Duplication In Species Research Articles

Evolution of immunogenetic components encoding ultralong CDR H3.

The genomes of most vertebrates contain many V, D, and J gene segments within their Ig loci to construct highly variable CDR3 sequences through combinatorial diversity. This nucleotide variability translates into an antibody population containing extensive paratope diversity. Cattle have relatively few functional VDJ gene segments, requiring innovative approaches for generating diversity like the use of ultralong-encoding IGHV and IGHD gene segments that yield dramatically elongated CDR H3. Unique knob and stalk microdomains create protracted paratopes, where the antigen-binding knob sits atop a long stalk, allowing the antibody to bind both surface and recessed antigen epitopes. We examined genomes of twelve species of Bovidae to determine when ultralong-encoding IGHV and IGHD gene segments evolved. We located the 8-bp duplication encoding the unique TTVHQ motif in ultralong IGHV segments in six Bovid species (cattle, zebu, wild yak, domestic yak, American bison, and domestic gayal), but we did not find evidence of the duplication in species beyond the Bos and Bison genera. Additionally, we analyzed mRNA from bison spleen and identified a rich repertoire of expressed ultralong CDR H3 antibody mRNA, suggesting that bison use ultralong IGHV transcripts in their host defense. We found ultralong-encoding IGHD gene segments in all the same species except domestic yak, but again not beyond the Bos and Bison clade. Thus, the duplication event leading to this ultralong-encoding IGHV gene segment and the emergence of the ultralong-encoding IGHD gene segment appears to have evolved in a common ancestor of the Bos and Bison genera 5-10 million years ago.

Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

BackgroundCommon carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event.ResultsWe have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp.ConclusionsThe assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future.

Seasonality, distribution and taxonomic status of avian haemosporidian parasites within the Greater Cape Town area, South Africa

A total of 9 304 birds representing 29 families, 55 genera and 78 species were captured at 10 sites within the Greater Cape Town area. Forty-one avian haemosporidian parasites from three genera were present in 20 avian families, with 1 978 (21.2%) individuals infected with one or more parasite species. Leucocytozoon spp. (12.6% of infected birds) exhibited the highest infection rate, followed by Haemoproteus spp. (9.6%) and Plasmodium spp. (0.6%). Prevalence of infection varied from 4.5% at Patryskraal to 28.0% at Tygerberg Nature Reserve. Columbidae had the highest infection rate by Haemoproteus spp. Ploceidae and Sylviidae were infected by all three haemosporidian genera, with Ploceidae the most heavily infected, with six species of avian haemosporidia. All study sites had similar seasonal patterns with two peaks. The first peak coincided with the end of the rainy season in August or September, and the second during January and February, when population sizes peaked on account of seasonal breeding and the presence of large numbers of immature birds susceptible to infection. The prevalence of infections had two seasonal lows, without a complete winter interruption, with the first low occurring in late autumn/early winter. The second low, known as ‘spring relapse’, resulted from acute primary parasitaemia, which follows a peak in haemosporidian infection. Seasonal prevalence patterns as recorded throughout the year in this study are typical of medium latitudes with mild climates and warm seasons. Avian haemosporidian parasites are classified according to the avian families or subfamilies that they infect; this is also taken as the maximum level of specificity for the practice of avian haemosporidian taxonomy. Description of a new species is based upon morphology of gametocyte development in the peripheral blood of the avian host. This does not distinguish between morphologically identical gametocytes from different avian host families, nor is species or family level a valid taxonomic character. Thus, Haemoproteus and Leucocytozoon spp. encountered in this study are considered to be relegated to synonymy with previously described, morphologically similar valid species in avian hosts of other families following the taxonomic path of Valkiunas, thereby eliminating duplication of species.

Genomic analysis of the carboxylesterases: Identification and classification of novel forms

Large species differences in the expression of carboxylesterases (CE) have been described, but the interrelationships of CEs across species are not well characterized. In the current analyses, sequences with genomic structures similar to human CEs were found in piscine, avian, and mammalian genomes. Analyses of these genes suggest that four CE groups existed prior to mammalian divergence, with another form occurring after eutherian–marsupial divergence, yielding five distinct mammalian CE groups. The CE1 and CE2 groupings appear to have undergone extensive gene duplication in species with herbivorous and omnivorous diets underscoring the potential importance of these two groups in xenobiotic metabolism. However, CE3, CE4, and CE5 have remained at one gene per species in almost all observed cases. In avian and piscine genomes, only two CE groupings each were observed in the currently available sequence data. Finally, this study presents considerations for a broader phylogenetic-based nomenclature that could encompass other serine hydrolases in addition to the CEs.

An apology for orthologs - or brave new memes.

An apology for orthologs - or brave new memes.