scholarly journals The Draft Genome and Transcriptome of the Atlantic Horseshoe Crab,Limulus polyphemus

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Stephen D. Simpson ◽  
Jordan S. Ramsdell ◽  
Winsor H. Watson III ◽  
Christopher C. Chabot
Keyword(s):  
Horseshoe Crab ◽  
Molecular Mechanisms ◽  
Transcriptome Assembly ◽  
Draft Genome ◽  
Limulus Polyphemus ◽  
Rna Seq ◽  
Accessory Gene ◽  
Large Dataset ◽  
Horseshoe Crabs ◽  
Atlantic Horseshoe Crab

The horseshoe crab,Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in7.4×105contigs with N50 of 4,736, while the transcriptome assembly resulted in9.3×104contigs and N50 of 3,497. Analysis of functional completeness by the identification of putative universal orthologs suggests that the transcriptome has three times more total expected orthologs than the genome. Interestingly, RNA-Seq analysis indicated no statistically significant changes in expression level for any circadian core or accessory gene, but there was significant cycling of several noncircadian transcripts. Overall, these assemblies provide a resource to investigate theLimulusclock systems and provide a large dataset for further exploration into the taxonomy and biology of the Atlantic horseshoe crab.

Limulus polyphemus (Atlantic Horseshoe Crab) Habitats in a Small Estuary and the Adjacent Inner Continental Shelf: Linkages Across Mid-Atlantic Bight Seascapes

2019 ◽  
Vol 26 (2) ◽  
pp. 287 ◽  
Author(s):  
Kenneth W. Able ◽  
Paola C. López-Duarte ◽  
Thomas M. Grothues ◽  
Linda Barry ◽  
Rosemarie Petrecca ◽  
...  
Keyword(s):  
Continental Shelf ◽  
Horseshoe Crab ◽  
Limulus Polyphemus ◽  
Inner Continental Shelf ◽  
Atlantic Horseshoe Crab

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang ◽  
Xian-zhi Sun ◽  
Sheng Zhang ◽  
Jing-hui Yang ◽  
Fang-fang Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
The Self ◽  
Rna Seq ◽  
Aphid Infestation ◽  
A Genome ◽  
Artemisia Scoparia

Abstract Abstract Background: Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum ( Chrysanthemum morifolium T. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results : The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion: In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding. Key words : Chrysanthemum, Grafting, Aphid stress, Gene expression, RNA-Seq

scholarly journals A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

2017 ◽  
Author(s):  
Mickael Orgeur ◽  
Marvin Martens ◽  
Stefan T. Börno ◽  
Bernd Timmermann ◽  
Delphine Duprez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Gene Annotation ◽  
Transcriptome Assembly ◽  
Draft Genome ◽  
Transcript Abundance ◽  
Accurate Estimation ◽  
Rna Seq ◽  
A Genome ◽  
Transcript Discovery

AbstractThe sequence of the chicken genome, like several other draft genome sequences, is presently not fully covered. Gaps, contigs assigned with low confidence and uncharacterized chromosomes result in gene fragmentation and imprecise gene annotation. Transcript abundance estimation from RNA sequencing (RNA-seq) data relies on read quality, library complexity and expression normalization. In addition, the quality of the genome sequence used to map sequencing reads and the gene annotation that defines gene features must also be taken into account. Partially covered genome sequence causes the loss of sequencing reads from the mapping step, while an inaccurate definition of gene features induces imprecise read counts from the assignment step. Both steps can significantly bias interpretation of RNA-seq data. Here, we describe a dual transcript-discovery approach combining a genome-guided gene prediction and ade novotranscriptome assembly. This dual approach enabled us to increase the assignment rate of RNA-seq data by nearly 20% as compared to when using only the chicken reference annotation, contributing therefore to a more accurate estimation of transcript abundance. More generally, this strategy could be applied to any organism with partial genome sequence and/or lacking a manually-curated reference annotation in order to improve the accuracy of gene expression studies.

Maternal transfer of trace elements in the Atlantic horseshoe crab (Limulus polyphemus)

Ecotoxicology ◽  
2016 ◽  
Vol 26 (1) ◽  
pp. 46-57 ◽  
Author(s):  
Aaron K. Bakker ◽  
Jessica Dutton ◽  
Matthew Sclafani ◽  
Nicholas Santangelo
Keyword(s):  
Trace Elements ◽  
Horseshoe Crab ◽  
Limulus Polyphemus ◽  
Maternal Transfer ◽  
Atlantic Horseshoe Crab

scholarly journals GENETIC VARIATION AND GEOGRAPHIC DIFFERENTIATION IN MITOCHONDRIAL DNA OF THE HORSESHOE CRAB, LIMULUS POLYPHEMUS

Genetics ◽  
1986 ◽  
Vol 112 (3) ◽  
pp. 613-627
Author(s):  
Nancy C Saunders ◽  
Louis G Kessler ◽  
John C Avise
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Horseshoe Crab ◽  
Gulf Coast ◽  
Sequence Divergence ◽  
Clonal Diversity ◽  
Limulus Polyphemus ◽  
Site Variation ◽  
Horseshoe Crabs ◽  
Or Gene

ABSTRACT Restriction site variation in mitochondrial DNA (mtDNA) of the horseshoe crab (Limulus polyphemus) was surveyed in populations ranging from New Hampshire to the Gulf Coast of Florida. MtDNA clonal diversity was moderately high, particularly in southern samples, and a major genetic "break" (nucleotide sequence divergence approximately 2%) distinguished all sampled individuals which were north vs. south of a region in northeastern Florida. The area of genotypic divergence in Limulus corresponds to a long-recognized zoogeographic boundary between warm-temperate and tropical marine faunas, and it suggests that selection pressures and/or gene flow barriers associated with water mass differences may also influence the evolution of species widely distributed across such transition zones. On the other hand, a comparison of the mtDNA divergence patterns in Limulus with computer models involving stochastic lineage extinction in species with limited gene flow demonstrates that deterministic explanations need not necessarily be invoked to account for the observations. Experiments to distinguish stochastic from deterministic possibilities are suggested. Overall, the pattern and magnitude of mtDNA differentiation in horseshoe crabs is very similar to that typically reported for freshwater and terrestrial species assayed over a comparable geographic range. Results demonstrate for the first time that, geographically, at least some continuously distributed marine organisms can show considerable mtDNA genetic differentiation.

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang ◽  
Xian-zhi Sun ◽  
Sheng Zhang ◽  
Jing-hui Yang ◽  
Fang-fang Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
The Self ◽  
Rna Seq ◽  
Aphid Infestation ◽  
A Genome ◽  
Artemisia Scoparia

Abstract Abstract Background: Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum ( Chrysanthemum morifolium T. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results : The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion: In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding. Key words : Chrysanthemum, Grafting, Aphid stress, Gene expression, RNA-Seq

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