scholarly journals Genome Report: A highly contiguous reference genome for Northern Bobwhite (Colinus virginianus)

2019 ◽  
Author(s):  
Jessie F. Salter ◽  
Oscar Johnson ◽  
Norman J. Stafford ◽  
William F. Herrin ◽  
Darren Schilling ◽  
...  
Keyword(s):  
Reference Genome ◽  
Colinus Virginianus ◽  
Phenotypic Diversity ◽  
Northern Bobwhite ◽  
Wild Female ◽  
Tissue Samples ◽  
Future Studies ◽  
Northern Bobwhites ◽  
Assembly Pipeline ◽  
Genomic Studies

ABSTRACTNorthern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. Using Dovetail Chicago and HiC libraries with the HiRise assembly pipeline, we produced an 866.8 Mbp assembly including 1,512 scaffolds with a contig N50 of 66.8 Mbp, a scaffold L50 of four, and a BUSCO completeness score of 90.8%. This new assembly greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome and provides an important tool for future studies of evolutionary and functional genomics in bobwhites.

scholarly journals A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus)

2019 ◽  
Vol 9 (12) ◽  
pp. 3929-3932 ◽  
Author(s):  
Jessie F. Salter ◽  
Oscar Johnson ◽  
Norman J. Stafford ◽  
William F. Herrin ◽  
Darren Schilling ◽  
...  
Keyword(s):  
Reference Genome ◽  
Colinus Virginianus ◽  
Northern Bobwhite

scholarly journals Predation on Artificial Nests of Northern Bobwhites, Colinus virginianus, by Mammalian Mesopredators: Does the Problem-Individual Paradigm Fit?

2006 ◽  
Vol 120 (4) ◽  
pp. 452 ◽  
Author(s):  
J. B. Jennings ◽  
M. L. Kennedy ◽  
A. E. Houston ◽  
B. D. Carver
Keyword(s):  
Prey Species ◽  
Colinus Virginianus ◽  
Management Strategies ◽  
Sampling Period ◽  
Northern Bobwhite ◽  
Didelphis Virginiana ◽  
Artificial Nests ◽  
Northern Bobwhites ◽  
Number Of Individuals ◽  
Striped Skunks

Using mark/recapture procedures, predation on artificial nests of Northern Bobwhites (Colinus virginianus) by mammalian mesopredators (Raccoons, Procyon lotor; Virginia Opossums, Didelphis virginiana; and Striped Skunks, Mephitis mephitis) was assessed in relation to the “problem-individual” paradigm. The paradigm, which is untested among mammalian mesopredators, predicts that most predation on a prey species is by a small number of individuals repeatedly involved. By examining number of captures and recaptures on artificial nests during non-nesting and nesting periods in 2000-2003, predation within and among species were gauged. Results varied by species, sampling period, and year; however, predation was by a small percentage of individuals and only within the population of Striped Skunks were individuals (2 of 49) captured on an artificial nest more than once. Raccoons, Virginia Opossums, and Striped Skunks were responsible for 10, 2, and 12% of the loss of all nests available to predators, respectively. Based on low occurrences of individuals repeatedly involved in predation on nests, the problem-individual paradigm was unsubstantiated. Although Raccoons, Virginia Opossums, and Striped Skunks (as individual predators) had only moderate impact on the population of Northern Bobwhites, they had a much greater impact collectively (preying upon 24% of all nests available). To maximize Northern Bobwhite success, the most productive management is probably best directed toward a vertebrate guild that includes mammalian, avian, and reptilian predators, and management strategies that use multiple techniques.

Antibiotic susceptibility of Edwardsiella hoshinae isolated from northern bobwhite quail (Colinus virginianus)

2004 ◽  
Vol 155 (1) ◽  
pp. 29-29 ◽  
Author(s):  
I. M. Singh ◽  
S. Singh ◽  
M. A. McMurphy ◽  
S. S. Crupper ◽  
F. Mills-Robertson ◽  
...  
Keyword(s):  
Antibiotic Susceptibility ◽  
Colinus Virginianus ◽  
Northern Bobwhite ◽  
Bobwhite Quail

scholarly journals Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 904
Author(s):  
Saif ur Rehman ◽  
Faiz-ul Hassan ◽  
Xier Luo ◽  
Zhipeng Li ◽  
Qingyou Liu
Keyword(s):  
Selective Breeding ◽  
Reference Genome ◽  
De Novo ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Genomic Diversity ◽  
Production Performance ◽  
Phylogeographic Structure ◽  
Economic Significance ◽  
And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

scholarly journals Evidence for the Use of Mucus Swabs to Detect Renibacterium salmoninarum in Brook Trout

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 460
Author(s):  
Tawni B. Riepe ◽  
Victoria Vincent ◽  
Vicki Milano ◽  
Eric R. Fetherman ◽  
Dana L. Winkelman
Keyword(s):  
Brook Trout ◽  
Sampling Methods ◽  
Kidney Tissue ◽  
Detection Methods ◽  
Fish Health ◽  
Wild Populations ◽  
Renibacterium Salmoninarum ◽  
Tissue Samples ◽  
Future Studies ◽  
Aquaculture Facilities

Efforts to advance fish health diagnostics have been highlighted in many studies to improve the detection of pathogens in aquaculture facilities and wild fish populations. Typically, the detection of a pathogen has required sacrificing fish; however, many hatcheries have valuable and sometimes irreplaceable broodstocks, and lethal sampling is undesirable. Therefore, the development of non-lethal detection methods is a high priority. The goal of our study was to compare non-lethal sampling methods with standardized lethal kidney tissue sampling that is used to detect Renibacterium salmoninarum infections in salmonids. We collected anal, buccal, and mucus swabs (non-lethal qPCR) and kidney tissue samples (lethal DFAT) from 72 adult brook trout (Salvelinus fontinalis) reared at the Colorado Parks and Wildlife Pitkin Brood Unit and tested each sample to assess R. salmoninarum infections. Standard kidney tissue detected R. salmoninarum 1.59 times more often than mucus swabs, compared to 10.43 and 13.16 times more often than buccal or anal swabs, respectively, indicating mucus swabs were the most effective and may be a useful non-lethal method. Our study highlights the potential of non-lethal mucus swabs to sample for R. salmoninarum and suggests future studies are needed to refine this technique for use in aquaculture facilities and wild populations of inland salmonids.

scholarly journals Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2631 ◽  
Author(s):  
Jinhui Shen ◽  
Qian Cong ◽  
Lisa N. Kinch ◽  
Dominika Borek ◽  
Zbyszek Otwinowski ◽  
...  
Keyword(s):  
Complete Genome ◽  
Evolutionary History ◽  
Reference Genome ◽  
Pieris Rapae ◽  
Defense Mechanism ◽  
Butterfly Species ◽  
Computational Simulations ◽  
Median Length ◽  
Future Studies ◽  
Anti Cancer

The Small Cabbage White (Pieris rapae) is originally a Eurasian butterfly. Being accidentally introduced into North America, Australia, and New Zealand a century or more ago, it spread throughout the continents and rapidly established as one of the most abundant butterfly species. Although it is a serious pest of cabbage and other mustard family plants with its caterpillars reducing crops to stems, it is also a source of pierisin, a protein unique to the Whites that shows cytotoxicity to cancer cells. To better understand the unusual biology of this omnipresent agriculturally and medically important butterfly, we sequenced and annotated the complete genome from USA specimens. At 246 Mbp, it is among the smallest Lepidoptera genomes reported to date. While 1.5% positions in the genome are heterozygous, they are distributed highly non-randomly along the scaffolds, and nearly 20% of longer than 1000 base-pair segments are SNP-free (median length: 38000 bp). Computational simulations of population evolutionary history suggest that American populations started from a very small number of introduced individuals, possibly a single fertilized female, which is in agreement with historical literature. Comparison to other Lepidoptera genomes reveals several unique families of proteins that may contribute to the unusual resilience of Pieris. The nitrile-specifier proteins divert the plant defense chemicals to non-toxic products. The apoptosis-inducing pierisins could offer a defense mechanism against parasitic wasps. While only two pierisins from Pieris rapae were characterized before, the genome sequence revealed eight, offering additional candidates as anti-cancer drugs. The reference genome we obtained lays the foundation for future studies of the Cabbage White and other Pieridae species.

scholarly journals Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4662 ◽  
Author(s):  
Iris Holmes ◽  
Alison R. Davis Rabosky
Keyword(s):  
Restriction Site ◽  
Tissue Sample ◽  
Host Tissue ◽  
Blood Parasites ◽  
Tissue Banks ◽  
Target Tissue ◽  
Tissue Samples ◽  
Reduced Representation ◽  
Assembly Pipeline ◽  
Hind Gut

Background Reduced representation genomic datasets are increasingly becoming available from a variety of organisms. These datasets do not target specific genes, and so may contain sequences from parasites and other organisms present in the target tissue sample. In this paper, we demonstrate that (1) RADseq datasets can be used for exploratory analysis of tissue-specific metagenomes, and (2) tissue collections house complete metagenomic communities, which can be investigated and quantified by a variety of techniques. Methods We present an exploratory method for mining metagenomic “bycatch” sequences from a range of host tissue types. We use a combination of the pyRAD assembly pipeline, NCBI’s blastn software, and custom R scripts to isolate metagenomic sequences from RADseq type datasets. Results When we focus on sequences that align with existing references in NCBI’s GenBank, we find that between three and five percent of identifiable double-digest restriction site associated DNA (ddRAD) sequences from host tissue samples are from phyla to contain known blood parasites. In addition to tissue samples, we examine ddRAD sequences from metagenomic DNA extracted snake and lizard hind-gut samples. We find that the sequences recovered from these samples match with expected bacterial and eukaryotic gut microbiome phyla. Discussion Our results suggest that (1) museum tissue banks originally collected for host DNA archiving are also preserving valuable parasite and microbiome communities, (2) that publicly available RADseq datasets may include metagenomic sequences that could be explored, and (3) that restriction site approaches are a useful exploratory technique to identify microbiome lineages that could be missed by primer-based approaches.

scholarly journals Unexpected cryptic species among streptophyte algae most distant to land plants

2021 ◽  
Vol 288 (1963) ◽  
Author(s):  
Iker Irisarri ◽  
Tatyana Darienko ◽  
Thomas Pröschold ◽  
Janine M. R. Fürst-Jansen ◽  
Mahwash Jamy ◽  
...  
Keyword(s):  
Land Plants ◽  
Comparative Genomic ◽  
Future Studies ◽  
Form And Function ◽  
Genomic Studies ◽  
Plant Form ◽  
Phylogenomic Analyses ◽  
And Function ◽  
Shed Light ◽  
Green Lineage

Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one billion years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp. and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes.

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