A first insight into the spleen transcriptome of the notothenioid fish Lepidonotothen nudifrons: Resource description and functional overview

Papetti, Chiara; Harms, Lars; Windisch, Heidrun Sigrid; Frickenhaus, Stephan; Sandersfeld, Tina; Jürgens, Jutta; Koschnick, Nils; Knust, Rainer; Pörtner, Hans‐Otto; Lucassen, Magnus

doi:10.1016/j.margen.2015.06.006

Cited by 14 publications

(8 citation statements)

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“…We therefore mined microsatellite sequences from the publicly available spleen transcriptome of L. nudifrons [ 13 ] and screened several promising candidate loci for amplification and polymorphism. We were able to isolate sixteen species-specific SSR markers from assembled transcript sequences of L. nudifrons.…”

Section: Resultsmentioning

confidence: 99%

“… The table reports: the name of each locus (Ln = Lepidonotothen nudifrons and the transcript number), Accession number of the de novo assembled transcripts of L. nudifrons (European Nucleotide Archive -ENA- project number PRJEB8919) [ 13 ], the putatively annotated loci (Blastx Top Hit, e-value < 10 −9 ), the repeat content, the forward (F) and reverse (R) primer sequences, the fluorescent label, the multiplex pool (mix). Variability, expressed in terms (P) polymorphic, (M) monomorphic or (-) unsuccessful locus, was assessed on 21 L. nudifrons (Ln), 20 L. squamifrons (Ls) and 18 L. larseni (Ll) individuals.…”

Section: Resultsmentioning

confidence: 99%

“…Gene-associated SSR markers were identified among 112,477 spleen transcripts of L. nudifrons [ 13 ]. The raw sequences were obtained from an Illumina MiSeq sequencer.…”

Section: Methodsmentioning

confidence: 99%

“…Adapter clipping and quality trimming was performed using Trimmomatic v.0.32 [ 14 ] with following parameters: seed mismatch of 2, palindrome clip threshold of 30, simple clip threshold of 10, a minimum adapter length of 2, keep both reads parameter set to true, headcrop of 7, leading and trailing quality of 3, sliding window size of 4 with an average quality of 15 and a minimum sequence length of 50 bases. The subsequent de novo assembly was performed using the trinity genome-independent transcriptome assembler [release 17 July 2014, 15 ] with a minimum transcript length of 300 bases (for further details see [ 13 ]). Transcripts were screened using SciRoKo v. 3.4 [ 16 ].…”

Section: Methodsmentioning

confidence: 99%

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Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species

et al. 2016

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BackgroundLoss of genetic variability due to environmental changes, limitation of gene flow between pools of individuals or putative selective pressure at specific markers, were previously documented for Antarctic notothenioid fish species. However, so far no studies were performed for the Gaudy notothen Lepidonotothen nudifrons. Starting from a species-specific spleen transcriptome library, we aimed at isolating polymorphic microsatellites (Type I; i.e. derived from coding sequences) suitable to quantify the genetic variability in this species, and additionally to assess the population genetic structure and demography in nototheniids.ResultsWe selected 43,269 transcripts resulting from a MiSeq sequencer run, out of which we developed 19 primer pairs for sequences containing microsatellite repeats. Sixteen loci were successfully amplified in L.nudifrons. Eleven microsatellites were polymorphic and allele numbers per locus ranged from 2 to 17. In addition, we amplified loci identified from L. nudifrons in two other congeneric species (L. squamifrons and L. larseni). Thirteen loci were highly transferable to the two congeneric species. Differences in polymorphism among species were detected.ConclusionsStarting from a transcriptome of a non-model organism, we were able to identify promising polymorphic nuclear markers that are easily transferable to other closely related species. These markers can be a key instrument to monitor the genetic structure of the three Lepidonotothen species if genotyped in larger population samples. When compared with anonymous loci isolated in other notothenioids, i.e. Type II (isolated from genomic libraries), they offer the possibility to test how the effects of occurring environmental change influence the population genetic structure in each species and subsequently the composition of the entire ecosystem.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…Gene-associated SSR markers were identified among 112,477 spleen transcripts of L. nudifrons [ 13 ]. The raw sequences were obtained from an Illumina MiSeq sequencer.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species

et al. 2016

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“…Parasitism is a very frequent occurrence in Antarctic teleosts, especially by nematodes [82]. The fish spleen is an organ primarily involved in immune defenses, being the site of leukocyte production [83], and ROS can form in large quantities during inflammatory processes and phagocytic cell activity. Therefore, it is important that antioxidant enzymes, such as SOD1, which are responsible for eliminating excessive levels of these molecules, act in a coordinated way with the immune defenses, so as to prevent negative effects of high levels of ROS from extending to host cells.…”

Section: Discussionmentioning

confidence: 99%

Copper/Zinc Superoxide Dismutase from the Crocodile Icefish Chionodraco hamatus: Antioxidant Defense at Constant Sub-Zero Temperature

et al. 2020

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In the present study, we describe the purification and molecular characterization of Cu,Zn superoxide dismutase (SOD) from Chionodraco hamatus, an Antarctic teleost widely distributed in many areas of the Ross Sea that plays a pivotal role in the Antarctic food chain. The primary sequence was obtained using biochemical and molecular biology approaches and compared with Cu,Zn SODs from other organisms. Multiple sequence alignment using the amino acid sequence revealed that Cu,Zn SOD showed considerable sequence similarity with its orthologues from various vertebrate species, but also some specific substitutions directly linked to cold adaptation. Phylogenetic analyses presented the monophyletic status of Antartic Teleostei among the Perciformes, confirming the erratic differentiation of these proteins and concurring with the theory of the “unclock-like” behavior of Cu,Zn SOD evolution. Expression of C. hamatus Cu,Zn SOD at both the mRNA and protein levels were analyzed in various tissues, highlighting the regulation of gene expression related to environmental stress conditions and also animal physiology. The data presented are the first on the antioxidant enzymes of a fish belonging to the Channichthyidae family and represent an important starting point in understanding the antioxidant systems of these organisms that are subject to constant risk of oxidative stress.

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Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar)

Zhang

et al. 2022

Mar Biotechnol

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Aeromonas salmonicida is a global fish pathogen. Aeromonas salmonicida subsp. masoucida (ASM) is classified as atypical A. salmonicida and caused huge losses to salmonid industry in China. Hence, it is of great significance to develop ASM vaccine and explore its protection mechanism in salmonids. In this regard, we conducted RNA-seq analysis with spleen tissue of Atlantic salmon after ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune protections. In our results, a total of 441.63 million clean reads were obtained, and 389.37 million reads were mapped onto the Atlantic salmon reference genome. In addition, 1125, 2126, 1098, 820, and 1351 genes were significantly up-regulated, and 747, 2626, 818, 254, and 908 genes were significantly down-regulated post-ASM vaccination at 12 h, 24 h, 1 month, 2 months, and 3 months, respectively. Subsequent pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cytokine-cytokine receptor interaction ( TNFRSF11b , IL-17RA , CCR9 , and CXCL11 ), HTLV-I infection ( MR1 and HTLV-1 ), MAPK signaling pathway ( MAPK , IL8 , and TNF-α-1 ), PI3K-Akt signaling pathway ( PIK3R3 , THBS4 , and COL2A1 ), and TNF signaling pathway ( PTGS2 , TNFRSF21-l , and CXCL10 ). Finally, the results of qRT-PCR showed a significant correlation with RNA-seq results, suggesting the reliability of RNA-seq for gene expression analysis. This study provided insights into regulation of gene expression and their involved pathways in Atlantic salmon spleen in responses to vaccine, and set the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species. Supplementary Information The online version contains supplementary material available at 10.1007/s10126-021-10089-6.

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A first insight into the spleen transcriptome of the notothenioid fish Lepidonotothen nudifrons: Resource description and functional overview

Cited by 14 publications

References 15 publications

Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species

Microsatellite markers for the notothenioid fish Lepidonotothen nudifrons and two congeneric species

Copper/Zinc Superoxide Dismutase from the Crocodile Icefish Chionodraco hamatus: Antioxidant Defense at Constant Sub-Zero Temperature

Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar)

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