Biomedical applications and studies of molecular evolution: a proposal for a primate genomic library resource

Searching for animal models and potential target species for emerging pathogens: Experience gained from Middle East respiratory syndrome (MERS) coronavirus

Emerging and re-emerging pathogens represent a substantial threat to public health, as demonstrated with numerous outbreaks over the past years, including the 2013-2016 outbreak of Ebola virus in western Africa. Coronaviruses are also a threat for humans, as evidenced in 2002/2003 with infection by the severe acute respiratory syndrome coronavirus (SARS-CoV), which caused more than 8000 human infections with 10% fatality rate in 37 countries. Ten years later, a novel human coronavirus (Middle East respiratory syndrome coronavirus, MERS-CoV), associated with severe pneumonia, arose in the Kingdom of Saudi Arabia. Until December 2016, MERS has accounted for more than 1800 cases and 35% fatality rate. Finding an animal model of disease is key to develop vaccines or antivirals against such emerging pathogens and to understand its pathogenesis. Knowledge of the potential role of domestic livestock and other animal species in the transmission of pathogens is of importance to understand the epidemiology of the disease. Little is known about MERS-CoV animal host range. In this paper, experimental data on potential hosts for MERS-CoV is reviewed. Advantages and limitations of different animal models are evaluated in relation to viral pathogenesis and transmission studies. Finally, the relevance of potential new target species is discussed.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes.

The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research

The genus Drosophila has been the subject of intense comparative phylogenomics characterization to provide insights into genome evolution under diverse biological and ecological contexts and to functionally annotate the Drosophila melanogaster genome, a model system for animal and insect genetics. Recent sequencing of 11 additional Drosophila species from various divergence points of the genus is a first step in this direction. However, to fully reap the benefits of this resource, the Drosophila community is faced with two critical needs: i.e., the expansion of genomic resources from a much broader range of phylogenetic diversity and the development of additional resources to aid in finishing the existing draft genomes. To address these needs, we report the first synthesis of a comprehensive set of bacterial artificial chromosome (BAC) resources for 19 Drosophila species from all three subgenera. Ten libraries were derived from the exact source used to generate 10 of the 12 draft genomes, while the rest were generated from a strategically selected set of species on the basis of salient ecological and life history features and their phylogenetic positions. The majority of the new species have at least one sequenced reference genome for immediate comparative benefit. This 19-BAC library set was rigorously characterized and shown to have large insert sizes (125-168 kb), low nonrecombinant clone content (0.3-5.3%), and deep coverage (9.1-42.9×). Further, we demonstrated the utility of this BAC resource for generating physical maps of targeted loci, refining draft sequence assemblies and identifying potential genomic rearrangements across the phylogeny.

PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer

To better understand the extent of Class II transposable element activity in mammals, we investigated the mouse lemur, Microcebus murinus, whole genome shotgun (2X) draft assembly. Analysis of this strepsirrhine primate extended previous research that targeted anthropoid primates and found no activity within the last 37 Myr. We tested the hypothesis that members of the piggyBac Class II superfamily have been inactive in the strepsirrhine lineage of primates during the same period. Evidence against this hypothesis was discovered in the form of three nonautonomous piggyBac elements with activity periods within the past 40 Myr and possibly into the very recent past. In addition, a novel family of piggyBac transposons was identified, suggesting introduction via horizontal transfer. A second autonomous element was also found with high similarity to an element recently described from the little brown bat, Myotis lucifugus, further implicating horizontal transfer in the evolution of this genome. These findings indicate a more complex history of transposon activity in mammals rather than a uniform shutdown of Class II transposition, which had been suggested by analyses of more common model organisms.

Sequencing primate genomes: what have we learned?

We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation, and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a significant challenge. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into the genetic basis of primate evolution. Next-generation sequencing technologies promise to greatly expand the number of available primate genome sequences; however, such draft genome sequences will likely miss critical genetic differences within complex genomic regions unless dedicated efforts are put forward to understand the full spectrum of genetic variation.

Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird

BACKGROUND

With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken.

RESULTS

From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes.

CONCLUSION

Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.

Spontaneous pathology of the common marmoset (Callithrix jacchus) and tamarins (Saguinus oedipus, Saguinus mystax)

BACKGROUND

Marmosets and tamarins are increasingly used in research, but their pathology remains poorly defined compared with Old World primates.

METHODS

Necropsy records of 129 marmosets and 52 tamarins were reviewed; none was used experimentally.

RESULTS

The most common marmoset lesions were dehydration, emaciation, nephritis, colitis, and inanition. The most common tamarin lesions were dehydration, ascites, emaciation, and congestive heart failure. Colitis and heart disease were the most common cause of death in marmosets and tamarins, respectively. Immature marmoset and tamarin deaths often occurred within the first month of life. Immature marmosets usually died from inanition, stillbirth, and colitis; immature tamarins from atelectasis, stillbirth, heart failure, and colitis. Lymphoma was the most common neoplasm for both marmosets and tamarins.

CONCLUSION

The findings were similar to prior reports with differences in frequency and severity. We report the first case of endometriosis in a marmoset.

Construction, characterization, and chromosomal mapping of a fosmid library of the white-cheeked gibbon (Nomascus leucogenys)

Gibbons have experienced extensive karyotype rearrangements during evolution and represent an ideal model for studying the underlying molecular mechanism of evolutionary chromosomal rearrangements. It is anticipated that the cloning and sequence characterization of evolutionary chromosomal breakpoints will provide vital insights into the molecular force that has driven such a radical karyotype reshuffle in gibbons. We constructed and characterized a high-quality fosmid library of the white-cheeked gibbon (Nomascus leucogenys) containing 192,000 non-redundant clones with an average insert size of 38 kb and 2.5-fold genome coverage. By end sequencing of 100 randomly selected fosmid clones, we generated 196 sequence tags for the library. These end-sequenced fosmid clones were then mapped onto the chromosomes of the white-cheeked gibbon by fluorescence in situ hybridization, and no spurious chimeric clone was detected. BLAST search against the human genome showed a good correlation between the number of hit clones and the number of chromosomes, an indication of unbiased chromosomal distribution of the fosmid library. The chromosomal distribution of the mapped clones is also consistent with the BLAST search result against human and white-cheeked gibbon genomes. The fosmid library and the mapped clones will serve as a valuable resource for further studying gibbons’ chromosomal rearrangements and the underlying molecular mechanism as well as for comparative genomic study in the lesser apes.

Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design

Cross-species sequence comparisons are a prominent method for analyzing genomic DNA and an ever increasing number of species are being selected for whole-genome sequencing. Targeted comparative genomic sequencing is a complementary approach to whole-genome shotgun sequencing and can produce high-quality sequence assemblies of orthologous chromosomal regions of interest from multiple species. Genomic libraries necessary to support targeted mapping and sequencing projects are available for more than 90 vertebrates. An essential step for utilizing these and other genomic libraries for targeted mapping and sequencing is the development of the hybridization-based probes, which are necessary to screen a genomic library of interest. The Uprobe website (http://uprobe.genetics.emory.edu) provides a public online resource for identifying or designing ‘universal’ overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species. Currently, Uprobe provides the ability to search or design probes for use in broad groups of species, including mammals and reptiles, as well as more specific clades, including marsupials, carnivores, rodents and nonhuman primates. In addition, Uprobe has the capability to design custom probes from multiple-species sequence alignments provided by the user, thus providing a general tool for targeted comparative physical mapping.

Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions

Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchromatin/heterochromatin transition regions (Yp11.2/Yp11.1, Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2). Several computational methods were applied to decipher the segmental duplication architecture and identify the ancestral origin of the 41 different duplicons. Combining computational and comparative FISH analysis, we reconstruct the evolutionary history of these regions. Our analysis indicates a continuous process of transposition of duplicated sequences onto the evolving higher primate Y chromosome, providing unique insights into the development of species-specific Y-chromosomal and autosomal duplicons. Phylogenetic sequence comparisons show that duplicons of the human Yp11.2/Yp11.1 region were already present in the macaque-human ancestor as multiple paralogs located predominantly in subtelomeric regions. In contrast, duplicons from the Yq11.1/Yq11.21, Yq11.23/Yq12, and Yq12/PAR2 regions show no evidence of duplication in rhesus macaque, but map to the pericentromeric regions in chimpanzee and human. This suggests an evolutionary shift in the direction of duplicative transposition events from subtelomeric in Old World monkeys to pericentromeric in the human/ape lineage. Extensive chromosomal relocation of autosomal-duplicated sequences from euchromatin/heterochromatin transition regions to interstitial regions as demonstrated on the pygmy chimpanzee Y chromosome support a model in which substantial reorganization and amplification of duplicated sequences may contribute to speciation.

A rhesus macaque radiation hybrid map and comparative analysis with the human genome

The genomes of nonhuman primates are powerful references for better understanding the recent evolution of the human genome. Here we compare the order of 802 genomic markers mapped in a rhesus macaque (Macaca mulatta) radiation hybrid panel with the human genome, allowing for nearly complete cross-reference to the human genome at an average resolution of 3.5 Mb. At least 23 large-scale chromosomal rearrangements, mostly inversions, are needed to explain the changes in marker order between human and macaque. Analysis of the breakpoints flanking inverted chromosomal segments and estimation of their duplication divergence dates provide additional evidence implicating segmental duplications as a major mechanism of chromosomal rearrangement in recent primate evolution.

Review on testicular development, structure, function, and regulation in common marmoset

BACKGROUND

The common marmoset (Callithrix jacchus) is a New World primate that has been used increasingly in toxicological evaluations including testing for testicular toxicity of pharmaceutical and environmental chemicals. Information on structural and functional characteristics of the testis in common marmosets ("marmoset" in this review) is critical for designing experiments, interpreting data collected, and determining relevance to humans in risk assessment.

METHODS

This study provides a comprehensive review on testicular development, structure, function, and regulation in common marmosets.

RESULTS

There is little information regarding testicular formation and development during gestation. Based on the overall pattern of embryonic development in marmosets, it is postulated that gonadal formation and testicular differentiation most likely takes place during gestational Week 6-12. After birth, the neonatal period of the first 2-3 weeks and the pubertal period from Months 6-12 are critical for establishment of spermatogenesis in the adult. In the adult, a nine-stage model has been used to describe the organization of seminiferous epithelium and multiple stages per tubular cross-section have been observed. Seminiferous epithelium is organized in a wave or partial-wave manner. There are on average two stages per cross-section of seminiferous tubules in adult marmoset testis. Sertoli cells in the marmoset have a uniform morphology. Marmoset spermatogenesis has a high efficiency. The prime determinant of germ cell production is proliferation and survival of spermatogonia. Sertoli cell proliferation during the neonatal period is regulated by follicle-stimulating hormone (FSH), but chorionic gonadotropin (CG), instead of luteinizing hormone (LH), is the only gonadotropin with luteinizing function in marmoset. The receptor gene for CG in marmoset is unique in that it does not have exon 10. Marmosets have a "generalized steroid hormone resistance," i.e., relatively high levels of steroid hormones in circulation and relatively low response to exogenous steroids. Blockage of FSH, CG, and testosterone production during the first 3 months after birth does not cause permanent damage to the male reproductive system. Initiation of spermatogenesis in the marmoset requires unique factors that are probably not present in other mammals. Normal male marmosets respond to estradiol injection positively (increased LH or CG levels), a pattern seen in normal females or castrated males, but not usually in normal males of other mammalian species.

CONCLUSIONS

It seems that the endocrine system including the testis in marmosets has some unique features that have not been observed in rodents, Old World primates, and humans, but detailed comparison in these features among these species will be presented in another review. Based on the data available, marmoset seems to be an interesting model for comparative studies. However, interpretation of experimental findings on the testicular effects in marmosets should be made with serious caution. Depending on potential mode of testicular actions of the chemical under investigation, marmoset may have very limited value in predicting potential testicular or steroid hormone-related endocrine effects of test chemicals in humans.

Comparative primate genomics

With the completion of the human genome sequence and the advent of technologies to study functional aspects of genomes, molecular comparisons between humans and other primates have gained momentum. The comparison of the human genome to the genomes of species closely related to humans allows the identification of genomic features that set primates apart from other mammals and of features that set certain primates notably humans apart from other primates. In this article, we review recent progress in these areas with an emphasis on how comparative approaches may be used to identify functionally relevant features unique to the human genome.

Fluorescence in situ hybridization to chromosomes as a tool to understand human and primate genome evolution

For the last 15 years molecular cytogenetic techniques have been extensively used to study primate evolution. Molecular probes were helpful to distinguish mammalian chromosomes and chromosome segments on the basis of their DNA content rather than solely on morphological features such as banding patterns. Various landmark rearrangements have been identified for most of the nodes in primate phylogeny while chromosome banding still provides helpful reference maps. Fluorescence in situ hybridization (FISH) techniques were used with probes of different complexity including chromosome painting probes, probes derived from chromosome sub-regions and in the size of a single gene. Since more recently, in silico techniques have been applied to trace down evolutionarily derived chromosome rearrangements by searching the human and mouse genome sequence databases. More detailed breakpoint analyses of chromosome rearrangements that occurred during higher primate evolution also gave some insights into the molecular changes in chromosome rearrangements that occurred in evolution. Hardly any "fusion genes" as known from chromosome rearrangements in cancer cells or dramatic "position effects" of genes transferred to new sites in primate genomes have been reported yet. Most breakpoint regions have been identified within gene poor areas rich in repetitive elements and/or low copy repeats (segmental duplications). The progress in various molecular and molecular-cytogenetic approaches including the recently launched chimpanzee genome project suggests that these new tools will have a significant impact on the further understanding of human genome evolution.

Genetic divergence of the rhesus macaque major histocompatibility complex

The major histocompatibility complex (MHC) is comprised of the class I, class II, and class III regions, including the MHC class I and class II genes that play a primary role in the immune response and serve as an important model in studies of primate evolution. Although nonhuman primates contribute significantly to comparative human studies, relatively little is known about the genetic diversity and genomics underlying nonhuman primate immunity. To address this issue, we sequenced a complete rhesus macaque MHC spanning over 5.3 Mb, and obtained an additional 2.3 Mb from a second haplotype, including class II and portions of class I and class III. A major expansion of from six class I genes in humans to as many as 22 active MHC class I genes in rhesus and levels of sequence divergence some 10-fold higher than a similar human comparison were found, averaging from 2% to 6% throughout extended portions of class I and class II. These data pose new interpretations of the evolutionary constraints operating between MHC diversity and T-cell selection by contrasting with models predicting an optimal number of antigen presenting genes. For the clinical model, these data and derivative genetic tools can be implemented in ongoing genetic and disease studies that involve the rhesus macaque.

Evolution of beta satellite DNA sequences: evidence for duplication-mediated repeat amplification and spreading

In this article, we report studies on the evolutionary history of beta satellite repeats (BSR) in primates. In the orangutan genome, the bulk of BSR sequences was found organized as very short stretches of approximately 100 to 170 bp, embedded in a 60-kb to 80-kb duplicated DNA segment. The estimated copy number of the duplicon that carries BSR sequences ranges from 70 to 100 per orangutan haploid genome. In both macaque and gibbon, the duplicon mapped to a single chromosomal region at the boundary of the rDNA on the marker chromosome (chromosome 13 and 12, respectively). However, only in the gibbon, the duplicon comprised 100 bp of beta satellite. Thus, the ancestral copy of the duplicon appeared in Old World monkeys ( approximately 25 to approximately 35 MYA), whereas the prototype of beta satellite repeats took place in a gibbon ancestor, after apes/Old World monkeys divergence ( approximately 25 MYA). Subsequently, a burst in spreading of the duplicon that carries the beta satellite was observed in the orangutan, after lesser apes divergence from the great apes-humans lineage ( approximately 18 MYA). The analysis of the orangutan genome also indicated the existence of two variants of the duplication that differ for the length (100 or 170 bp) of beta satellite repeats. The latter organization was probably generated by nonhomologous recombination between two 100-bp repeated regions, and it likely led to the duplication of the single Sau3A site present in the 100-bp variant, which generated the prototype of Sau3A 68-bp beta satellite tandem organization. The two variants of the duplication, although with a different ratios, characterize the hominoid genomes from the orangutan to humans, preferentially involving acrocentric chromosomes. At variance to alpha satellite, which appeared before the divergence of New World and Old World monkeys, the beta satellite evolutionary history began in apes ancestor, where we have first documented a low-copy, nonduplicated BSR sequence. The first step of BSR amplification and spreading occurred, most likely, because the BSR was part of a large duplicon, which underwent a burst dispersal in great apes' ancestor after the lesser apes' branching. Then, after orangutan divergence, BSR acquired the clustered structural organization typical of satellite DNA.

Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey (Ateles geoffroyi). A total of 193 152 BAC clones were generated in this library. The average insert size of the BAC clones was estimated to be 184.6 kb with the small inserts (50-100 kb) accounting for less than 3% and the non-recombinant clones only 1.2%. Assuming a similar genome size with humans, the spider monkey BAC library has about 11× genome coverage. In addition, by end sequencing of randomly selected BAC clones, we generated 367 sequence tags for the library. When blasted against human genome, they showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the library. This black-handed spider monkey BAC library would serve as a valuable resource in comparative genomic study and large-scale genome sequencing of nonhuman primates.Key words: black-handed spider monkeys, Ateles geoffroyi, BAC library.

Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome

We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Using a human genomic reference, optimal global alignments were constructed from large (>50-kb) genomic sequence clones. These alignments were examined for the pattern, frequency, and nature of mutational events. Whereas rates of single-nucleotide substitution remain relatively constant (1-2 x 10(-9) substitutions/site/year), rates of retrotransposition vary radically among different primate lineages. These differences have lead to a 15%-20% expansion of human genome size over the last 50 million years of primate evolution, 90% of it due to new retroposon insertions. Orthologous comparisons with the chimpanzee suggest that the human genome continues to significantly expand due to shifts in retrotransposition activity. Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively.

Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization

Large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of the genetic history and evolution of our species. Here, we present the results of an evolutionary analysis utilizing array comparative genomic hybridization (array CGH), measuring copy-number gains and losses among these species. Using an array of 2460 human bacterial artificial chromosomes (BACs) (12% of the genome), we identified a total of 63 sites of putative DNA copy-number variation between humans and the great apes (chimpanzee, bonobo, gorilla, and orangutan). Detailed molecular characterization of a subset of these sites confirmed rearrangements ranging from 40 to at least 175 kb in size. Surprisingly, the majority of variant sites differentiating great ape and human genomes were found within interstitial euchromatin. These data suggest that such large-scale events are not restricted solely to subtelomeric or pericentromeric regions, but also occur within genic regions. In addition, 5/9 of the verified variant sites localized to areas of intrachromosomal segmental duplication within the human genome. On the basis of the frequency of duplication in humans, this represents a 14-fold positional bias. In contrast to previous cytogenetic and comparative mapping studies, these results indicate extensive local repatterning of hominoid chromosomes in euchromatic regions through a duplication-driven mechanism of genome evolution.

Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence

BACKGROUND

In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues.

RESULT

The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl. We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously.

CONCLUSIONS

In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies.