Genome Biology and Evolution - Advance Access

The mechanism of expansion and the volatility it created in three pheromone gene clusters in the mouse (Mus musculus) genome

Karn, R. C., Laukaitis, C. M. — Fri, 20 Nov 2009 08:45:53 PST

Three families of proteinaceous pheromones have been described in the house mouse: androgen-binding proteins (ABPs), exocrine-gland-secreting peptides (ESPs) and major urinary proteins (MUPs), each of which is thought to communicate different information. All three are encoded by large gene clusters in different regions of the mouse genome, clusters that have expanded dramatically during mouse evolutionary history. We report copy number variation (CNV) among the most recently duplicated Abp genes, which suggests substantial volatility in this gene region. It appears that groups of these genes behave as low copy repeats (LCRs), duplicating as relatively large blocks of genes by non-allelic homologous recombination (NAHR). An analysis of gene conversion suggested that it did not contribute to the very low or absent divergence among the paralogs duplicated in this way. We evaluated the ESP and MUP gene regions for signs of the LCR pattern but could find no compelling evidence for duplication of gene blocks of any significant size.. Assessment of the entire Abp gene region with the Mouse Paralogy Browser supported the conclusion that substantial volatility has occurred there. This was especially evident when comparing strains with all or part of the M. m. musculus or M. m. castaneus Abp region. No particularly remarkable volatility was observed in the other two gene families and we discuss the significance of this in light of the various roles proposed for the three families of mouse proteinaceous pheromones.

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.

Wed, 18 Nov 2009 06:51:21 PST

Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is to identify questions that shallow-depth genomic data can address successfully, and to develop corresponding analytical methods that are statistically sound. Here we apply the Roche/454 platform to survey natural variation in strains of Drosophila melanogaster from an African (n=3) and a North American (n=6) population. Reads were aligned to the reference D. melanogaster genomic assembly, SNPs were identified, and nucleotide variation was quantified genome-wide. Simulations and empirical results suggest that nucleotide diversity can be accurately estimated from sparse data with as little as 0.2x coverage per line. The unbiased genomic sampling provided by random short read sequencing also allows insight into distributions of transposable elements and copy number polymorphisms found within populations, and demonstrates that short-read sequencing methods provide an efficient means to quantify variation in genome organization and content. Continued development of methods for statistical inference of shallow-depth genome-wide sequencing data will allow such sparse, partial datasets to become the norm in the emerging field of population genomics.

Population genomics of intron splicing in 38 Saccharomyces cerevisiae genome sequences

Skelly, D. A., Ronald, J., Connelly, C. F., Akey, J. M. — Tue, 17 Nov 2009 06:32:46 PST

Introns are a ubiquitous feature of eukaryotic genomes, and the dynamics of intron evolution between species has been extensively studied. However, comparatively few analyses have focused on the evolutionary forces shaping patterns of intron variation within species. To better understand the population genetic characteristics of introns, we performed an extensive population genetics analysis on key intron splice sequences obtained from 38 strains of Saccharomyces cerevisiae. As expected, we found that purifying selection is the dominant force governing intron splice sequence evolution in yeast, formally confirming that intron-containing alleles are a mutational liability. In addition, through extensive coalescent simulations, we obtain quantitative estimates of the strength of purifying selection (2N_es 19) and use diffusion approximations to provide insights into the evolutionary dynamics and sojourn times of newly arising splice sequence mutations in natural yeast populations. In contrast to previous functional studies, evolutionary analyses comparing the prevalence of introns in essential and non-essential genes suggest that introns in non-ribosomal protein genes are functionally important and tend to be actively maintained in natural populations of S. cerevisiae. Finally, we demonstrate that heritable variation in splicing efficiency is common in intron-containing genes with splice sequence polymorphisms. More generally, our study highlights the advantages of population genomics analyses for exploring the forces that have generated extant patterns of genome variation and for illuminating basic biological processes.

The complete plastid genome sequence of the secondarily non-photosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate

Fri, 13 Nov 2009 09:26:42 PST

The cryptomonads are a group of unicellular algae that acquired photosynthesis through the engulfment of a red algal cell, a process called secondary endosymbiosis. Here we present the complete plastid genome sequence of the secondarily non-photosynthetic species Cryptomonas paramecium CCAP977/2a. The ~78 kilobase pair (Kbp) C. paramecium genome contains 82 predicted protein genes, 29 tRNA genes, and a single pseudogene (atpF). The C. paramecium plastid genome is approximately 50 Kbp smaller than those of the photosynthetic cryptomonads Guillardia theta and Rhodomonas salina; 71 genes present in the G. theta and/or R. salina plastid genomes are missing in C. paramecium. The pet, psa and psb photosynthetic gene families are almost entirely absent. Interestingly, the ribosomal RNA operon, present as inverted repeats in most plastid genomes (including G. theta and R. salina), exists as a single copy in C. paramecium. The G+C content (38%) is higher in C. paramecium than in other cryptomonad plastid genomes, and C. paramecium plastid genes are characterized by significantly different codon usage patterns and increased evolutionary rates. The content and structure of the C. paramecium plastid genome provides insight into the changes associated with recent loss of photosynthesis in a predominantly photosynthetic group of algae, and reveals features shared with the plastid genomes of other secondarily non-photosynthetic eukaryotes.

Lateral transfer of genes and gene fragments in prokaryotes

Chan, C. X., Beiko, R. G., Darling, A. E., Ragan, M. A. — Wed, 04 Nov 2009 09:18:52 PST

Lateral genetic transfer (LGT) involves the movement of genetic material from one lineage into another, and its subsequent incorporation into the new host genome via genetic recombination. Studies in individual taxa have indicated lateral origins for stretches of DNA of greatly varying length, from a few nucleotides to chromosome size. Here we analyse 1462 sets of single-copy, putatively orthologous genes from 144 fully sequenced prokaryote genomes, asking to what extent complete genes and fragments of genes have been transferred and recombined in LGT. Using a rigorous phylogenetic approach, we find evidence for LGT in at least 476 (32.6%) of these 1462 gene sets: 286 (19.6%) clearly show one or more observable recombination breakpoints within the boundaries of the open reading frame, while a further 190 (13.0%) yield trees that are topologically incongruent with the reference tree but do not contain a recombination breakpoint within the open reading frame. We refer to these gene sets as observable recombination breakpoint positive (ORB⁺) and negative (ORB^-) respectively. The latter are prima facie instances of lateral transfer of an entire gene or beyond. We observe little functional bias between ORB⁺ and ORB^- gene sets, but find that incorporation of entire genes is potentially more frequent in pathogens than in non-pathogens. As ORB⁺ gene sets are almost twice as common as ORB^- sets in our data, the transfer of gene fragments has been relatively frequent, and the frequency of LGT may have been systematically underestimated in phylogenetic studies.