Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates.

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events of Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.

Analyses of Genome Regulatory Evolution Following Whole-Genome Duplication Using the Phylogenetic EVE Model.

Whole-genome duplications (WGDs) are important in shaping the evolution of complex genomes, including rewiring of genome regulation. To address key questions about how WGDs impact the evolution of genome regulation, we need to understand the relative importance of selection versus drift and temporal evolutionary dynamics. One promising class of statistical models that can help address such questions are phylogenetic Ornstein-Uhlenbeck (OU) models.Here we present a computational pipeline for the comparative phylogenetic analyses of genome regulation using an OU model. We have implemented this model in R and provide a step-by-step protocol for the use of this model, including example scripts and simulated test data. We provide the nonspecialist a brief overview of how this model works and how to perform tests for signatures of selection on genome regulation as well as power simulations to aid in experimental design and interpretation of results. We believe that these resources could help polyploidy research move forward in an era of rapidly increasing functional genomics data across the tree of life.

Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution.

The long-term evolutionary impacts of whole-genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologs) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnolog sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent "explosion" of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnolog divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial "wave" of rediploidization in the late Cretaceous (85-106 Ma). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnolog divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication.

BACKGROUND: Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. RESULTS: We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of "toxic mutations". Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. CONCLUSIONS: Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar).

BACKGROUND: One objective of this study was to identify putative quantitative trait loci (QTL) that affect indicator phenotypes for growth, nitrogen, and carbon metabolism in muscle, liver, and adipose tissue, and for feed efficiency. Another objective was to perform an RNAseq analysis (184 fish from all families), to identify genes that are associated with carbon and nitrogen metabolism in the liver. The material consisted of a family experiment that was performed in freshwater and included 2281 individuals from 23 full-sib families. During the 12-day feed conversion test, families were randomly allocated to family tanks (50 fish per tank and 2 tanks per family) and fed a fishmeal-based diet labeled with the stable isotopes 15N and 13C at inclusion levels of 2 and 1%, respectively. RESULTS: Using a linear mixed-model algorithm, a QTL for pre-smolt growth was identified on chromosome 9 and a QTL for carbon metabolism in the liver was identified on chromosome 12 that was closely related to feed conversion ratio on a tank level. For the indicators of feed efficiency traits that were derived from the stable isotope ratios (15N and 13C) of muscle tissue and growth, no convincing QTL was detected, which suggests that these traits are polygenic. The transcriptomic analysis showed that high carbon and nitrogen metabolism was associated with individuals that convert protein from the feed more efficiently, primarily due to higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. In addition, we identified seven transcription factors that were associated with carbon and nitrogen metabolism and located in the identified QTL regions. CONCLUSIONS: Analyses revealed one QTL associated with pre-smolt growth and one QTL for carbon metabolism in the liver. Both of these traits are associated with feed efficiency. However, more accurate mapping of the putative QTL will require a more diverse family material. In this experiment, fish that have a high carbon and nitrogen metabolism in the liver converted protein from the feed more efficiently, potentially because of a higher expression of the proteasome, lipid, and carbon metabolic pathways in liver. Within the QTL regions, we detected seven transcription factors that were associated with carbon and nitrogen metabolism.

Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae.

The grass subfamily Pooideae dominates the grass floras in cold temperate regions and has evolved complex physiological adaptations to cope with extreme environmental conditions like frost, winter, and seasonality. One such adaptation is cold acclimation, wherein plants increase their frost tolerance in response to gradually falling temperatures and shorter days in the autumn. However, understanding how complex traits like cold acclimation evolve remains a major challenge in evolutionary biology. Here, we investigated the evolution of cold acclimation in Pooideae and found that a phylogenetically diverse set of Pooideae species displayed cold acclimation capacity. However, comparing differential gene expression after cold treatment in transcriptomes of five phylogenetically diverse species revealed widespread species-specific responses of genes with conserved sequences. Furthermore, we studied the correlation between gene family size and number of cold-responsive genes as well as between selection pressure on coding sequences of genes and their cold responsiveness. We saw evidence of protein-coding and regulatory sequence evolution as well as the origin of novel genes and functions contributing toward evolution of a cold response in Pooideae. Our results reflect that selection pressure resulting from global cooling must have acted on already diverged lineages. Nevertheless, conservation of cold-induced gene expression of certain genes indicates that the Pooideae ancestor may have possessed some molecular machinery to mitigate cold stress. Evolution of adaptations to seasonally cold climates is regarded as particularly difficult. How Pooideae evolved to transition from tropical to temperate biomes sheds light on how complex traits evolve in the light of climate changes.

Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome.

KEY MESSAGE: A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.

Single-incision laparoscopic versus conventional laparoscopic ventral hernia repair: a comparison of short-term surgical results.

AIM: To demonstrate the feasibility of single-port incisional hernia repair, quantify incision size, and compare results of patients operated by standard laparoscopy (SL) with those operated by the single-port technique [laparoendoscopic single-site surgery (LESS)]. METHODS: Prospective data collected on patients operated from March 2008 to June 2010. Indication for surgery was incisional hernia >3 cm. There were no selection criteria for the enrollment of patients or the operative technique used. RESULTS: Thirty-four patients were operated (18 women and 16 men): 15 with LESS and 19 with SL. There was no difference for age, body mass index, ASA scores, or number of previous surgical procedures. LESS patients had slightly larger (82 ± 54 vs. 64 ± 34 mm) and more numerous hernias: 3 (1 to 7) versus 1 (1 to 3). Adhesion grades, severity scores, and operating times (78.2 SD ± 31.2 vs. 73.5 SD ± 25.4 min, P=0.76) did not differ between the groups. The mean fascia incision size in LESS was digitally measured as 12.93 ± 2.01 mm. The hospital stay was a median of 1 day in both groups. There was 1 conversion in the SL group. The median follow-up time was 26 months (range, 25 to 31 mo) for LESS and 34 months (range, 31 to 42 mo) for SL. COMPLICATIONS: There were 2 seromas and 1 hematoma in the LESS group. In the SL group, there were 2 small-bowel injuries and 2 seromas. There were no recurrences in the SL group, 1 in LESS, and no port-site hernia so far. CONCLUSIONS: LESS incisional hernia repair through 1 minimal fascia incision is feasible. Early results do not indicate a longer operation time, higher complication, or higher recurrence rates.

The anatomical and surgical consequences of right colectomy for cancer.

BACKGROUND: Current practice when performing right colectomy for cancer is to divide the feeding vessels for the right colon on the right side of the superior mesenteric vein. OBJECTIVE: This study aims to show that arterial stumps can be visualized through an early postoperative CT and analyze their anatomical and surgical characteristics. DESIGN: This study presents a retrospective review of prospective data. SETTINGS: :The study was conducted at the Department of Surgery, Vestfold Hospital, Tonsberg, Norway. PATIENTS: Patients with leakage after a right colectomy for cancer (2003-2011) were identified through a local prospective complication registry (FileMaker Pro 9.0v3 software). INTERVENTIONS: Both preoperative and postoperative CTs were retrieved, reanalyzed, and 3-dimensionally reconstructed (Osirix v.3.0.2./Mimics v.13.1.). Patients without postoperative CTs were excluded. MAIN OUTCOME MEASURES: The main outcomes measured were length, caliber of presumed and actual arterial stumps, and their position relative to the superior mesenteric vein. RESULTS: Eighteen patients, median age 69 (10 men) were included. All patients had postoperative CTs, and 15 patients had preoperative CTs. Median time from operation to postoperative CT was 5 days. The ileocolic artery was found in 14 (11 CT pairs) patients, and the right colic artery was found in 5 (4 pairs) patients. Actual stump lengths were 28.0 mm (SD 9.3) and 37.3 mm (SD 14.9). A significant statistical difference between presumed and actual ileocolic artery stump lengths was found (P = .002). Posterior crossing to the superior mesenteric vein was noticed in 8 of 14 ileocolic arteries and in 3 of 5 right colic arteries. There was no statistical difference in mean caliber for the preoperative and postoperative right colic artery (P = .505) and ileocolic artery (P = .474). LIMITATIONS: Difficulties when interpreting the postoperative images, due to intra-abdominal effusion, staples, edema, and altered syntopy of blood vessels, were overcome through comparison with preoperative CTs. CONCLUSION: An early postoperative CT can show arterial stumps after right colectomy for cancer. These stumps appear to be significantly longer than presumed; implying a significant improvement potential when specimen size is concerned.