scholarly journals Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli

2019 ◽  
Vol 11 (8) ◽  
pp. 2071-2077 ◽  
Author(s):  
Wansheng Jiang ◽  
Yunyun Lv ◽  
Le Cheng ◽  
Kunfeng Yang ◽  
Chao Bian ◽  
...  
Keyword(s):  
Body Size ◽  
Ictalurus Punctatus ◽  
Genome Assembly ◽  
De Novo ◽  
Large Body ◽  
Single Copy ◽  
The Body ◽  
Flesh Color ◽  
Fish Muscles ◽  
Freshwater Aquaculture

AbstractAs one economically important fish in the southeastern Himalayas, the giant devil catfish (Bagarius yarrelli) has been known for its extraordinarily large body size. It can grow up to 2 m, whereas the non-Bagarius sisorids only reach 10–30 cm. Another outstanding characteristic of Bagarius species is the salmonids-like reddish flesh color. Both body size and flesh color are interesting questions in science and also valuable features in aquaculture that worth of deep investigations. Bagarius species therefore are ideal materials for studying body size evolution and color depositions in fish muscles, and also potential organisms for extensive utilization in Asian freshwater aquaculture. In a combination of Illumina and PacBio sequencing technologies, we de novo assembled a 571-Mb genome for the giant devil catfish from a total of 153.4-Gb clean reads. The scaffold and contig N50 values are 3.1 and 1.6 Mb, respectively. This genome assembly was evaluated with 93.4% of Benchmarking Universal Single-Copy Orthologs completeness, 98% of transcripts coverage, and highly homologous with a chromosome-level-based genome of channel catfish (Ictalurus punctatus). We detected that 35.26% of the genome assembly is composed of repetitive elements. Employing homology, de novo, and transcriptome-based annotations, we annotated a total of 19,027 protein-coding genes for further use. In summary, we generated the first high-quality genome assembly of the giant devil catfish, which provides an important genomic resource for its future studies such as the body size and flesh color issues, and also for facilitating the conservation and utilization of this valuable catfish.

scholarly journals New records of ring nematodes, Bakernema enormese n. sp. and Criconema (Nothocriconemella) graminicola Loof, Wouts & Yeates, 1997 (Nematoda: Criconematidae) from natural forests of Vietnam

2019 ◽  
Vol 41 (3) ◽  
Author(s):  
Nguyen Ngoc Chau
Keyword(s):  
New Species ◽  
Body Size ◽  
New Records ◽  
Large Body ◽  
Lateral View ◽  
The Body ◽  
Natural Forests ◽  
Large Body Size ◽  
Stylet Length ◽  
North Vietnam

Bakernema enormese sp. n., collected from rhizosphere of forest wood trees in Muong Phang, Dien Bien Province (north Vietnam) is described and illustrated. The new species is characterized by large body size and stylet. In general, this new species is close to two existing species of the same genus, B. inaequale and B. dauniense by cuticle structure in transparent membranous projections which appear in lateral view as spine-like structures on each annulus. These structure arranged into several rows along the body. In morphology, the new species differs from B. inaequale and B. dauniense  by body and stylet length, i.e. 609–842 µm and 143.5–150 µm vs. 391–578 µm and 59–74 µm for B. inaequale and vs. 391–461 µm and 65–74 µm for B. dauniense. In addition, new species can be distinguished from B. inaequale by the longer membranous projection, 8–12 vs. 6–10 µm and vagina shape, curved vs. sigmoid. From B. dauniense, the new species differs by the much longer membranous projection, 8–12 vs. 1.4–2.2 µm and less number annules between vulva and tail end (RV), 3–4 vs. 7.8 annules. The presence of Criconema (Nothocriconemella) graminicola Loof, Wouts & Yeates, in Vietnam with morphometrics, illustrators and remarks given.

Body size and the risk of multiple sclerosis in Norway and Italy: The EnvIMS study

2014 ◽  
Vol 21 (4) ◽  
pp. 388-395 ◽  
Author(s):  
Kristin Wesnes ◽  
Trond Riise ◽  
Ilaria Casetta ◽  
Jelena Drulovic ◽  
Enrico Granieri ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Risk Factor ◽  
Body Size ◽  
Case Control Study ◽  
Disease Onset ◽  
Large Body ◽  
Population Based ◽  
The Body ◽  
Outdoor Activity ◽  
Control Study

Background: Obesity may be a risk factor for developing multiple sclerosis (MS). Objective: We examined if body size influences the risk of MS in a population-based, case control study. Methods: A total of 953 cases and 1717 controls from Norway and 707 cases and 1333 controls from Italy reported their body size by choosing a silhouette 1 to 9 (largest) every fifth year from age 5 to 30 and at time of study. The body size-related MS risk was defined by odds ratios (ORs) in logistic regression analyses adjusting for age, smoking and outdoor activity. Results: In Norway a large body size (silhouettes 6–9) compared to silhouette 3 increased the risk of MS, especially at age 25 (OR 2.21; 95% CI 1.09–4.46 for men and OR 1.43; 95% CI 0.90–2.27 for women). When comparing silhouette 9 to 1, we found a significant dose-response from age 10 until age 30 peaking at age 25 (sex-adjusted OR 2.83; 95% CI 1.68–4.78). The association was present for at least 15 years prior to disease onset. No significant associations were found in Italy. Conclusions: Obesity from childhood until young adulthood is a likely risk factor for MS with a seemingly stronger effect in Norway than in Italy.

scholarly journals De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris)

2019 ◽  
Vol 10 (2) ◽  
pp. 475-478 ◽  
Author(s):  
Nicholas A. Mason ◽  
Paulo Pulgarin ◽  
Carlos Daniel Cadena ◽  
Irby J. Lovette
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Single Copy ◽  
Single Copy Gene ◽  
High Quality ◽  
Data Set ◽  
Copy Gene ◽  
Assembly Pipeline ◽  
Horned Lark ◽  
Gene Orthologs

The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for the Horned Lark and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for E. alpestris generated from a blood sample of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2713 scaffolds, with a largest scaffold size of 31.81 Mb, a scaffold N50 of 9.42 Mb, and a scaffold L50 of 30. These scaffolds were assembled from 23685 contigs, with a largest contig size of 1.69 Mb, a contig N50 of 193.81 kb, and a contig L50 of 1429. Our assembly pipeline also produced a single mitochondrial DNA contig of 14.00 kb. After polishing the genome, we identified 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, which further demonstrates the high quality of our assembly. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of larks, which comprise a widespread, yet understudied lineage of songbirds.

scholarly journals De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 69 ◽  
Author(s):  
Nagesh Kancharla ◽  
Saakshi Jalali ◽  
J. Narasimham ◽  
Vinod Nair ◽  
Vijay Yepuri ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genome Assembly ◽  
Jatropha Curcas ◽  
Quantitative Trait ◽  
De Novo ◽  
Mapping Population ◽  
Single Copy ◽  
Sequencing Data ◽  
De Novo Genome Assembly ◽  
Sequencing Technologies

Jatropha curcas is an important perennial, drought tolerant plant that has been identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of J. curcas generated using Illumina and PacBio sequencing technologies, and identification of quantitative loci for Jatropha Mosaic Virus (JMV) resistance. In this study, we generated scaffolds of 265.7 Mbp in length, which correspond to 84.8% of the gene space, using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Additionally, 96.4% of predicted protein-coding genes were captured in RNA sequencing data, which reconfirms the accuracy of the assembled genome. The genome was utilized to identify 12,103 dinucleotide simple sequence repeat (SSR) markers, which were exploited in genetic diversity analysis to identify genetically distinct lines. A total of 207 polymorphic SSR markers were employed to construct a genetic linkage map for JMV resistance, using an interspecific F2 mapping population involving susceptible J. curcas and resistant Jatropha integerrima as parents. Quantitative trait locus (QTL) analysis led to the identification of three minor QTLs for JMV resistance, and the same has been validated in an alternate F2 mapping population. These validated QTLs were utilized in marker-assisted breeding for JMV resistance. Comparative genomics of oil-producing genes across selected oil producing species revealed 27 conserved genes and 2986 orthologous protein clusters in Jatropha. This reference genome assembly gives an insight into the understanding of the complex genetic structure of Jatropha, and serves as source for the development of agronomically improved virus-resistant and oil-producing lines.

scholarly journals Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yaoxi He ◽  
Xin Luo ◽  
Bin Zhou ◽  
Ting Hu ◽  
Xiaoyu Meng ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Genome Assembly ◽  
De Novo ◽  
Gene Annotation ◽  
Large Body ◽  
Phenotypic Traits ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Chinese Rhesus Macaque ◽  
Long Read

Abstract We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), rheMacS increases sequence contiguity 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). We improve gene annotation by generating more than two million full-length transcripts from ten different tissues by long-read RNA sequencing. We sequence resolve 53,916 structural variants (96% novel) and identify 17,000 ape-specific structural variants (ASSVs) based on comparison to ape genomes. Many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a subset that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. The rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies.

scholarly journals Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome

GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Yan Li ◽  
Guangliang Gao ◽  
Yu Lin ◽  
Silu Hu ◽  
Yi Luo ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Spatial Organization ◽  
De Novo ◽  
Single Copy ◽  
Interaction Patterns ◽  
Anser Anser ◽  
Pacific Biosciences ◽  
Eukaryotic Genes ◽  
Chromosome Level

ABSTRACT Background The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing. Findings We generated a 1.11-Gb goose genome with contig and scaffold N50 values of 1.85 and 33.12 Mb, respectively. The assembly contains 39 pseudo-chromosomes (2n = 78) accounting for ∼88.36% of the goose genome. Compared with previous goose assemblies, our assembly has more continuity, completeness, and accuracy; the annotation of core eukaryotic genes and universal single-copy orthologs has also been improved. We have identified 17,568 protein-coding genes and a repeat content of 8.67% (96.57 Mb) in this genome assembly. We also explored the spatial organization of chromatin and gene expression in the goose liver tissues, in terms of inter-pseudo-chromosomal interaction patterns, compartments, topologically associating domains, and promoter-enhancer interactions. Conclusions We present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese.

scholarly journals Selection on morphological traits and fluctuating asymmetry by a fungal parasite in the yellow dung fly

2017 ◽  
Author(s):  
Wolf U. Blanckenhorn
Keyword(s):  
Body Size ◽  
Fungal Infection ◽  
Fluctuating Asymmetry ◽  
Large Body ◽  
The Body ◽  
Female Size ◽  
Adult Body Size ◽  
Scathophaga Stercoraria ◽  
Evolutionary Response ◽  
Adult Body

AbstractA Preprint reviewed and recommended by Peer Community Evolutionary Biology: http://dx.doi.org/10.24072/pci.evolbiol.100027Evidence for selective disadvantages of large body size remains scarce in general. Previous phenomenological studies of the yellow dung fly Scathophaga stercoraria have demonstrated strong positive sexual and fecundity selection on male and female size. Nevertheless, the body size of flies from a Swiss study population has declined by almost 10% from 1993 to 2009. Given substantial heritability of body size, this negative evolutionary response of an evidently positively selected trait suggests important selective factors being missed (e.g. size-selective predation or parasitism). A periodic epidemic outbreak of the fungus Entomophthora scatophagae allowedassessment of selection exerted by this parasite fatal to adult flies. Fungal infection varied over the season from ca. 50% in the cooler and more humid spring and autumn to almost 0% in summer. The probability of dying from fungal infection increased with adult body size. All infected females died before laying eggs, so there was no fungus impact on female fecundity beyond its impact on mortality. Large males showed the typical mating advantage in the field, but this pattern of positive sexual selection was nullified by fungal infection. Mean fluctuating asymmetry of paired appendages (legs, wings) did not affect the viability, fecundity or mating success of yellow dung flies in the field. This study demonstrates rare parasite-mediated disadvantages of large adult body size in the field. Reduced ability to combat parasites such as Entomophthora may be an immunity cost of large size in dung flies, although the hypothesized trade-off between fluctuating asymmetry, a presumed indicator of developmental instability and environmental stress, and immunocompetence was not found here.

scholarly journals Genome Report: De novo assembly of a high-quality reference genome for the Horned Lark (Eremophila alpestris)

2019 ◽  
Author(s):  
Nicholas A. Mason ◽  
Paulo Pulgarin ◽  
Carlos Daniel Cadena ◽  
Irby J. Lovette
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Single Copy ◽  
Single Copy Gene ◽  
Data Set ◽  
Copy Gene ◽  
Assembly Pipeline ◽  
Horned Lark ◽  
Genomic Resource ◽  
Gene Orthologs

AbstractThe Horned Lark (Eremophila alpestris) is a species of small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris and related species have been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for horned larks and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for horned larks generated from blood samples of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2708 contigs with an N50 of 10.58 Mb and a L50 of 29. After polishing the genome, we were able to identify 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, indicating that our de novo assembly is near complete. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of a widespread, yet understudied lineage of songbirds.

The effects of temperature change and domestication on the body size of Late Pleistocene to Holocene mammals of Israel

Paleobiology ◽  
1981 ◽  
Vol 7 (1) ◽  
pp. 101-114 ◽  
Author(s):  
Simon J. M. Davis
Keyword(s):  
Body Size ◽  
Temperature Change ◽  
Late Pleistocene ◽  
Eastern Mediterranean ◽  
Large Body ◽  
Size Variation ◽  
The Body ◽  
Main Body ◽  
Fossil Species ◽  
Late Pleistocene To Holocene

Size variation among several species of large mammals is examined both throughout a wide geographical range today and within the Late Pleistocene-Holocene archaeo-faunal sequence of Israel. A regression of log dental size on environmental temperature produces similar negative slopes for recent Palaearctic foxes, wolves and boars as well as for Nearctic foxes. These species, and others which also exhibit an inverse correlation between size and temperature today, became dwarfed at the end of the Pleistocene in Israel. Abundant fossil gazelle and fox mensural data indicate that this diminution coincided with the temperature elevation 12,000 yr ago. Both the similarity of regression slopes for the recent material and the temporal coincidence of dwarfing among fossil species, representing different ecologies, strongly implicate temperature as the main body-size determining factor. Changes evidenced in the fossil record for boar, wolf and fox approximate a 15°C temperature change (Δt) based on their respective present-day size-temperature regressions. This Δt, if taken as an estimate for the eastern Mediterranean, is considerably higher than generally accepted values.An additional size reduction of aurochs, wolf and boar at the end of the Pleistocene or several millenia later is associated with their domestication. It may reflect man's preference for a large “head count” over individual large body size.

Analysis about the Effect on the Design of the Diffusers

2012 ◽  
Vol 174-177 ◽  
pp. 2016-2019
Author(s):  
Hui Yu Chen ◽  
Jing Gong
Keyword(s):  
Body Size ◽  
Absorption Coefficient ◽  
High Frequency ◽  
Large Body ◽  
Low Frequency ◽  
Groove Depth ◽  
The Body ◽  
Frequency Sound ◽  
High Absorption Coefficient ◽  
High Absorption

In order to study the effect of the diffusers,there has been designed a variety of diffusers.If groove depth is large , the diffuser will become a high absorption coefficient, low-frequency sounds will reduce significantly. So we have spread the body size nested within each other, a small has been nested in a large body .The smaller parts expand of high-frequency sound, the larger parts for low-frequency sound, so over a wide frequency band can been spreading.

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