplicity of defensins and their preferential overexpression in the urogenital tract indicate that defensins function in the protection and maintenance of fertility.

Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo)

The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

Somatic cell hybrid mapping of expressed sequence tags for genes showing early embryonic death-associated changes of expression patterns in the fetal placenta of the cow carrying somatic nuclear-derived cloned embryo

We previously detected 368 expressed sequence tags showing early embryonic death-associated changes of expression patterns in the fetal placenta of the cow carrying somatic nuclear-derived cloned embryo. In the present study 7 (presumed expressed sequence tags for HYPC, SPTBN1 and TNNC2, and four expressed sequence tags for unknown novel genes) out of the 368 expressed sequence tags were mapped to bovine chromosomes by analyzing deoxyribonucleic acids of bovine/murine somatic cell hybrid panel with polymerase chain reaction using primers specific for those bovine genes.

Isochores and replication time zones: a perfect match

The mammalian genome is not a random sequence but shows a specific, evolutionarily conserved structure that becomes manifest in its isochore pattern. Isochores, i.e. stretches of DNA with a distinct sequence composition and thus a specific GC content, cause the chromosomal banding pattern. This fundamental level of genome organization is related to several functional features like the replication timing of a DNA sequence. GC richness of genomic regions generally corresponds to an early replication time during S phase. Recently, we demonstrated this interdependency on a molecular level for an abrupt transition from a GC-poor isochore to a GC-rich one in the NF1 gene region; this isochore boundary also separates late from early replicating chromatin. Now, we analyzed another genomic region containing four isochores separated by three sharp isochore transitions. Again, the GC-rich isochores were found to be replicating early, the GC-poor isochores late in S phase; one of the replication time zones was discovered to consist of one single replicon. At the boundaries between isochores, that all show no special sequence elements, the replication machinery stopped for several hours. Thus, our results emphasize the importance of isochores as functional genomic units, and of isochore transitions as genomic landmarks with a key function for chromosome organization and basic biological properties.

Chromosome painting and molecular dating indicate a low rate of chromosomal evolution in golden moles (Mammalia, Chrysochloridae)

Golden moles (Chrysochloridae) are poorly known subterranean mammals endemic to Southern Africa that are part of the superordinal clade Afrotheria. Using G-banding and chromosome painting we provide a comprehensive comparison of the karyotypes of five species representing five of the nine recognized genera: Amblysomus hottentotus, Chrysochloris asiatica, Chrysospalax trevelyani, Cryptochloris zyli and Eremitalpa granti. The species are karyotypically highly conserved. In total, only four changes were detected among them. Eremitalpa granti has the most derived karyotype with 2n = 26 and differs from the remaining species (all of whom have 2n = 30) by one centric and one telomere:telomere fusion. In addition, two intrachromosomal rearrangements were detected in A. hottentotus. The painting probes also suggest the presence of a unique satellite DNA family located on chromosomes 11 and 12 of both C. asiatica and C. zyli. This represents a synapomorphy linking these two sympatric species as sister taxa. A molecular clock was calibrated adopting a relaxed Bayesian approach for multigene data sets comprising publicly available sequences derived from five gene fragments representative of three golden moles and 39 other eutherian species. The data suggest that golden moles diverged from a common ancestor approximately 28.5 mya (95% credibility interval = 21.5-36.5 mya). Based on an inferred chrysochlorid ancestral karyotype of 2n = 30, the estimated rate of 0.7 rearrangements per 10 my (95% Credibility Interval = 0.54-0.93) differs from the 'default rate' of mammalian chromosomal evolution which has been estimated at one change per 10 million years, thus placing the Chrysochloridae among the slower-evolving chromosomal lineages thus far recorded.

Embryonic stem cells in companion animals (horses, dogs and cats): present status and future prospects

Reproductive technologies have made impressive advances since the 1950s owing to the development of new and innovative technologies. Most of these advances were driven largely by commercial opportunities and the potential improvement of farm livestock production and human health. Companion animals live long and healthy lives and the greatest expense for pet owners are services related to veterinary care and healthcare products. The recent development of embryonic stem cell and nuclear transfer technology in primates and mice has enabled the production of individual specific embryonic stem cell lines in a number of species for potential cell-replacement therapy. Stem cell technology is a fast-developing area in companion animals because many of the diseases and musculoskeletal injuries of cats, dogs and horses are similar to those in humans. Nuclear transfer-derived stem cells may also be selected and directed into differentiation pathways leading to the production of specific cell types, tissues and, eventually, even organs for research and transplantaton. Furthermore, investigations into the treatment of inherited or acquired pathologies have been performed mainly in mice. However, mouse models do not always faithfully represent the human disease. Naturally occurring diseases in companion animals can be more ideal as disease models of human genetic and acquired diseases and could help to define the potential therapeutic efficiency and safety of stem cell therapies. In the present review, we focus on the economic implications of companion animals in society, as well as recent biotechnological progress that has been made in horse, dog and cat embryonic stem cell derivation.

A scaffold for the Chinese hamster genome

Chinese hamster ovary (CHO) cells are a prevalent tool in biological research and are among the most widely used host cell lines for production of recombinant therapeutic proteins. While research in other organisms has been revolutionized through the development of DNA sequence-based tools, the lack of comparable genomic resources for the Chinese hamster has impeded similar work in CHO cell lines. A comparative genomics approach, based upon the completely sequenced mouse genome, can facilitate genomic work in this important organism. Using chromosome synteny to define regions of conserved linkage between Chinese hamster and mouse chromosomes, a working scaffold for the Chinese hamster genome has been developed. Mapping CHO and Chinese hamster sequences to the mouse genome creates direct access to relevant information in public databases. Additionally, mapping gene expression data onto a chromosome scaffold affords the ability to interpret information in a genomic context, potentially revealing important structural and regulatory features in the Chinese hamster genome. Further development of this genomic scaffold will provide opportunities to use biomolecular tools for research in CHO cell lines today and will be an asset to future efforts to sequence the Chinese hamster genome.

Practicable approaches to facilitate rapid and accurate molecular cytogenetic mapping in birds and mammals

Molecular cytogenetic mapping by FISH is a common feature of most genome projects as it provides a global, low-resolution overview of the genome and facilitates comparative genomics. An essential prerequisite for cytogenetic mapping is the ability to identify accurately the chromosome on which the clone (e.g. BAC) resides. This is not usually a barrier to human mapping as knowledge of the human karyotype is commonplace. For other species however accurate assignment can be problematic either because, as in birds, the karyotype is too complex to analyze by standard means or because of the paucity of individuals skilled to perform the karyotyping. Using chicken as a model we have developed a reproducible approach for accurate cytogenetic mapping that involves: a single colour FISH, measurement of the ratio of the size of the signal bearing chromosome to that of chromosome 8, and final assignment through a small series of dual colour experiments. Reference values for size ratios were established using base pair estimate information from the Ensembl browser. By this method cytogenetic mapping to highly complex karyotypes can be achieved in a small number of simple steps. We have also developed and tested a karyotyping tutorial programme adapted from one previously reported in this journal. That is, we have used pig as an example of a model species with a relatively tractable karyotype and demonstrated that scientists and students, even after only one hour using our tutorial, can readily identify pig chromosomes and thus make appropriate assignments using FISH. Simple, practicable means often provide preferable solutions than complex alternatives (e.g. m-FISH) to the solution of scientific problems. Such is the case for the approaches described here.

An unusual mode of concerted evolution of the EGF-TM7 receptor chimera EMR2

The epidermal growth factor (EGF)-TM7 receptors CD97, EMR1, EMR2, EMR3, and EMR4 form a group of adhesion class heptahelical molecules predominantly expressed by cells of the immune system. These receptors bind cellular ligands through EGF-like domains, localized N-terminal to a large extracellular region. Remarkably, EMR2 possesses a chimeric structure with a seven-span transmembrane (TM7) region most related to EMR3 and an EGF domain region nearly identical to CD97. By comparing EGF-TM7 receptors in primates and dogs, we identified an intriguing pattern of concerted evolution, apparently mediated by gene conversion, among EMR2 and the oppositely orientated and physically adjacent genes CD97 and EMR3. This concerted evolution has continuously maintained the chimeric structure of EMR2 since early mammal radiation. Most highly conserved between EMR2 and CD97 is the fourth EGF domain, which mediates binding to chondroitin sulfate, a ligand specificity shared by both receptors. Another ligand, CD55, is bound effectively only by CD97. We show that different molecular mechanisms (mutations vs. alternative splicing) prevent CD55 binding by EMR2 in hominoids. Our findings illustrate how various and partially opposing evolutionary events have shaped the structure and ligand specificity of a modern mammalian gene family.

A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics

We describe the first genetic linkage map for Daphnia pulex using 185 microsatellite markers, including 115 new markers reported in this study. Our approach was to study the segregation of polymorphisms in 129 F2 progeny of one F1 hybrid obtained by crossing two genetically divergent lineages of Daphnia isolated from two Oregon populations. The map spanned 1206 Kosambi cM and had an average intermarker distance of 7 cM. Linkage groups ranged in size from 7 to 185 cM and contained 4 to 27 markers. The map revealed 12 linkage groups corresponding to the expected number of chromosomes and covers approximately 87% of the genome. Tests for random segregation of alleles at individual loci revealed that 21% of the markers showed significant transmission ratio distortion (primarily homozygote deficiency) likely due to markers being linked to deleterious recessive alleles. This map will become the anchor for the physical map of the Daphnia genome and will serve as a starting point for mapping single and quantitative trait loci affecting ecologically important phenotypes. By mapping 342 tentative orthologous gene pairs (Daphnia/Drosophila) into the Daphnia linkage map, we facilitate future comparative projects.

Biomedical knowledge navigation by literature clustering

There is an urgent need for a system that facilitates surveys by biomedical researchers and the subsequent formulation of hypotheses based on the knowledge stored in literature. One approach is to cluster papers discussing a topic of interest and reveal its sub-topics that allow researchers to acquire an overview of the topic. We developed such a system called McSyBi. It accepts a set of citation data retrieved with PubMed and hierarchically and non-hierarchically clusters them based on the titles and the abstracts using statistical and natural language processing methods. A novel point is that McSyBi allows its users to change the clustering by entering a MeSH term or UMLS Semantic Type, and therefore they can see a set of citation data from multiple aspects. We evaluated McSyBi quantitatively and qualitatively: clustering of 27 sets of citation data (40643 different papers) and scrutiny of several resultant clusters. While non-hierarchical clustering provides us with an overview of the target topic, hierarchical clustering allows us to see more details and relationships among citation data. McSyBi is freely available at http://textlens.hgc.jp/McSyBi/.

Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS

Research studies of infectious disease outbreaks in wild species of the cat family Felidae have revealed unusual details regarding forces that shape population survival and genetic resistance in these species. A highly virulent feline coronavirus epidemic in African cheetahs, a disease model for human SARS, illustrates the critical role of ancestral population genetic variation. Widespread prevalence of species specific feline immunodeficiency virus (FIV), a relative of HIV-AIDS, occurs with little pathogenesis in felid species, except in domestic cats, suggesting immunological adaptation in species where FIV is endemic. Resolving the interaction of host and pathogen genomes can shed new light on the process of disease outbreak in wildlife and in humankind. The role of disease in endangered populations and species is difficult to access as opportunities to monitor outbreaks in natural populations are limited. Conservation management may benefit greatly from advances in molecular genetic tools developed for human biomedical research to assay the biodiversity of both host species and emerging pathogen. As these examples illustrate, strong parallels exist between disease in human and endangered wildlife and argue for an integration of the research fields of comparative genomics, infectious disease, epidemiology, molecular genetics and population biology for an effective proactive conservation approach.

Chromosome organization and chromatin modification: influence on genome function and evolution

Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.