A comparative gene index for the white sturgeon Acipenser transmontanus

Lazzari, Barbara; Mariani, Valentina; Malinverni, Roberto; Caprera, Andrea; Giuffra, Elisabetta

doi:10.1016/j.margen.2008.04.002

Cited by 4 publications

(2 citation statements)

References 30 publications

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“…The Swiss-Prot part of the UniProt database (downloaded on 2012/02/24) was also queried. Local TBLASTX 2.2.25+ similarity searches were conducted locally against (1) 6,088 EST sequences of the genus Acipenser downloaded from NCBI-taxonomy (2011/04/18), mainly obtained from A. sinensis [39] and A. transmontanus [40] (2) a super-set of all transcripts resulting from Ensembl (release-66) including known-, novel- and pseudo-gene predictions for the following list of reference species (hereafter RS-list): Petromyzon marinus, Latimeria chalumnae, Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, Tetraodon nigroviridis and Homo sapiens. In order to identify non-coding sequences, BLASTN 2.2.25+ similarity searches were conducted locally against whole non-coding RNA gene and pseudogene sequences from Ensembl release-66 for the species of the RS-list.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

et al. 2013

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BackgroundSturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The intense fishing pressure on wild stocks to harvest caviar has caused in the last decades a dramatic decline of their distribution and abundance leading the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, the characterization of the genes involved in sex determination could provide relevant information for the selective farming of the more profitable females.ResultsThe 454 sequencing of two cDNA libraries from the gonads and brain of one male and one female full-sib A. naccarii, yielded 182,066 and 167,776 reads respectively, which, after strict quality control, were iterative assembled into more than 55,000 high quality ESTs. The average per-base coverage reached by assembling the two libraries was 4X. The multi-step annotation process resulted in 16% successfully annotated sequences with GO terms. We screened the transcriptome for 32 sex-related genes and highlighted 7 genes that are potentially specifically expressed, 5 in male and 2 in females, at the first life stage at which sex is histologically identifiable. In addition we identified 21,791 putative EST-linked SNPs and 5,295 SSRs.ConclusionsThis study represents the first large massive release of sturgeon transcriptome information that we organized into the public database AnaccariiBase, which is freely available at http://compgen.bio.unipd.it/anaccariibase/. This transcriptomic data represents an important source of information for further studies on sturgeon species. The hundreds of putative EST-linked molecular makers discovered in this study will be invaluable for sturgeon reintroduction and breeding programs.

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Section: Methodsmentioning

confidence: 99%

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

et al. 2013

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“…Given such equivocal results, some revision of Acipenseriform classification is needed to guide conservation efforts. Ultimately, this lack of genomic resources for sturgeons hinders mechanistic study (but see [15]). …”

Section: Introductionmentioning

confidence: 99%

A Nuclear DNA Perspective on Delineating Evolutionarily Significant Lineages in Polyploids: The Case of the Endangered Shortnose Sturgeon (Acipenser brevirostrum)

King

Henderson²,

Kynard³

et al. 2014

PLoS ONE

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The shortnose sturgeon, Acipenser brevirostrum, oft considered a phylogenetic relic, is listed as an “endangered species threatened with extinction” in the US and “Vulnerable” on the IUCN Red List. Effective conservation of A. brevirostrum depends on understanding its diversity and evolutionary processes, yet challenges associated with the polyploid nature of its nuclear genome have heretofore limited population genetic analysis to maternally inherited haploid characters. We developed a suite of polysomic microsatellite DNA markers and characterized a sample of 561 shortnose sturgeon collected from major extant populations along the North American Atlantic coast. The 181 alleles observed at 11 loci were scored as binary loci and the data were subjected to multivariate ordination, Bayesian clustering, hierarchical partitioning of variance, and among-population distance metric tests. The methods uncovered moderately high levels of gene diversity suggesting population structuring across and within three metapopulations (Northeast, Mid-Atlantic, and Southeast) that encompass seven demographically discrete and evolutionarily distinct lineages. The predicted groups are consistent with previously described behavioral patterns, especially dispersal and migration, supporting the interpretation that A. brevirostrum exhibit adaptive differences based on watershed. Combined with results of prior genetic (mitochondrial DNA) and behavioral studies, the current work suggests that dispersal is an important factor in maintaining genetic diversity in A. brevirostrum and that the basic unit for conservation management is arguably the local population.

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Metabolomics in sturgeon research: a mini-review

Liu,

Naganuma

2024

Fish Physiol Biochem

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Sturgeons are ancient fish, with 27 species distributed in the Northern Hemisphere. This review first touches upon the significance of sturgeons in the context of their biological, ecological, and economic importance, highlighting their status as “living fossils” and the challenges they face in genomic research due to their diverse chromosome numbers. This review then discusses how omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have been used in sturgeon research, which so far has only been done on Acipenser species. It focuses on metabolomics as a way to better understand how sturgeons work and how they react to their environment. Specific studies in sturgeon metabolomics are cited, showing how metabolomics has been used to investigate various aspects of sturgeon biology, such as growth, reproduction, stress responses, and nutrition. These studies demonstrate the potential of metabolomics in improving sturgeon aquaculture practices and conservation efforts. Overall, the review suggests that metabolomics, as a relatively new scientific tool, has the potential to enhance our understanding of sturgeon biology and aid in their conservation and sustainable aquaculture, contributing to global food security efforts.

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A comparative gene index for the white sturgeon Acipenser transmontanus

Cited by 4 publications

References 30 publications

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon

A Nuclear DNA Perspective on Delineating Evolutionarily Significant Lineages in Polyploids: The Case of the Endangered Shortnose Sturgeon (Acipenser brevirostrum)

Metabolomics in sturgeon research: a mini-review

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