SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

Wyffels, Jennifer T.; King, Benjamin L.; Vincent, James J.; Chen, Chuming; Wu, Cathy H.; Polson, Shawn W.

doi:10.12688/f1000research.4996.1

Cited by 69 publications

(64 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Overall 159 thornback rays were sampled in the Bay of Biscay be- We aligned ca 54.6M paired-end Miseq reads to the little skate (Leucoraja erinacea) genome assembly (Wang et al, 2012;Wyffels et al, 2014) using BWA-SW (version 0.7.12-r1039, default parameters) to build up thornback ray consensus sequences from high quality mapped reads (mapQ score = 60). The result was used as a reference for further analyses.…”

Section: Samplingmentioning

confidence: 99%

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Marandel

Charrier

Lamy

et al. 2020

Ecology and Evolution

View full text Add to dashboard Cite

Effective population size (Ne) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.

show abstract

Section: Samplingmentioning

confidence: 99%

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Marandel

Charrier

Lamy

et al. 2020

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…Even though jawed vertebrates consist of only two major groups, cartilaginous fishes and bony vertebrates, there have not been enough studies focusing on the former. One of the advantages of the bamboo shark is that its genome assembly, which will be released by our laboratory, has better continuity and coverage than that of other elasmobranchs, such as the whale shark and the little skate (Read et al, ; Wyffels et al, ; S. Kuraku, unpubl. data, 2017).…”

Section: Perspectivementioning

confidence: 99%

A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum)

Onimaru¹,

Motone²,

Kiyatake

et al. 2018

Developmental Dynamics

View full text Add to dashboard Cite

Background: Studying cartilaginous fishes (chondrichthyans) has helped us understand vertebrate evolution and diversity. However, resources such as genome sequences, embryos, and detailed staging tables are limited for species within this clade. To overcome these limitations, we have focused on a species, the brownbanded bamboo shark (Chiloscyllium punctatum), which is a relatively common aquarium species that lays eggs continuously throughout the year. In addition, because of its relatively small genome size, this species is promising for molecular studies. Results: To enhance biological studies of cartilaginous fishes, we establish a normal staging table for the embryonic development of the brownbanded bamboo shark. Bamboo shark embryos take around 118 days to reach the hatching period at 25°C, which is approximately 1.5 times as fast as the small‐spotted catshark (Scyliorhinus canicula) takes. Our staging table divides the embryonic period into 38 stages. Furthermore, we found culture conditions that allow early embryos to grow in partially opened egg cases. Conclusions: In addition to the embryonic staging table, we show that bamboo shark embryos exhibit relatively fast embryonic growth and are amenable to culture, key characteristics that enhance their experimental utility. Therefore, the present study is a foundation for cartilaginous fish research. Developmental Dynamics 247:712–723, 2018. © 2017 Wiley Periodicals, Inc.

show abstract

“…To determine skate Pax6, Cbln1 and Grid2 sequences, human PAX6, CBLN1 and GRID2 amino acid sequences were blasted against the skate transcriptomebuild2.0 or skate genomicbuild2.0 using Skate-BLAST (http://skatebase.org/skateBLAST, RRID:SCR_005302; Wang et al, 2004Wang et al, , 2012Waterhouse et al, 2009;Wyffels et al, 2014). Contigs containing regions of high homology were taken from the contig lookup, translated using EMBL-EBI EMBOSS Transeq and aligned with the human amino acid sequence using EMBL-EBI Clustal OMEGA (RRID:SCR_001591; Goujon et al, 2010;Rice et al, 2000;Sievers et al, 2011).…”

Section: Sequence Analysismentioning

confidence: 99%

Evidence for generative homology of cerebellum and cerebellum‐like structures in an elasmobranch fish based on Pax6, Cbln1 and Grid2 expression

Suriano

Bodznick

2018

J of Comparative Neurology

View full text Add to dashboard Cite

The majority of neurons in the mammalian brain reside within the cerebellum (Cb). Yet, the evolutionary origins of the Cb are not well understood. There are several sensory nuclei present across vertebrate phylogeny collectively termed cerebellum-like structures (CbLS) due to a shared anatomy and physiology with the Cb. Despite the similarities, the CbLS are clearly not phylogenetically homologous with the Cb. Common structure and function may arise due to a shared genetic and developmental toolkit. To examine this possibility, we used sequence analysis, western blotting, immunohistochemistry and RT-qPCR to test for the expression of three genes that are critical for mammalian cerebellar development in the Cb and CbLS of an elasmobranch fish, Leucoraja erinacea. In the mammalian Cb, Pax6 is necessary for parallel fiber development, while Cbln1 and Grid2 code for proteins necessary for parallel fiber-principal cell synaptogenesis. Pax6 and Cbln1 are expressed by granule cells in the Cb and CbLS of the adult skate and stage 31 embryo. Grid2 is expressed by principal cells in the Cb and CbLS of the adult and stage 31 embryo. RT-qPCR showed this expression is spatially and temporally restricted to the Cb and CbLS. If Pax6, Cbln1 and Grid2 perform the same functions in the skate Cb and CbLS as they do in the mammalian Cb, then these structures may develop using a shared genetic toolkit and be considered generatively homologous. It is possible that the evolutionary genesis of the Cb was the result of duplication or expansion of the cerebellum-like developmental toolkit.

show abstract

SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

Cited by 69 publications

References 76 publications

Estimating effective population size using RADseq: Effects of SNP selection and sample size

Estimating effective population size using RADseq: Effects of SNP selection and sample size

A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum)

Evidence for generative homology of cerebellum and cerebellum‐like structures in an elasmobranch fish based on Pax6, Cbln1 and Grid2 expression

Contact Info

Product

Resources

About