Non-random genomic integration - an intrinsic property of retrogenes in Drosophila?

ABSTRACT: BACKGROUND: The Drosophila X-chromosome shows a significant underrepresentation of genes with male-biased gene expression (demasculinization). This trend is matched by retrogenes, which typically have a male biased gene expression pattern and show a significant movement bias from X-chromosomes to autosomes. It is currently assumed that these patterns are best explained by selection, either mediated by male meiotic sex chromosome inactivation (MSCI) or sexually antagonistic forces. We scrutinized the evolutionary dynamics of retroposition by focusing on retrogenes for which the parental copy has degenerated. RESULTS: Consistent with a functional substitution of the degenerated gene by the retrogene, patterns of sequence evolution and gene expression were similar between retroposed and parental genes. Like previous studies, our set of retrogenes showed a significant movement off the X-chromosome. In contrast to data sets where retroposition caused gene duplication, the genes in our study showed primarily female-biased or unbiased gene expression. CONCLUSIONS: Based on our results, the biased transposition pattern cannot be explained by MSCI and probably not by sexual antagonism. Rather, we propose that the movement away from the X-chromosome represents a general property of retroposition in Drosophila

Male-biased genes are overrepresented among novel Drosophila pseudoobscura sex-biased genes

BACKGROUND: The origin of functional innovation is among the key questions in biology. Recently, it has been shown that new genes could arise from non-coding DNA and that such novel genes are often involved in male reproduction. RESULTS: With the aim of identifying novel genes, we used the technique "generation of longer cDNA fragments from serial analysis of gene expression (SAGE) tags for gene identification (GLGI)" to extend 84 sex-biased 3'end SAGE tags that previously could not be mapped to the D. pseudoobscura transcriptome. Eleven male-biased and 33 female-biased GLGI fragments were obtained, of which 5 male-biased and 3 female-biased tags corresponded to putatively novel genes. This excess of novel genes with a male-biased gene expression pattern is consistent with previous results, which found novel genes to be primarily expressed in male reproductive tissues. 5' RACE analysis indicated that these novel transcripts are very short in length and could contain introns. Interspecies comparisons revealed that most novel transcripts show evidence for purifying selection. CONCLUSION: Overall, our data indicate that among sex-biased genes a considerable number of novel genes (approximately 2-4%) exist in D. pseudoobscura, which could not be predicted based on D. melanogaster gene models

Molecular phylogeny of silkmoths reveals the origin of domesticated silkmoth, Bombyx mori from chinese Bombyx mandarina and paternal inheritance of Antheraea proylei mitochondrial DNA

Molecular phylogeny of some of the economically important silkmoths was derived using three mitochondrial genes, 12S rRNA, 16S rRNA, and COI, and the control region (CR). Maximum likelihood (ML) analyses showed two distinct clades, one consisting of moths from Bombycidae family and the other from Saturniidae family. The mitochondrial CR showed length polymorphisms with indels. The ML analyses for complete mitochondrial genome sequences of Bombyx mori (strains Aojuku, C108, Backokjam, and Xiafang), Japanese and Chinese strains of B. mandarina (Japanese mandarina and Chinese mandarina) and, Antheraea pernyi revealed two distinct clades, one comprising of B. mori strains and the other with B. mandarina, and A. pernyi forming an outgroup. Pairwise distances revealed that all of the strains of B. mori studied are closer to Chinese than to Japanese mandarina. Phylogenetic analyses based on whole mitochondrial genome sequences, the finding of a tandem triplication of a 126 bp repeat element only in Japanese mandarina, and chromosome number variation in B. mandarina suggest that B. mori must have shared its recent common ancestor with Chinese mandarina. Another wild species of the Bombycidae family, Theophila religiosa, whose phylogenetic status was not clear, clustered together with the other bombycid moths in the study. Analysis of the interspecific hybrid, A. proylei gave evidence for paternal inheritance of mitochondrial DNA

Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken

<p>Abstract</p> <p>Background</p> <p>Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), <it>Gallus gallus murghi </it>in previous studies has left a big gap in understanding the relationship of this major group of birds. In the present study, we addressed this issue by analyzing 76 Indian birds that included 56 <it>G. g. murghi </it>(RJF), 16 <it>G. g. domesticus </it>(domestic chicken) and 4 <it>G. sonneratii </it>(Grey JF) using both microsatellite markers and mitochondrial D-loop sequences. We also compared the D-loop sequences of Indian birds with those of 779 birds obtained from GenBank.</p> <p>Results</p> <p>Microsatellite marker analyses of Indian birds indicated an average F_STof 0.126 within <it>G. g. murghi</it>, and 0.154 within <it>G. g. domesticus </it>while it was more than 0.2 between the two groups. The microsatellite-based phylogenetic trees showed a clear separation of <it>G. g. domesticus </it>from <it>G. g. murghi</it>, and <it>G. sonneratii</it>. Mitochondrial DNA based mismatch distribution analyses showed a lower Harpending's raggedness index in both <it>G. g. murghi </it>(0.001515) and in Indian <it>G. g. domesticus </it>(0.0149) birds indicating population expansion. When meta analysis of global populations of 855 birds was carried out using median joining haplotype network, 43 Indian birds of <it>G. g. domesticus </it>(19 haplotypes) were distributed throughout the network sharing haplotypes with the RJFs of different origins.</p> <p>Conclusion</p> <p>Our results suggest that the domestication of chicken has occurred independently in different locations of Asia including India. We found evidence for domestication of Indian birds from <it>G. g. spadiceus </it>and <it>G. g. gallus </it>as well as from <it>G. g. murghi</it>, corroborating multiple domestication of Indian and other domestic chicken. In contrast to the commonly held view that RJF and domestic birds hybridize in nature, the present study shows that <it>G. g. murghi </it>is relatively pure. Further, the study also suggested that the chicken populations have undergone population expansion, especially in the Indus valley.</p

Genetic characterization of the Indian cattle breeds, Ongole and Deoni (Bos indicus), using microsatellite markers – a preliminary study

BACKGROUND: Molecular characterization of cattle breeds is important for the prevention of germplasm erosion by cross breeding. The Indian zebu cattle have their significant role in evolution of present day cattle breeds and development of some of the exotic breeds. Microsatellites are the best available molecular tools for characterization of cattle breeds. The present study was carried out to characterize two Indian cattle breeds, Ongole and Deoni, using microsatellite markers. RESULTS: Using 5 di- and 5 tri-nucleotide repeat loci, 17 Ongole and 13 Deoni unrelated individuals were studied. Of the ten loci, eight revealed polymorphism in both the breeds. The di-nucleotide repeat loci were found to be more polymorphic (100%) than tri-nucleotide repeat loci (60%). A total of 39 polymorphic alleles were obtained at 4.5 alleles per locus in Ongole and 4.1 in Deoni. The average expected heterozygosity was 0.46 (±0.1) and 0.50 (±0.1) in Ongole and Deoni breeds, respectively. The PIC values of the polymorphic loci ranged from 0.15 to 0.79 in Ongole and 0.13 to 0.80 in Deoni breeds. Six Ongole specific and three Deoni specific alleles were identified. The two breeds showed a moderate genetic relationship between themselves with a F(ST )value of 0.117 (P = 0.01). CONCLUSIONS: This preliminary study shows that microsatellite markers are useful in distinguishing the two zebu breeds namely, Ongole and Deoni. Further studies of other zebu breeds using many microsatellite loci with larger sample sizes can reveal the genetic relationships of Indian breeds

ioinformatička karakterizacija transmembranskog proteina gena 95 (TMEM95) u murah bivola (Bubalus bubalis)

Idiopathic male subfertility is often a neglected phenotype with respect to male fertility in bovines. The gene TMEM95 plays a crucial role in idiopathic male subfertility in cattle. Using the DNA sequence information from cattle TMEM95 gene, we characterized the gene in Murrah buffalo. A total of 2.6 kb of a fragment orthologous to cattle was sequenced from Murrah buffalo and Gir cattle. A 2 bp deletion is present in Murrah buffalo, causing missense mutations in three isoforms that are present in cattle. The functional effects of various non-synonymous mutations were predicted using the SNAP2 program, and showed that the non-synonymous SNPs could affect the protein function. Functional motif annotation revealed the presence of a Casein kinase II phosphorylation site that plays an important role in sperm morphology, Leucine zipper pattern, N-myristoylation site, protein kinase C phosphorylation site, CHRD domain profile, N-glycosylation site and HIT zinc finger motifs in cattle. The HIT ZF motif is absent in all of the functional isoforms in buffalo. The results together suggest that the subfertility gene TMEM95 in cattle and buffalo must have evolved with different functions but plays a role in male fertility as in other mammals.Pri razmatranju plodnosti goveda, idiopatska neplodnost mužjaka često je zanemareno fenotipsko obilježje. S obzirom na gensku osnovu, smatra se da je obilježje povezano s genom TMEM9. U radu je, upotrebom DNA sekvencijskih informacija dobivenih od goveđeg TMEM95, provedena karakterizaciju tog gena u murah bivola. Uz bivola, fragment od ukupno 2.6 kb koji je ortologan govedima, sekvenciran je i u gir goveda. Delecija od 2 bp prisutna je u murah bivola što uzrokuje pogrešnu mutaciju u tri izoformna oblika prisutna u goveda. Funkcijski učinci nesinonimnih mutacija predviđani su primjenom SNAP2 programa koji je pokazao da nesinonimni SNP-i mogu utjecati na funkciju proteina. Funkcionalna bilješka motiva pokazala je prisustvo kazein kinaze II fosforilacijskog mjesta koje ima važnu ulogu u morfologiji spermija, zatim prisustvo leucin patentnog-zatvarača, N-miristoilacijskog mjesta, protein kinaze C-fosforilacijskog mjesta, CHRD domene profila, N-glikokosilacijskog mjesta i HIT motiva cinkovog prsta u goveda. U nijednoj od funkcionalnih izoformi u bivola nije prisutan HIT motiv cinkovog prsta. Rezultati skupno ukazuju da se gen subfertilnosti TMEM95 između goveda i bivola razvijao sa različitim funkcijama ali ima ulogu u muškoj plodnosti kao i u drugih sisavaca

No accelerated rate of protein evolution in male-biased Drosophila pseudoobscura genes.

Sexually dimorphic traits are often subject to diversifying selection. Genes with a male-biased gene expression also are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex-biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex-related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in the rate of evolution for genes with a male-biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male-biased genes, our data imply a radically different selection regime in D. pseudoobscura

Gene expression profiling by massively parallel sequencing

Massively parallel sequencing holds great promise for expression profiling, as it combines the high throughput of SAGE with the accuracy of EST sequencing. Nevertheless, until now only very limited information had been available on the suitability of the current technology to meet the requirements. Here, we evaluate the potential of 454 sequencing technology for expression profiling using Drosophila melanogaster. We show that short (< ∼80 bp) and long (> ∼300–400 bp) cDNA fragments are under-represented in 454 sequence reads. Nevertheless, sequencing of 3′ cDNA fragments generated by nebulization could be used to overcome the length bias of the 454 sequencing technology. Gene expression measurements generated by restriction analysis and nebulization for fragments within the 80- to 300-bp range showed correlations similar to those reported for replicated microarray experiments (0.83–0.91); 97% of the cDNA fragments could be unambiguously mapped to the genomic DNA, demonstrating the advantage of longer sequence reads. Our analyses suggest that the 454 technology has a large potential for expression profiling, and the high mapping accuracy indicates that it should be possible to compare expression profiles across species