The Chlamydomonas genome has been sequenced, assembled and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. However, the current reference genome contains ~1000 blocks of unknown sequence (‘N-islands’), which are frequently placed in introns of annotated gene models. We developed a strategy, using careful bioinformatics analysis of short-sequence cDNA and genomic DNA reads, to search for previously unknown exons hidden within such blocks, and determine the sequence and exon/intron boundaries of such exons. These methods are based on assembly and alignment completely independent of prior reference assembly or reference annotation. Our evidence indicates that ~one-quarter of the annotated intronic N-islands actually contain hidden exons. For most of these our algorithm recovers full exonic sequence with associated splice junctions and exon-adjacent intron sequence, that can be joined to the reference genome assembly and annotated transcript models. These new exons represent de novo sequence generally present nowhere in the assembled genome, and the added sequence can be shown in many cases to greatly improve evolutionary conservation of the predicted encoded peptides. At the same time, our results confirm the purely intronic status for a substantial majority of N-islands annotated as intronic in the reference annotated genome, increasing confidence in this valuable resource.

Rawcopy is an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). It uses data from a large number of reference samples to produce log ratio for total copy number analysis and B-allele frequency for allele-specific copy number and heterozygosity analysis. Rawcopy achieves higher signal-to-noise ratio than commonly used free and proprietary alternatives, leading to improved identification of copy number alterations. In addition, Rawcopy visualises each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states.

Sex chromosomes play a prominent role in development and evolution and have several characteristic features that distinguish them from autosomes. Across diverse taxa, recombination is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the remainder of the chromosome or pseudoautosomal region (PAR). However, in most model taxa the sex chromosomes are ancient and highly differentiated from autosomes, and thus little is known about recombination dynamics of homomorphic sex chromosomes with incipient sex-determining mechanisms. Here we examine male function (pollen production) and female function (fruit production) in crosses of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the young ZW chromosome. The SDR occurs in a narrow 280kb window, in which the maternal recombination rate is lower than in the orthologous paternal region and the genome-wide average rate, but within the range of autosomal rate variation. In contrast to the SDR, the ZW recombination rate in the PAR is much higher than the rates of the ZZ or autosomal linkage groups, substantially overcompensating for the SDR rate. By extensively sequencing sections of the SDR vicinity in several crosses and unrelated plants, we show that W-specific divergence is elevated within a portion of the SDR and find only a single SNP to be in high linkage disequilibrium with sex, suggesting that any W-specific haplotype protected from recombination is not large. We hypothesize that selection for recombination suppression within the small SDR may be weak, but that fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutation on the W. Thus these results illuminate the recombination dynamics of a nascent sex chromosome with a modestly diverged SDR, which could be typical of other dioecious plants.

Due to the lack of recombination, the male-specific region of the Y chromosome (MSY) is a unique resource for tracking the genetic history of populations. The MSY is also enriched for large, nearly identical repetitive regions known as amplicons, which harbor many of the genes essential for spermatogenesis. In humans, sequence diversity on the unique segment of the MSY is greatly reduced compared to the autosomes, an observation consistent with the action of strong selection. Here, we analyze 9 chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and two Pan paniscus male whole-genome sequences to assess Y chromosome nucleotide and ampliconic copy-number diversity across the Pan genus. In total, we identified 23,946 Pan spp. SNVs across 4.2 million callable sites. Comparisons with autosomal, X chromosome, and mitochondrial sequences from the same samples indicate that nucleotide diversity on the chimpanzee MSY is reduced relative to neutral expectations with an equal sex ratio. Additionally, the estimated common chimpanzee Y chromosome TMRCA (0.44 mya [0.31-0.56]) is half the age of the mitochondria TMRCA (0.97 mya [0.65-1.35]), indicating an unequal sex ratio or Y chromosome selection in the common chimpanzee ancestral population. We observe that the copy-number of Y chromosome amplicons is variable amongst chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy-number of the testis-expressed genes RBMY and DAZ. We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.

Motivation: Bioinformatics analyses have become increasingly intensive computing processes, with lowering costs and increasing numbers of samples. Each laboratory spends time creating and maintaining a set of pipelines, which may not be robust, scalable, or efficient. Further, the existence of different computing environments across institutions hinders both collabo-ration and the portability of analysis pipelines. Results: Flowr is a robust and scalable framework for designing and deploying computing pipelines in an easy-to-use fashion. It implements a scatter-gather approach using computing clusters, simplifying the concept to the use of five simple terms (in submission and dependency types). Most importantly, it is flexible, such that customizing existing pipelines is easy, and since it works across several computing environments (LSF, SGE, Torque, and SLURM), it is portable. Availability: http://docs.flowr.space