Comparison Of Single Nucleotide Polymorphisms Research Articles

A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology

In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.

Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid-zone mammals with high dispersal capacity.

Landscape genetics is increasingly transitioning away from microsatellites, with single nucleotide polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial-genetic structure. This is particularly pertinent for research in arid-zone mammals due to challenges associated with unique life history traits, such as boom-bust population dynamics and long-distance dispersal capacities. Here, we provide a case study comparing SNPs versus microsatellites for testing three explicit landscape genetic hypotheses (isolation-by-distance, isolation-by-barrier, and isolation-by-resistance) in a suite of small, arid-zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi, and two native rodents, Pseudomys chapmani and P. hermannsburgensis. SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation-by-distance and isolation-by-resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best-performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.

Genetic Analysis and QTL Mapping of Parthenocarpy in <i>Cucumis sativus</i> L

Breeding of cucumber cultivars with high parthenocarpy rate are the prerequisite that ensuring yield and quality under undesirable environment. The mixed major gene plus polygene inheritance model was used to analyze cucumber parthenocarpy trait in the six generations, including P 1 , P 2 , F 1 , BC 1 , BC 2  and F 2 , derived from a cross between the highly parthenocarpic line DDX and low parthenocarpic line ZK. The major-effect quantitative trait locus (QTL) was identified by genome-wide comparison of single nucleotide polymorphisms (SNPs) between high- and low- parthenocarpy rate F 2  pools, and confirmed by traditional QTL mapping with genetic map. Genetic analysis showed that the genetic model E-2, mixed two additive-dominant-epistatic major genes and additive-dominant polygenes, is the best-fitting genetic model for cucumber parthenocarpy phenotype. A major-effect QTL, namely  par2.1 , were identified by the method of Δ(SNP_index).  par2.1  was confirmed by traditional markers based QTL mapping method with least likelihood (LOD) peak score of 12.6, genetic distance of 11.5cM and accounting for 26.6% of the total phenotypic variance.  par2.1  was narrowed down to a 765kb region through comparison of markers physical locations on chromosome 2. The major-effect QTL,  par2.1  on Chr2, for parthenocarpy identified by this study was not reported previously. Our findings shed light on the genetic architecture underlying cucumber parthenocarpy trait, and lay a solid basis for innovation of cucumber parthenocarpy germplasm and breed of new cucumber varieties with high parthenocarpy.

Successful Dissemination of Plasmid-Mediated Extended-Spectrum β-Lactamases in Enterobacterales over Humans to Wild Fauna

Background: The emergence of multidrug-resistant bacteria remains poorly understood in the wild ecosystem and at the interface of habitats. Here, we explored the spread of Escherichia coli containing IncI1-ST3 plasmid encoding resistance gene cefotaximase-Munich-1 (blaCTX-M-1) in human-influenced habitats and wild fauna using a genomic approach. Methods. Multilocus sequence typing (MLST), single-nucleotide polymorphism comparison, synteny-based analysis and data mining approaches were used to analyse a dataset of genomes and circularised plasmids. Results. CTX-M-1 E. coli sequence types (STs) were preferentially associated with ecosystems. Few STs were shared by distinct habitats. IncI1-ST3-blaCTX-M-1 plasmids are disseminated among all E. coli phylogroups. The main divergences in plasmids were located in a shuffling zone including blaCTX-M-1 inserted in a conserved site. This insertion hot spot exhibited diverse positions and orientations in a zone-modulating conjugation, and the resulting synteny was associated with geographic and biological sources. Conclusions. The ecological success of IncI1-ST3-blaCTX-M-1 appears less linked to the spread of their bacterial recipients than to their ability to transfer in a broad spectrum of bacterial lineages. This feature is associated with the diversity of their shuffling conjugation region that contain blaCTX-M-1. These might be involved in the resistance to antimicrobials, but also in their spread.

Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Hematopoietic Stem Cell Transplant Unit.

A recent surge in human mastadenovirus (HAdV) cases, including five deaths, amongst a haematopoietic stem cell transplant population led us to use whole genome sequencing (WGS) to investigate. We compared sequences from 37 patients collected over a 20-month period with sequences from GenBank and our own database of HAdVs. Maximum likelihood trees and pairwise differences were used to evaluate genotypic relationships, paired with the epidemiological data from routine infection prevention and control (IPC) records and hospital activity data. During this time period, two formal outbreaks had been declared by IPC, while WGS detected nine monophyletic clusters, seven were corroborated by epidemiological evidence and by comparison of single-nucleotide polymorphisms. One of the formal outbreaks was confirmed, and the other was not. Of the five HAdV-associated deaths, three were unlinked and the remaining two considered the source of transmission. Mixed infection was frequent (10%), providing a sentinel source of recombination and superinfection. Immunosuppressed patients harboring a high rate of HAdV positivity require comprehensive surveillance. As a consequence of these findings, HAdV WGS is being incorporated routinely into clinical practice to influence IPC policy contemporaneously.

Comparison of single nucleotide polymorphisms and short tandem repeats as markers for differentiating between donors and recipients in solid organ transplantation.

BackgroundTo analyze transplant rejection and to distinguish between donor and recipient, it is necessary to select a marker from single nucleotide polymorphism (SNP), short tandem repeat (STR), and human leukocyte antigen (HLA) testing. SNPs are bi-allelic and the polymerase chain reaction method used for SNP testing has the advantage of lower cost than sequencing methods. In this study, we aimed to distinguish donors from recipients using a combination of existing commercialized STRs and the SNPs identified.MethodsAll selected SNPs complied with the following criterion known and validated minor allele frequency (MAF) ≥43% in Korean and reported ethnicities from global populations (HapMap, 1000 Genomes, and the Korean Reference Genome project). The STR assays were performed for 16 tetranucleotide repeat loci.ResultsDNA from the 52 donor/recipient pairs were tested for informative markers. The median age of the recipients was 47 years. MAF in the 52 pairs was 1.0%–76.0%. The probability of informative genotypes (I) was 0.001–0.124. The summation of I was 0.680. In the 52 donor recipient pairs, the selected SNPs showed a 0.031 average probability of being informative. The probability of identity in our study was 0.122–0.348. SNP panel configuration distinguished 100% of 52 donors/recipient pairs.ConclusionsDonors and recipients were distinguished by STR and 22 SNPs with MAF identified from SNP databases. Seventeen SNPs were able to distinguish between donors and recipients (I value=0.039).

1456. Resistance Mechanisms of Tigecycline in Enterococcus faecalis

Background Enterococcus faecalis have been regarded as one of the leading causes of the nosocomial infections worldwide. Tigecycline (TGC) is considered as a choice of last resort for the treatment of infections caused by multidrug-resistant E. faecalis, however, the emergence of TGC non-susceptibility has posted the therapeutic challenge. Non-susceptibility in clinical strains could be due to resistance (MIC >0.5 mg/l) or heteroresistance. Therefore, this study aimed to understand the underlying molecular mechanisms of TGC resistance and heteroresistance in E. faecalis.Methods In vitro induction experiments were carried out under TGC pressure with two TGC- sensitive E. faecalis strains. Heteroresistance was evaluated by population analysis profiling (PAP) in 270 clinical TGC- sensitive E. faecalis strains. TGC susceptibility was determined by the agar dilution method. Resistance and heteroresistance mechanisms were investigated by identifying genetic mutations in tetracycline (Tet) target sites and susceptibility testing in the presence of the efflux protein inhibitors phenylalanine-arginine-β-naphthylamide (PaβN) and carbonyl cyanide m chlorophenylhydrazine (CCCP). Comparison of single nucleotide polymorphism in the whole genome between the parental isolate and two TGC-resistant strains were investigated by next-generation sequencing.ResultsNo mutations in Tet target sites in seven TGC heteroresistant strains were present, whereas the mutations in Tet target sites of seven TGC-resistant E. faecalis were frequently found (Table 1). TGC MICs in heteroresistant strains were reduced by CCCP (Table 2). Whole genome sequencing revealed the same non-synonymous mutations and transcoding deletions in the exons of several genes encoding for various enzymes or transfer systems (Table 3).Table 1. The characteristics of the antimicrobial susceptibility, resistance mechanism of TGC-induced resistant isolates Table 2. Characteristics of clinical heteroresistant mother E. faecalis strains and heteroresistance-derived E. faecalis clones Table 3. List of mutation-related genes, amino acids and proteins by comparison of whole genome between the parental isolate and the TGC-induced resistant strains ConclusionOur data indicated that the main mechanism of TGC heteroresistance in E. faecalis might be associated with the efflux pumps. TGC resistance in E. faecalis was associated with mutations in the 16SrRNA site or 30S ribosome protein S10. The genetic mutations in several enzymes and transfer systems might also participate in the resistance development to TGC in E. faecalis.Disclosures All Authors: No reported disclosures

Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit.

Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total of 21 organisms (10 patient-derived isolates and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis Strains isolated from multiple detergent-dispensing bottles were either identical or closely related by single-nucleotide polymorphism comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk expression equipment. No new cases were identified once the detergent bottles were removed. Environmental reservoirs may be an important source in outbreaks of multidrug-resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.

The major-effect quantitative trait locus Fnl7.1 encodes a late embryogenesis abundant protein associated with fruit neck length in cucumber.

SummaryFruit neck length (FNL) is an important quality trait in cucumber because it directly affects its market value. However, its genetic basis remains largely unknown. We identified a candidate gene for FNL in cucumber using a next‐generation sequencing‐based bulked segregant analysis in F2 populations, derived from a cross between Jin5‐508 (long necked) and YN (short necked). A quantitative trait locus (QTL) on chromosome 7, Fnl7.1, was identified through a genome‐wide comparison of single nucleotide polymorphisms between long and short FNL F2 pools, and it was confirmed by traditional QTL mapping in multiple environments. Fine genetic mapping, sequences alignment and gene expression analysis revealed that CsFnl7.1 was the most likely candidate Fnl7.1 locus, which encodes a late embryogenesis abundant protein. The increased expression of CsFnl7.1 in long‐necked Jin5‐508 may be attributed to mutations in the promoter region upstream of the gene body. The function of CsFnl7.1 in FNL control was confirmed by its overexpression in transgenic cucumbers. CsFnl7.1 regulates fruit neck development by modulating cell expansion. Probably, this is achieved through the direct protein–protein interactions between CsFnl7.1 and a dynamin‐related protein CsDRP6 and a germin‐like protein CsGLP1. Geographical distribution differences of the FNL phenotype were found among the different cucumber types. The East Asian and Eurasian cucumber accessions were highly enriched with the long‐necked and short‐necked phenotypes, respectively. A further phylogenetic analysis revealed that the Fnl7.1 locus might have originated from India. Thus, these data support that the CsFnl7.1 has an important role in increasing cucumber FNL.

Genome Analysis of A Novel South African Cydia pomonella granulovirus (CpGV-SA) with Resistance-Breaking Potential.

The complete genome of an endemic South African Cydia pomonella granulovirus isolate was sequenced and analyzed. Several missing or truncated open reading frames (ORFs) were identified, including a 24 bp deletion in the pe38 gene which is reported to be associated with type I resistance-breaking potential. Comparison of single nucleotide polymorphisms (SNPs) with five other fully sequenced CpGV isolates identified 67 unique events, 47 of which occurred within ORFs, leading to several amino acid changes. Further analysis of single nucleotide variations (SNVs) within CpGV-SA revealed that this isolate consists of mixed genotypes. Phylogenetic analysis using complete genome sequences placed CpGV-SA basal to M, I12 and E2 and distal to S and I07 but with no distinct classification into any of the previously defined CpGV genogroups. These results suggest that CpGV-SA is a novel and genetically distinct isolate with significant potential as a biopesticide for management of codling moth (CM), not only in South Africa, but potentially in other pome fruit producing countries, particularly where CM resistance to CpGV has been reported.

Overlap in the Genetic Architecture of Stroke Risk, Early Neurological Changes, and Cardiovascular Risk Factors.

Background and Purpose- The genetic relationships between stroke risk, stroke severity, and early neurological changes are complex and not completely understood. Genetic studies have identified 32 all stroke risk loci. Polygenic risk scores can be used to compare the genetic architecture of related traits. In this study, we compare the genetic architecture of stroke risk, stroke severity, and early neurological changes with that of 2 stroke risk factors: type 2 diabetes mellitus (T2DM) and hypertension. Methods- We assessed the degree of overlap in the genetic architecture of stroke risk, T2DM, hypertension, and 2 acute stroke phenotypes based on the National Institutes of Health Stroke Scale (NIHSS), which ranges from 0 for no stroke symptoms to 21 to 42 for a severe stroke: baseline (within 6 hours after onset) and change in NIHSS (ΔNIHSS=NIHSS at baseline-NIHSS at 24 hours). This was done by (1) single-nucleotide polymorphism by single-nucleotide polymorphism comparison, (2) weighted polygenic risk scores with sentinel variants, and (3) whole-genome polygenic risk scores using multiple P thresholds. Results- We found evidence of genetic architecture overlap between stroke risk and T2DM ( P=2.53×10-169), hypertension ( P=3.93×10-04), and baseline NIHSS ( P=0.03). However, there was no evidence of overlap between ΔNIHSS and stroke risk, T2DM, or hypertension. Conclusions- The genetic architecture of stroke risk is correlated with that of T2DM, hypertension, and initial stroke severity (NIHSS within 6 hours of stroke onset). However, the genetic architecture of early neurological change after stroke (ΔNIHSS) is not correlated with that of ischemic stroke risk, T2DM, or hypertension. Thus, stroke risk and early neurological change after stroke have distinct genetic architectures.

Comparison of biochemical and genotypic speciation methods for vancomycin-resistant enterococci isolated from urban wastewater treatment plants

Enterococci species in wastewater including Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus and Enterococcus gallinarum isolates (n = 308) with low or high level vancomycin resistance were determined and compared using a phenotypic method (RapID™ STR system), 16S rRNA sequencing, and multi-locus (atpA, groESL, and pheS) sequence analysis (MLSA). Error rates for the RapID™ STR system were E. faecalis (15.9%), E. faecium (21.5%), and E. casseliflavus/E. gallinarum (56.9%) when referenced to the consensus of all methods tested. Comparison of single nucleotide polymorphism (SNP) distances and phylogenetic trees suggested that the groESL locus delineated species more effectively than other loci. The groESL locus was the most reliable loci for the correct identification of Enterococcus spp., including E. casseliflavus and E. gallinarum, with high congruence compared to the consensus (Adjusted Rand Index = 0.954; Adjusted Wallace Co-efficient = 0.941). All of the methods were compared to whole genome sequencing, which acted as a gold standard, for the isolates from this study and those downloaded from NCBI.

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

BackgroundNanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity.ResultsFrom 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs.ConclusionsThis population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations.

ANKRD9 is associated with tumor suppression as a substrate receptor subunit of ubiquitin ligase

BackgroundHuman ANKRD9 (ankyrin repeat domain 9) expression is altered in some cancers. MethodsWe tested genetic association of ANKRD9 with gastric cancer susceptibility and examined functional association of ANKRD9 with altered proliferation of MKN45 gastric cancer cells. We then identified ANKRD9-binding partners in HEK 293 embryonic kidney cells using quantitative proteomics, western blotting and complex reconstitution assays. We finally demonstrated ANKRD9's role of recognizing substrates for ubiquitination using in vitro ubiquitylation assay. ResultsANKRD9 is associated with cancer susceptibility in a comparison of single-nucleotide polymorphisms between 1092 gastric cancer patients and 1206 healthy controls. ANKRD9 depletion accelerates tumor progression by increasing cellular proliferation, piling up, and anchorage-independent growth of MKN45 cells. We discovered that ANKRD9 is a ubiquitin ligase substrate receptor subunit and has an anti-proliferative activity. ANKRD9 associates with CUL5 (not CUL2), ELOB, ELOC, and presumably RNF7 subunits, which together assemble into a cullin-RING superfamily E3 ligase complex. ANKRD9 belongs to the ASB family of proteins, which are characterized by the presence of ankyrin repeats and a SOCS box. In addition to its interactions with the other E3 ligase subunits, ANKRD9 interacts with two isoforms of inosine monophosphate dehydrogenase (IMPDH). These IMPDH isoforms are cognate substrates of the ANKRD9-containing E3 enzyme, which ubiquitinates them for proteasomal degradation. Their ubiquitination and turnover require the presence of ANKRD9. ConclusionANKRD9, a previously unidentified E3 substrate receptor subunit, functions in tumor suppression by recognizing the oncoprotein IMPDH isoforms for E3 ubiquitination and proteasomal degradation.

Clonal diversity and geographic distribution of methicillin-resistant Staphylococcus pseudintermedius from Australian animals: Discovery of novel sequence types

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an increasingly prevalent pathogen in veterinary medicine. This study examined the molecular epidemiology of clinical MRSP isolated from Australian animals. Clinical staphylococci submitted to all Australian veterinary diagnostic laboratories were collected during 2013 and identified using traditional phenotypic tests and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Phenotypic antimicrobial resistance was determined using broth microdilution and disk diffusion. MRSP isolates were characterized by whole genome sequencing which included identification of the mecA gene. Phylogenetic relationships were inferred by comparison of single nucleotide polymorphisms. Of the 669 S. pseudintermedius isolates collected from dogs, cats and cattle, 77 (11.5%) were MRSP. Nineteen multilocus sequence types (STs) were identified, with most isolates belonging to one of five STs (ST71, ST497, ST316, ST496 and ST45). Phylogenetic analysis revealed that Australian ST71 appears closely related to ST71 from overseas. ST497 and ST496 represented novel sequence types, not previously reported outside Australia. Most other STs were novel and only distantly related to each other. Geographical clustering of STs was observed. All isolates belonging to the five main STs were multi- to extensively- drug resistant while isolates from singleton STs generally had lower levels of antimicrobial resistance. The frequency of ciprofloxacin, trimethoprim-sulfamethoxazole, gentamicin, chloramphenicol and tetracycline resistance varied significantly between STs (p<0.01). Australian MRSP isolates are phylogenetically diverse, with a mix of previously unreported and well known international MRSP clones that demonstrate geographic clustering and exhibit both multidrug-resistant and extensively drug-resistant phenotypes.

Fine-mapping and candidate gene analysis of the Brassica juncea white-flowered mutant Bjpc2 using the whole-genome resequencing.

Flower color in Brassica spp. is an important trait and considered a major visual signal for insect-pollinated plants. In previous study, we isolated and identified two genes (BjPC1 and BjPC2) that control the flower color in B. juncea, and mapped BjPC1 to a 0.13-cM region. In this study, we report the fine-mapping and candidate analysis of BjPC2. We conducted whole-genome resequencing, using bulked segregant analysis (BSA) to determine the BjPC2 candidate intervals. Crossing, allelism testing, and repeated full-sib mating were used to generate XG3, a near isogenic line (NIL) population that segregated on the BjPC2 locus. Through a genome-wide comparison of single nucleotide polymorphism (SNP) profiles between the yellow- and white-flowered bulks, a candidate interval for BjPC2 was identified on chromosome B04 (2.45Mb). The BjPC2 linkage map was constructed with the newly developed simple sequence repeat (SSR) markers in the candidate interval to narrow the candidate BjPC2 region to 31-kb. Expression profiling and RNA-seq analysis partially confirmed that the AtPES2 homolog, BjuB027334 is the most promising candidate gene for BjPC2. Furthermore, analyses with high pressure liquid chromatography and transmission electron microscopy demonstrated that BjPC2 might be important in xanthophyll esterification, a process that limits xanthophyll degradation and increases sequestration. Overall, we mapped the BjPC2 to a 31-kb region on the B04 in B. juncea and identified BjuB027334 as a valuable candidate gene. Our results provide a basis for understanding the molecular mechanisms underlying the white-flowered trait and for molecular marker-assisted selection of flower color in B. juncea breeding.

The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs

Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charrSalvelinus alpinuspopulations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr.The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, includinglysozymeandnatterin-likewhich was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr.The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.

The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs.

Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr Salvelinus alpinus populations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr. The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, including lysozyme and natterin-like which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide.We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr. The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.

The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs

Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr Salvelinus alpinus populations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr.The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, including lysozyme and natterin-like which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr.The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.

The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs.

Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr Salvelinus alpinus populations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr. The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, including lysozyme and natterin-like which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide.We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr. The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.