Exploring single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes in the jellyfish (Rhopilema esculentum) by transcriptome sequencing

Li, Yunfeng; Zhou, Zunchun; Tian, Meilin; Yi, Tian; Dong, Ying; Li, Shilei; Liu, Weidong; He, Chongbo

doi:10.1016/j.margen.2017.01.007

Cited by 6 publications

(3 citation statements)

References 18 publications

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“…SNP markers as one of the molecular markers were genotyped easily to construct the genetic linkage maps for guiding the genetic breeding of aquaculture animals 17 . Researchers have identified 1,034,708 SNPs in R. esculentum by transcriptome sequencing 15 , yet we only identified 9100 SNPs by 2b-RAD sequencing, much lower than that in the previous study 15 . The difference in SNP numbers between the two studies may be caused by the SNP analysis method.…”

Section: Discussioncontrasting

confidence: 59%

“…Although the R. esculentum genome has been released 1 , 13 , the genetic linkage map and QTL for growth in R. esculentum have not been reported yet. In previous studies, the researchers only identified some markers in R. esculentum , such as microsatellite for detection of genetic diversity and conservation of germplasm resources 14 and SNPs and simple sequence repeats (SSRs) for assisting MAS breeding 15 . To improve the growth of R. esculentum through MAS breeding, we identified SNP markers by 2b-RAD method and constructed the first genetic linkage map of R. esculentum .…”

Section: Introductionmentioning

confidence: 99%

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Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

Chen

Tian

et al. 2022

Sci Rep

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R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the genetic linkage map and growth-related molecular markers are still lacking, hindering marker assisted selection (MAS) for genetic improvement of R. esculentum. Therefore, we firstly used 2b-restriction site-associated DNA (2b-RAD) method to sequence 152 R. esculentum specimens and obtained 9100 single nucleotide polymorphism (SNP) markers. A 1456.34 cM linkage map was constructed using 2508 SNP markers with an average interval of 0.58 cM. Then, six quantitative trait loci (QTLs) for umbrella diameter and body weight were detected by QTL analysis based on the new linkage map. The six QTLs are located on four linkage groups (LGs), LG4, LG13, LG14 and LG15, explaining 9.4% to 13.4% of the phenotypic variation. Finally, 27 candidate genes in QTLs regions of LG 14 and 15 were found associated with growth and one gene named RE13670 (sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1-like) may play an important role in controlling the growth of R. esculentum. This study provides valuable information for investigating the growth mechanism and MAS breeding in R. esculentum.

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Section: Discussioncontrasting

confidence: 59%

Section: Introductionmentioning

confidence: 99%

Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

Chen

Tian

et al. 2022

Sci Rep

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“…The resulting analysis ready reads are parsed to detect SNPs using GATK-UniiedGenotyper tool with parameters of "-stand_call_conf 30" and "-stand_emit_conf 10". Following this step, SNP calls are hardiltered using GATK-VariantFiltration tool with parameters of "quality by depth > 5", "uniltered read depth ≥ 10" and "read mapping quality ≥ 40" to obtain reliable and accurate SNPs [85][86][87].…”

Section: Transcriptomics Tells More: Focusing On Speciic Annotation Tmentioning

confidence: 99%

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Eldem¹,

Zararsız²,

Taşçi³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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Since transcriptome analysis provides genome-wide sequence and gene expression information, transcript reconstruction using RNA-Seq sequence reads has become popular during recent years. For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via de novo transcriptome assembly approaches to produce large numbers of contigs corresponding to coding or non-coding, but expressed, part of genome. In spite of immense potential of RNA-Seq-based methods, particularly in recovering full-length transcripts and spliced isoforms from short-reads, the accurate results can be only obtained by the procedures to be taken in a step-by-step manner. In this chapter, we aim to provide an overview of the state-of-the-art methods including (i) quality check and pre-processing of raw reads, (ii) the pros and cons of de novo transcriptome assemblers, (iii) generating non-redundant transcript data, (iv) current quality assessment tools for de novo transcriptome assemblies, (v) approaches for transcript abundance and diferential expression estimations and inally (vi) further mining of transcriptomic data for particular biological questions. Our intention is to provide an overview and practical guidance for choosing the appropriate approaches to best meet the needs of researchers in this area and also outline the strategies to improve on-going projects.

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Population Genomics of Marine Zooplankton

Bucklin

DiVito

Smolina

et al. 2018

Population Genomics

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The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many -but not all -marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic "noise" in large and patchy populations from local adaptation to environmental conditions and change.

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Exploring single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes in the jellyfish (Rhopilema esculentum) by transcriptome sequencing

Cited by 6 publications

References 18 publications

Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Population Genomics of Marine Zooplankton

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