An improved genome reference for the African cichlid, Metriaclima zebra

Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.Background: Problems associated with using draft genome assemblies are well documented and have become more pronounced with the use of short read data for de novo genome assembly. We set out to improve the draft genome assembly of the African cichlid fish, Metriaclima zebra, using a set of Pacific Biosciences SMRT sequencing reads corresponding to 16.5x coverage of the genome. Here we characterize the improvements that these long reads allowed us to make to the state-of-the-art draft genome previously assembled from short read data. Results: Our new assembly closed 68 % of the existing gaps and added 90.6Mbp of new non-gap sequence to the existing draft assembly of M. zebra. Comparison of the new assembly to the sequence of several bacterial artificial chromosome clones confirmed the accuracy of the new assembly. The closure of sequence gaps revealed thousands of new exons, allowing significant improvement in gene models. We corrected one known misassembly, and identified and fixed other likely misassemblies. 63.5 Mbp (70 %) of the new sequence was classified as repetitive and the new sequence allowed for the assembly of many more transposable elements. Conclusions: Our improvements to the M. zebra draft genome suggest that a reasonable investment in long reads could greatly improve many comparable vertebrate draft genome assemblies.https://doi.org/10.1186/s12864-015-1930-

Cone opsin genes of African cichlid fishes: tuning spectral sensitivity by differential gene expression.

Spectral tuning of visual pigments is typically accomplished through changes in opsin amino acid sequence. Within a given opsin class, changes at a few key sites control wavelength specificity. To investigate known differences in the visual pigment spectral sensitivity of the Lake Malawi cichlids, Metriaclima zebra (368, 488, and 533 nm) and Dimidiochromis compressiceps (447, 536, and 569 nm), we sequenced cone opsin genes from these species as well as Labeotropheus fuelleborni and Oreochromis niloticus. These cichlids have five distinct classes of cone opsin genes, including two unique SWS-2 genes. Comparisons of the inferred amino acid sequences from the five cone opsin genes of M. zebra, D. compressiceps, and L. fuelleborni show the sequences to be nearly identical. Therefore, evolution of key opsin sites cannot explain the differences in visual pigment sensitivities. Real-time PCR demonstrates that different cichlid species express different subsets of the available cone opsin genes. Metriaclima zebra and L. fuelleborni express a complement of genes which give them UV-shifted visual pigments, while D. compressiceps expresses a different set to produce a red-shifted visual system. Thus, variations in cichlid spectral sensitivity have arisen through evolution of gene regulation, rather than through changes in opsin amino acid sequence

Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron

Background Inversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping techniques. Here we compare distantly related species of tilapia that each segregate an XY system of sex-determination on linkage group 1. We use whole genome sequencing to identify shared sex-patterned polymorphisms, which are candidates for the ancestral sex-determination mutation. Results We found that Sarotherodon melanotheron segregates an XY system on LG1 in the same region identified in Oreochromis niloticus. Both species have higher densities of sex-patterned SNPs, as well as elevated number of ancestral copy number variants in this region when compared to the rest of the genome, but the pattern of differentiation along LG1 differs between species. The number of sex-patterned SNPs shared by the two species is small, but larger than expected by chance, suggesting that a novel Y-chromosome arose just before the divergence of the two species. We identified a shared sex-patterned SNP that alters a Gata4 binding site near Wilms tumor protein that might be responsible for sex-determination. Conclusions Shared sex-patterned SNPs, insertions and deletions suggest an ancestral sex-determination system that is common to both S. melanotheron and O. niloticus. Functional analyses are needed to evaluate shared SNPs near candidate genes that might play a role in sex-determination of these species. Interspecific variation in the sex chromosomes of tilapia species provides an excellent model system for understanding the evolution of vertebrate sex chromosomes. (Résumé d'auteur

Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus

Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.Sex-determination genes drive the evolution of adjacent chromosomal regions. Sexually antagonistic selection favors the accumulation of inversions that reduce recombination in regions adjacent to the sex-determination gene. Once established, the clonal inheritance of sex-linked inversions leads to the accumulation of deleterious alleles, repetitive elements and a gradual decay of sex-linked genes. This in turn creates selective pressures for the evolution of mechanisms that compensate for the unequal dosage of gene expression. Here we use whole genome sequencing to characterize the structure of a young sex chromosome and quantify sex-specific gene expression in the developing gonad. We found an 8.8 Mb block of strong differentiation between males and females that corresponds to the location of a previously mapped sex-determiner on linkage group 1 of Oreochromis niloticus. Putatively disruptive mutations are found in many of the genes within this region. We also found a significant female-bias in the expression of genes within the block of differentiation compared to those outside the block of differentiation. Eight candidate sex-determination genes were identified within this region. This study demonstrates a block of differentiation on linkage group 1, suggestive of an 8.8 Mb inversion encompassing the sex-determining locus. The enrichment of female-biased gene expression inside the proposed inversion suggests incomplete dosage compensation. This study helps establish a model for studying the early-to-intermediate stages of sex chromosome evolution.https://doi.org/10.1186/1471-2164-15-97

Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra

Pigmentation patterns are one of the most recognizable phenotypes across the animal kingdom. They play an important role in camouflage, communication, mate recognition and mate choice. Most progress on understanding the genetics of pigmentation has been achieved via mutational analysis, with relatively little work done to understand variation in natural populations. Pigment patterns vary dramatically among species of cichlid fish from Lake Malawi, and are thought to be important in speciation. In this study, we crossed two species, Metriaclima zebra and M. mbenjii, that differ in several aspects of their body and fin color. We genotyped 798 SNPs in 160 F2 male individuals to construct a linkage map that was used to identify quantitative trait loci (QTL) associated with the pigmentation traits of interest. We also used the linkage map to anchor portions of the M. zebra genome assembly. We constructed a linkage map consisting of 834 markers in 22 linkage groups that spanned over 1,933 cM. QTL analysis detected one QTL each for dorsal fin xanthophores, caudal fin xanthophores, and pelvic fin melanophores. Dorsal fin and caudal fin xanthophores share a QTL on LG12, while pelvic fin melanophores have a QTL on LG11. We used the mapped markers to anchor 66.5% of the M. zebra genome assembly. Within each QTL interval we identified several candidate genes that might play a role in pigment cell development. This is one of a few studies to identify QTL for natural variation in fish pigmentation. The QTL intervals we identified did not contain any pigmentation genes previously identified by mutagenesis studies in other species. We expect that further work on these intervals will identify new genes involved in pigment cell development in natural populations

A BAC-based physical map of the Nile tilapia genome

BACKGROUND: Cichlid fishes, particularly tilapias, are an important source of animal protein in tropical countries around the world. To support selective breeding of these species we are constructing genetic and physical maps of the tilapia genome. Physical maps linking collections of BAC clones are a critical resource for both positional cloning and assembly of whole genome sequences. RESULTS: We constructed a genome-wide physical map of the tilapia genome by restriction fingerprinting 35,245 bacterial artificial chromosome (BAC) clones using high-resolution capillary polyacrylamide gel electrophoresis. The map consists of 3,621 contigs and is estimated to span 1.752 Gb in physical length. An independent analysis of the marker content of four contigs demonstrates the reliability of the assembly. CONCLUSION: This physical map is a powerful tool for accelerating genomic studies in cichlid fishes, including comparative mapping among fish species, long-range assembly of genomic shotgun sequences, and the positional cloning of genes underlying important phenotypic traits. The tilapia BAC fingerprint database is freely available at

An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags

<p>Abstract</p> <p>Background</p> <p>Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research.</p> <p>Results</p> <p>The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10^-10) to the UniProt database.</p> <p>Conclusion</p> <p>Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.</p

On reminder effects, drop-outs and dominance: evidence from an online experiment on charitable giving

We present the results of an experiment that (a) shows the usefulness of screening out drop-outs and (b) tests whether different methods of payment and reminder intervals affect charitable giving. Following a lab session, participants could make online donations to charity for a total duration of three months. Our procedure justifying the exclusion of drop-outs consists in requiring participants to collect payments in person flexibly and as known in advance and as highlighted to them later. Our interpretation is that participants who failed to collect their positive payments under these circumstances are likely not to satisfy dominance. If we restrict the sample to subjects who did not drop out, but not otherwise, reminders significantly increase the overall amount of charitable giving. We also find that weekly reminders are no more effective than monthly reminders in increasing charitable giving, and that, in our three months duration experiment, standing orders do not increase giving relative to one-off donations