ArticlePloS one2011
Expression profiling without genome sequence information in a non-model species, Pandalid shrimp (Pandalus latirostris), by next-generation sequencing.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the LerayEcology and evolution · 2024Article
- Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management ofAnimals : an open access journal from MDPI · 2024Article
- Single-molecule long-read sequencing facilitates shrimp transcriptome research.Scientific reports · 2018Article
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- Transcriptome analysis of the livers of ducklings hatched normally and with assistance.Asian-Australasian journal of animal sciences · 2017Article
- Comparative Transcriptome Analysis Reveals Related Regulatory Mechanisms of Androgenic Gland inBioMed research international · 2017Article
- Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways ofFrontiers in plant science · 2017Article
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- Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes.Molecular ecology resources · 2016Article
- Gene expression profiling in gills of the great spider crab Hyas araneus in response to ocean acidification and warming.BMC genomics · 2014Article
- Identification of twenty novel polymorphic microsatellite DNA markers from transcripts of the pearl oyster Pinctada fucata using next-generation sequencing approach.Journal of genetics · 2014Article
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- Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes.Physiological genomics · 2014Article
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- Transcriptomic analysis of Prunus domestica undergoing hypersensitive response to plum pox virus infection.PloS one · 2014Article
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- Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants.BMC genomics · 2012Article
- De novo sequencing and transcriptome analysis of the central nervous system of mollusc Lymnaea stagnalis by deep RNA sequencing.PloS one · 2012Article
- Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).PloS one · 2012Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While the study of phenotypic variation is a central theme in evolutionary biology, the genetic approaches available to understanding this variation are usually limited because of a lack of genomic information in non-model organisms. This study explored the utility of next-generation sequencing (NGS) technologies for studying phenotypic variations between 2 populations of a non-model species, the Hokkai shrimp (Pandalus latirostris; Decapoda, Pandalidae). Before we performed transcriptome analyses using NGS, we examined the genetic and phenotypic differentiation between the populations. Analyses using microsatellite DNA markers suggested that these populations genetically differed from one another and that gene flow is restricted between them. Moreover, the results of our 4-year field observations indicated that the egg traits varied genetically between the populations. Using mRNA extracted from the ovaries of 5 females in each population of Hokkai shrimp, we then performed a transcriptome analysis of the 2 populations. A total of 13.66 gigabases (Gb) of 75-bp reads was obtained. Further, 58,804 and 33,548 contigs for the first and second population, respectively, and 47,467 contigs for both populations were produced by de novo assembly. We detected 552 sequences with the former approach and 702 sequences with the later one; both sets of sequences showed greater than twofold differences in the expression levels between the 2 populations. Twenty-nine sequences were found in both approaches and were considered to be differentially expressed genes. Among them, 9 sequences showed significant similarity to functional genes. The present study showed a de novo assembly approach for the transcriptome of a non-model species using only short-read sequence data, and provides a strategy for identifying sequences showing significantly different expression levels between populations.
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