BackgroundTo facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear how comparable these tools are or what their relative merits in real-world scenarios might be.MethodsWe sequenced 15 exomes from four families using commercial kits (Illumina HiSeq 2000 platform and Agilent SureSelect version 2 capture kit), with approximately 120X mean coverage. We analyzed the raw data using near-default parameters with five different alignment and variant-calling pipelines (SOAP, BWA-GATK, BWA-SNVer, GNUMAP, and BWA-SAMtools). We additionally sequenced a single whole genome using the sequencing and analysis pipeline from Complete Genomics (CG), with 95% of the exome region being covered by 20 or more reads per base. Finally, we validated 919 single-nucleotide variations (SNVs) and 841 insertions and deletions (indels), including similar fractions of GATK-only, SOAP-only, and shared calls, on the MiSeq platform by amplicon sequencing with approximately 5000X mean coverage.ResultsSNV concordance between five Illumina pipelines across all 15 exomes was 57.4%, while 0.5 to 5.1% of variants were called as unique to each pipeline. Indel concordance was only 26.8% between three indel-calling pipelines, even after left-normalizing and intervalizing genomic coordinates by 20 base pairs. There were 11% of CG variants falling within targeted regions in exome sequencing that were not called by any of the Illumina-based exome analysis pipelines. Based on targeted amplicon sequencing on the MiSeq platform, 97.1%, 60.2%, and 99.1% of the GATK-only, SOAP-only and shared SNVs could be validated, but only 54.0%, 44.6%, and 78.1% of the GATK-only, SOAP-only and shared indels could be validated. Additionally, our analysis of two families (one with four individuals and the other with seven), demonstrated additional accuracy gained in variant discovery by having access to genetic data from a multi-generational family.ConclusionsOur results suggest that more caution should be exercised in genomic medicine settings when analyzing individual genomes, including interpreting positive and negative findings with scrutiny, especially for indels. We advocate for renewed collection and sequencing of multi-generational families to increase the overall accuracy of whole genomes.

Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed for gene duplication to explain how new gene copies are preserved by natural selection, but these models have rarely been tested using empirical data. Opsin proteins, when combined with a chromophore, form a photopigment that is responsible for the absorption of light, the first step in the phototransduction cascade. Adaptive gene duplications have occurred many times within the animal opsins' gene family, leading to novel wavelength sensitivities. Consequently, opsins are an attractive choice for the study of gene duplication evolutionary models. Odonata (dragonflies and damselflies) have the largest opsin repertoire of any insect currently known. Additionally, there is tremendous variation in opsin copy number between species, particularly in the long-wavelength-sensitive (LWS) class. Using comprehensive phylotranscriptomic and statistical approaches, we tested various evolutionary models of gene duplication. Our results suggest that both the blue-sensitive (BS) and LWS opsin classes were subjected to strong positive selection that greatly weakens after multiple duplication events, a pattern that is consistent with the permanent heterozygote model. Due to the immense interspecific variation and duplicability potential of opsin genes among odonates, they represent a unique model system to test hypotheses regarding opsin gene duplication and diversification at the molecular level.

Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically “intermediate” species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.

exchange of inter-specific genetic information via various biological processes. In particular, 51 lateral gene transfer, incomplete lineage sorting (ILS) and introgression can result in gene trees 52 that are discordant with the species tree [3, 4]. Lateral transfer and introgression both involve 53 gene flow following speciation, thereby producing "reticulate" phylogenies. Incomplete lineage 54 sorting (ILS), on the other hand, occurs when three or more lineages coalesce in their ancestral 55 population. This often arises in an order that conflicts with that of the true species tree, and thus 56 involves no post-speciation gene flow and therefore does not contribute to reticulate evolution. 57 Thus, phylogenetic species-gene tree incongruence observed in empirical data can provide 58 insight into underlying biological factors that shape the evolutionary trajectories of a set of taxa. 59The major source of reticulate evolution for eukaryotes is introgression where it affects 60 approximately 25% of flowering plant and 10% of animal species [1, 5]. Introgressed alleles can 61 be fitness-neutral, deleterious [6] or adaptive. For example, adaptive introgression has been 62 shown to provide an evolutionary rescue from polluted habitats in gulf killifish (Fundulus 63 grandis) [7], yielded mimicry adaptations among Heliconius butterflies [8] and archaic 64 introgression has facilitated adaptive evolution of altitude tolerance [9], immunity and 65 metabolism in modern humans [10]. Additionally, hybridization and introgression are important 66 and often overlooked mechanisms of invasive species establishment and spread [11]. 67Odonata, the insect order that contains dragonflies and damselflies, lacks a strongly 68 supported backbone tree to clearly resolve higher-level phylogenetic relationships [12, 13]. 69 Current evidence places odonates together with Ephemeroptera (mayflies) as the living 70 representatives of the most ancient insect lineages to have evolved wings and active flight [14]. 71Odonates possess unique anatomical and morphological features such as a specialized body 72 form, specialized wing venation, a distinctive form of muscle attachment to the wing base [15] 73 allowing for direct flight and accessory (secondary) male genitalia that support certain unique 74 behaviors (e.g., sperm competition). They are among the most adept flyers of all animals and are 75 exclusively carnivorous insects relying primarily on vision [16, 17] to capture prey. They spend 76 much of their adult life in flight [18]. Biogeographically, odonates exhibit worldwide dispersal 77[19] and play crucial ecological roles in local freshwater communities, being a top invertebrate 78 predator [20]. Due to this combination of characteristics, odonates are quickly becoming model 79 organisms to study specific questions in ecology, physiology and evolution [21, 22]. However, 80 the extent of introgression at the genomic scale within Odonata remains primarily unknown. 81Two early attempts to tackle introgression/hybridization patterns wi...

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species.