scholarly journals It’s okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana)

2017 ◽  
Author(s):  
S. Austin Hammond ◽  
René L. Warren ◽  
Benjamin P. Vandervalk ◽  
Erdi Kucuk ◽  
Hamza Khan ◽  
...  
Keyword(s):  
North American ◽  
Draft Genome ◽  
Food Sources ◽  
Model Organisms ◽  
Population Declines ◽  
American Bullfrog ◽  
The North ◽  
Long Reads ◽  
Frog Species ◽  
Lithobates Catesbeiana

AbstractFrogs play important ecological roles as sentinels, insect control and food sources. Several species are important model organisms for scientific research to study embryogenesis, development, immune function, and endocrine signaling. The globally-distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Consequently, the extensive Xenopus genomic resources are of limited utility for Ranids and related frog species. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines.Herein, we report on the first genome sequence of a Ranid species, an adult male North American bullfrog (Rana [Lithobates] catesbeiana). We assembled high-depth Illumina reads (66-fold coverage), into a 5.8 Gbp (NG50 = 57.7 kbp) draft genome using ABySS v1.9.0. The assembly was scaffolded with LINKS and RAILS using pseudo-long-reads from targeted denovo assembler Kollector and Illumina Synthetic Long-Reads, as well as reads from long fragment (MPET) libraries. We predicted over 22,000 protein-coding genes using the MAKER2 pipeline and identified the genomic loci of 6,227 candidate long noncoding RNAs (IncRNAs) from a composite reference bullfrog transcriptome. Mitochondrial sequence analysis supported Lithobates as a subgenus of Rana. RNA-Seq experiments identified ~6,000 thyroid hormone– responsive transcripts in the back skin of premetamorphic tadpoles; the majority of which regulate DNA/RNA processing. Moreover, 1/6th of differentially-expressed transcripts were putative lncRNAs. Our draft bullfrog genome will serve as a useful resource for the amphibian research community.

scholarly journals The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
S. Austin Hammond ◽  
René L. Warren ◽  
Benjamin P. Vandervalk ◽  
Erdi Kucuk ◽  
Hamza Khan ◽  
...  
Keyword(s):  
North American ◽  
Long Noncoding Rna ◽  
Hormonal Regulation ◽  
Noncoding Rna ◽  
Draft Genome ◽  
American Bullfrog ◽  
The North ◽  
Insight Into

scholarly journals Reproductive phenology of the American Bullfrog in subtropical Brazil: photoperiod as a main determinant of seasonal activity

2016 ◽  
Vol 88 (3 suppl) ◽  
pp. 1909-1921 ◽  
Author(s):  
CAMILA I. MEDEIROS ◽  
CAMILA BOTH ◽  
IGOR L. KAEFER ◽  
SONIA Z. CECHIN
Keyword(s):  
Life Histories ◽  
Management Strategies ◽  
Reproductive Activity ◽  
Ex Situ ◽  
Reproductive Phenology ◽  
High Fertility ◽  
Seasonal Activity ◽  
Population Declines ◽  
American Bullfrog ◽  
The North

ABSTRACT The North American bullfrog Lithobates catesbeianus continues to invade ecosystems worldwide, potentially causing population declines and even extinctions. Within its native distribution, bullfrogs show prolonged reproductive seasons and high fertility. However, data on breeding biology of bullfrogs ex-situ in invaded localities mainly comes from anecdotal reports. Understanding how invasive species are adjusting their life histories to new colonized environments is important for conservation purposes. Here we describe temporal and spatial abundance, calling activity, spawning and tadpole distribution of bullfrogs in southern Brazil. Eighteen samplings occurred during one year. The abundance of individuals was positively related to longer photoperiods and higher temperatures. Reproductive activity was also positively associated with longer photoperiods. Calling sites, spawning and tadpoles were associated with microhabitats presenting hydrophytes, which may provide shelter and thermal stability to bullfrogs. The reproductive seasonal activity of bullfrogs can be highly variable across its growing geographical range, but in subtropical Brazil it is associated with photoperiod, a highly predictable abiotic determinant. In our study area, bullfrogs presented a breeding season twice as long as that observed in some native localities. We suggest that management strategies directed to bullfrog populations must consider the habitat structures and seasonal regimes determined by each invaded environment.

Olfactory epithelium ontogenesis and function in postembryonic North American Bullfrog (Rana (Lithobates) catesbeiana) tadpoles

2020 ◽  
Vol 98 (6) ◽  
pp. 367-375 ◽  
Author(s):  
J.L. Heerema ◽  
S.J. Bogart ◽  
C.C. Helbing ◽  
G.G. Pyle
Keyword(s):  
Olfactory Epithelium ◽  
North American ◽  
Olfactory System ◽  
Postembryonic Development ◽  
Acid Mixture ◽  
Epithelial Surface ◽  
American Bullfrog ◽  
Olfactory Stimuli ◽  
And Function ◽  
Lithobates Catesbeiana

During metamorphosis, the olfactory system remodelling in anuran tadpoles — to transition from detecting waterborne odorants to volatile odorants as frogs — is extensive. How the olfactory system transitions from the larval to frog form is poorly understood, particularly in species that become (semi-)terrestrial. We investigated the ontogeny and function of the olfactory epithelium of North American Bullfrog (Rana (Lithobates) catesbeiana Shaw, 1802) tadpoles at various stages of postembryonic development. Changes in sensory components observable at the epithelial surface were examined by scanning electron microscopy. Functionality of the developing epithelium was tested using a neurophysiological technique (electro-olfactography (EOG)), and behaviourally, using a choice maze to assess tadpole response to olfactory stimuli (algae extract, amino acids). The youngest (premetamorphic) tadpoles responded behaviourally to an amino acid mixture despite having underdeveloped olfactory structures (cilia, olfactory knobs) and no EOG response. The consistent appearance of olfactory structures in older (prometamorphic) tadpoles coincided with reliably obtaining EOG responses to olfactory stimuli. However, as tadpoles aged further, and despite indistinguishable differences in sensory components, behavioural- and EOG-based olfactory responses were drastically reduced, most strongly near metamorphic climax. This work demonstrates a more complex relationship between structure and function of the olfactory system during tadpole life history than originally thought.

scholarly journals LongStitch: High-quality genome assembly correction and scaffolding using long reads

2021 ◽  
Author(s):  
Lauren Coombe ◽  
Janet X Li ◽  
Theodora Lo ◽  
Johnathan Wong ◽  
Vladimir Nikolic ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Model Organisms ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Long Reads ◽  
Long Read ◽  
Genomic Regions ◽  
Genome Assemblies

Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 2.0-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently runs in under five hours using less than 23GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.

scholarly journals The North American bullfrog as a reservoir for the spread of Batrachochytrium dendrobatidis in Brazil

2010 ◽  
Vol 13 ◽  
pp. 53-61 ◽  
Author(s):  
L. M. Schloegel ◽  
C. M. Ferreira ◽  
T. Y. James ◽  
M. Hipolito ◽  
J. E. Longcore ◽  
...  
Keyword(s):  
North American ◽  
Batrachochytrium Dendrobatidis ◽  
American Bullfrog ◽  
The North

Effects of Intramuscular Meloxicam Administration on Prostaglandin E2 Synthesis in the North American Bullfrog (Rana catesbeiana)

2011 ◽  
Vol 42 (4) ◽  
pp. 680-685 ◽  
Author(s):  
Larry J. Minter ◽  
Elsburgh O. Clarke ◽  
Jenessa L. Gjeltema ◽  
Kate E. Archibald ◽  
Lysa P. Posner ◽  
...  
Keyword(s):  
Prostaglandin E2 ◽  
North American ◽  
Rana Catesbeiana ◽  
American Bullfrog ◽  
The North

scholarly journals LongStitch: high-quality genome assembly correction and scaffolding using long reads

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lauren Coombe ◽  
Janet X. Li ◽  
Theodora Lo ◽  
Johnathan Wong ◽  
Vladimir Nikolic ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Model Organisms ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Long Reads ◽  
Long Read ◽  
Genomic Regions ◽  
Genome Assemblies

Abstract Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.

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