The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, ...these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.
Abstract Skeletal muscle is the most abundant tissue in the body and serves various physiological functions including the generation of movement and support. Whole body motor function requires ...adequate quantity, geometry, and distribution of muscle. This raises the question: how do muscles scale with subject size in order to achieve similar function across humans? While much of the current knowledge of human muscle architecture is based on cadaver dissection, modern medical imaging avoids limitations of old age, poor health, and limited subject pool, allowing for muscle architecture data to be obtained in vivo from healthy subjects ranging in size. The purpose of this study was to use novel fast-acquisition MRI to quantify volumes and lengths of 35 major lower limb muscles in 24 young, healthy subjects and to determine if muscle size correlates with bone geometry and subject parameters of mass and height. It was found that total lower limb muscle volume scales with mass ( R2 =0.85) and with the height–mass product ( R2 =0.92). Furthermore, individual muscle volumes scale with total muscle volume (median R2 =0.66), with the height–mass product (median R2 =0.61), and with mass (median R2 =0.52). Muscle volume scales with bone volume ( R2 =0.75), and muscle length relative to bone length is conserved (median s.d.=2.1% of limb length). These relationships allow for an arbitrary subject's individual muscle volumes to be estimated from mass or mass and height while muscle lengths may be estimated from limb length. The dataset presented here can further be used as a normative standard to compare populations with musculoskeletal pathologies.
The giant sugarcane borer Telchin licus (Drury, 1773) (Lepidoptera: Castniidae) is a day-flying moth pest of sugarcane, pineapples and bananas. To better understand the chemical communication in this ...species, we examined the morphology of its olfactory system and the chemical composition of its body parts. The ventral surface of the clubbed antennae of T. licus has six morphological types of sensilla: sensilla trichodea, basiconica, chaetica, squamiforma, coeloconica, and auricillica. The telescopic ovipositor shows no evidence of a sexual gland, or female-specific compounds. On the other hand, the midleg basitarsus of males releases (E,Z)-2,13-octadecadienol and (Z,E)-2,13-octadecadienol, which are electroantennographically active in both sexes. These compounds are known female sex pheromones in the Sesiidae family and are male-specific compounds in another castniid moth, although further investigations are necessary to elucidate their ecological role in the Castniidae family.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical ...Andean regions in Peru (Pasco and Puno), and three alpaca farms within each region. The samples were genotyped using an Affymetrix Custom Alpaca genotyping array containing 76,508 SNPs. After the quality controls, 960 samples and 51,742 SNPs were retained. Three association study methodologies were performed. The GWAS based on a linear model allowed us to identify 11 and 35 SNPs (−log10(p-values) > 4) using information on all alpacas and alpacas with extreme values of fiber diameter, respectively. The haplotype and marker analysis method allowed us to identify nine haplotypes with standardized haplotype heritability higher than six standard deviations. The selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) allowed us to identify 180 SNPs with XP-EHH values greater than |3|. Four candidate regions with adjacent SNPs identified via two association methods of analysis are located on VPA6, VPA9, VPA29 and one chromosomally unassigned scaffold. This study represents the first analysis of alpaca whole genome association with fiber diameter, using a recently assembled alpaca SNP microarray.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
The alpaca (
) is an economically important and cultural signature species in Peru. Thus, molecular genomic information about the genes underlying the traits of interest, such as fiber properties and ...color, is critical for improved breeding and management schemes. Current knowledge about the alpaca genome, particularly the chromosomal location of such genes of interest is limited and lags far behind other livestock species. The main objective of this work was to localize alpaca candidate genes for fiber growth and color using fluorescence
hybridization (FISH). We report the mapping of candidate genes for fiber growth
,
,
,
,
, and
to chromosomes 16, 17, 4, 16, 1, and 16, respectively. Likewise, we report the mapping of candidate genes for fiber color
,
,
,
, and
to chromosomes 9, 19, 16, 1, and 14, respectively. In addition, since
clusters with five other keratin genes (
,
,
,
, and
) in scaffold 450 (Vic.Pac 2.0.2), the entire gene cluster was assigned to chromosome 16. Similarly, mapping
to chromosome 19, anchored scaffold 34 with 8 genes, viz.,
,
,
,
,
,
,
, and
to chromosome 19. These results are concordant with known conserved synteny blocks between camelids and humans, cattle and pigs.
Alpaca is a camelid species of broad economic, biological and biomedical interest, and an essential part of the cultural and historical heritage of Peru. Recently, efforts have been made to improve ...knowledge of the alpaca genome, and its genetics and cytogenetics, to develop molecular tools for selection and breeding. Here, we report cytogenetic mapping of 35 new markers to 19 alpaca autosomes and the X chromosome. Twenty-eight markers represent alpaca SNPs, of which 17 are located inside or near protein-coding genes, two are in ncRNA genes and nine are intergenic. The remaining seven markers correspond to candidate genes for fiber characteristics (
, coat color (
) and development (
). The results take the tally of cytogenetically mapped markers in alpaca to 281, covering all 36 autosomes and the sex chromosomes. The new map assignments overall agree with human-camelid conserved synteny data, except for mapping
to VPA3, suggesting a hitherto unknown homology with HSA14. The findings validate, refine and correct the current alpaca assembly
by anchoring unassigned sequence scaffolds, and ordering and orienting assigned scaffolds. The study contributes to the improvement in the alpaca reference genome and advances camelid molecular cytogenetics.
Spinal muscular atrophy is a rare, autosomal recessive, neuromuscular disease caused by biallelic loss of the survival motor neuron 1 (SMN1) gene, resulting in motor neuron dysfunction. In this ...STR1VE-EU study, we aimed to evaluate the safety and efficacy of onasemnogene abeparvovec gene replacement therapy in infants with spinal muscular atrophy type 1, using broader eligibility criteria than those used in STR1VE-US.
STR1VE-EU was a multicentre, single-arm, single-dose, open-label phase 3 trial done at nine sites (hospitals and universities) in Italy (n=4), the UK (n=2), Belgium (n=2), and France (n=1). We enrolled patients younger than 6 months (180 days) with spinal muscular atrophy type 1 and the common biallelic pathogenic SMN1 exon 7–8 deletion or point mutations, and one or two copies of SMN2. Patients received a one-time intravenous infusion of onasemnogene abeparvovec (1·1 × 1014 vector genomes vg/kg). The outpatient follow-up consisted of assessments once per week starting at day 7 post-infusion for 4 weeks and then once per month until the end of the study (at age 18 months or early termination). The primary outcome was independent sitting for at least 10 s, as defined by the WHO Multicentre Growth Reference Study, at any visit up to the 18 months of age study visit, measured in the intention-to-treat population. Efficacy was compared with the Pediatric Neuromuscular Clinical Research (PNCR) natural history cohort. This trial is registered with ClinicalTrials.gov, NCT03461289 (completed).
From Aug 16, 2018, to Sept 11, 2020, 41 patients with spinal muscular atrophy were assessed for eligibility. The median age at onasemnogene abeparvovec dosing was 4·1 months (IQR 3·0–5·2). 32 (97%) of 33 patients completed the study and were included in the ITT population (one patient was excluded despite completing the study because of dosing at 181 days). 14 (44%, 97·5% CI 26–100) of 32 patients achieved the primary endpoint of functional independent sitting for at least 10 s at any visit up to the 18 months of age study visit (vs 0 of 23 untreated patients in the PNCR cohort; p<0·0001). 31 (97%, 95% CI 91–100) of 32 patients in the ITT population survived free from permanent ventilatory support at 14 months compared with six (26%, 8–44) of 23 patients in the PNCR natural history cohort (p<0·0001). 32 (97%) of 33 patients had at least one adverse event and six (18%) had adverse events that were considered serious and related to onasemnogene abeparvovec. The most common adverse events were pyrexia (22 67% of 33), upper respiratory infection (11 33%), and increased alanine aminotransferase (nine 27%). One death, unrelated to the study drug, occurred from hypoxic-ischaemic brain damage because of a respiratory tract infection during the study.
STR1VE-EU showed efficacy of onasemnogene abeparvovec in infants with symptomatic spinal muscular atrophy type 1. No new safety signals were identified, but further studies are needed to show long-term safety. The benefit–risk profile of onasemnogene abeparvovec seems favourable for this patient population, including those with severe disease at baseline.
Novartis Gene Therapies.
Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of alpaca fiber contributes to the economy of the region and the livelihood of many rural ...families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies to fiber production characteristics. The aim of this study was to discover alpaca SNPs by genotyping forty alpaca DNA samples using the BovineHD Genotyping Beadchip. Data analysis was performed with GenomeStudio (Illumina) software. Because different filters and thresholds are reported in the literature we investigated the effects of no-call threshold (≥0.05, ≥0.15, and ≥0.25) and call frequency (≥0.9 and =1.0) in identifying positive SNPs. Average GC Scores, calculated as the average of the 10% and 50% GenCall scores for each SNP (≥0.70) and the GenTrain score ≥ 0.25 parameters were applied to all comparisons. SNPs with minor allele frequency (MAF) ≥ 0.05 or ≥ 0.01 were retained. Since detection of SNPs is based on the stable binding of oligonucleotide probes to the target DNA immediately adjacent to the variant nucleotide, all positive SNP flanking sequences showing perfect alignments between the bovine and alpaca genomes for the first 21 or 26 nucleotides flanking the variant nucleotide at either side were selected. Only SNPs localized in one scaffold were assumed unique. Unique SNPs identified in both reference genomes were kept and mapped on the Vicugna_pacos 2.0.2 genome. The effects of the no-call threshold ≥ 0.25, call frequency = 1 and average GC ≥ 0.7 were meaningful and identified 6756 SNPs of which 400 were unique and polymorphic (MAF ≥ 0.01). Assignment to alpaca chromosomes was possible for 292 SNPs. Likewise, 209 SNPs were localized in 202 alpaca gene loci and 29 of these share the same loci with the dromedary. Interestingly, 69 of 400 alpaca SNPs have 100% similarity with dromedary.
Leucoptera sinuella
is a leaf-miner moth present in several regions in the world, which has been recently introduced into Chile. The larvae feed exclusively on the leaves of poplar and willow trees, ...and the damage caused by the feeding behavior poses a threat to the wood-producing industry. Besides,
L. sinuella
larvae invade nearby orchards for pupation, causing rejections in Chilean fresh fruit for export. Here we report the identification of the female-produced sex pheromone of
L. sinuella
as a first step towards the development of pheromone-based methods for pest management of this species. First, we analyzed hexane extracts of the abdominal glands of virgin females by gas chromatography coupled with mass spectrometry and identified the major compound in these extracts to be 3,7-dimethylpentadecane, while minor compounds in the extracts proved to be 3,7-dimethyltetradecane and 7-methylpentadecane. Structure assignments were carried out by comparison of retention times and mass spectra of the natural products with those of authentic reference samples. Second, we conducted field tests, which showed that traps baited with synthetic 3,7-dimethylpentadecane were significantly attractive to males in a dose-dependent response. Our results also showed that a mixture of 3,7-dimethylpentadecane, 3,7-dimethyltetradecane, and 7-methylpentadecane in proportions similar to those found in gland extracts was the most attractive lure.
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