Maser: one-stop platform for NGS big data from analysis to visualization

Kinjo, Sonoko; Monma, Norikazu; Misu, Sadahiko; Kitamura, Norikazu; Imoto, Junichi; Yoshitake, Kazutoshi; Gojobori, Takashi; Ikeo, Kazuho

doi:10.1093/database/bay027

Cited by 49 publications

(34 citation statements)

References 47 publications

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“…The sequence data were deposited in the DNA Data Bank Japan Sequence Read Archive (accession numbers are shown in Supplementary file 1). The raw reads were subjected to de novo assembly using the Trinity program (Grabherr et al, 2011) implemented in the MASER pipeline (Kinjo et al, 2018). After automatic assembling, we checked and manually corrected the sequences of genes that are highly expressed in mature males using the Integrative Genomics Viewer (Thorvaldsdóttir et al, 2013) as reported previously (Futahashi, 2017).…”

Section: Methodsmentioning

confidence: 99%

Molecular basis of wax-based color change and UV reflection in dragonflies

Futahashi

Yamahama

Kawaguchi

et al. 2019

eLife

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Many animals change their body color for visual signaling and environmental adaptation. Some dragonflies show wax-based color change and ultraviolet (UV) reflection, but the biochemical properties underlying the phenomena are totally unknown. Here we investigated the UV-reflective abdominal wax of dragonflies, thereby identifying very long-chain methyl ketones and aldehydes as unique and major wax components. Little wax was detected on young adults, but dense wax secretion was found mainly on the dorsal abdomen of mature males of Orthetrum albistylum and O. melania, and pruinose wax secretion was identified on the ventral abdomen of mature females of O. albistylum and Sympetrum darwinianum. Comparative transcriptomics demonstrated drastic upregulation of the ELOVL17 gene, a member of the fatty acid elongase gene family, whose expression reflected the distribution of very long-chain methyl ketones. Synthetic 2-pentacosanone, the major component of dragonfly’s wax, spontaneously formed light-scattering scale-like fine structures with strong UV reflection, suggesting its potential utility for biomimetics.

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Section: Methodsmentioning

confidence: 99%

Molecular basis of wax-based color change and UV reflection in dragonflies

Futahashi

Yamahama

Kawaguchi

et al. 2019

eLife

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“…The dataset was downloaded and edited by the FASTX‐TOOLKIT 0.0.13 software. The de novo transcriptome assembly was implemented using Trinity software in the MASER pipeline . The nucleotide sequences were translated by the TransDecoder v.5.3.0 tool.…”

Section: Methodsmentioning

confidence: 99%

Characterizing the Bioluminescence of the Humboldt Squid, Dosidicus gigas (d'Orbigny, 1835): One of the Largest Luminescent Animals in the World

Galeazzo

Mirza

Pinto

et al. 2019

Photochem & Photobiology

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Bioluminescence is found in a number of cephalopods, such as Watasenia scintillans and Sthenoteuthis oualaniensis; however, many species remain poorly studied, including the Humboldt squid, Dosidicus gigas. This is the largest member of the Ommastrephidae family and grows to 2 m in length, making it one of the largest luminescent animals ever observed. Humboldt squid have small photophores all over their body that emit a brilliant blue luminescence. Using lyophilized photophores from squid caught off the coast of Chile, experiments were conducted to isolate the luciferin and protein involved in its bioluminescence. Methanolic extracts of the photophores were shown to contain dehydrocoelenterazine, and a membrane‐bound photoprotein was shown to be involved. This photoprotein was purified using ion exchange chromatography, and SDS‐PAGE showed a clean band of approximately 60 kDa. The excised band was analyzed by LC/MS, and the obtained data were compared against the transcriptome data of D. gigas, allowing us to find two gene products which displayed high coverage (>80%), the enzymes symplectin and vanin‐2, which potentially associate with light emission process in this organism. Finally, the purified photoprotein was shown to emit a blue light (470 nm) in the presence of dehydrocoelenterazine.

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“…The transposon sequence analysis was analyzed using BLAST program with TREP database [14] (data file 8, data file 9). Transcriptome reference was assessed using Busco v.3.2 [15] under Maser platform [16] (data file 10). The SwissProt-annotated contigs were used to analyze GO and KEGG pathways using Blast2GO 5.2 (data file 11).…”

Section: Data Descriptionmentioning

confidence: 99%

De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media

et al. 2020

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Objectives: Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socioeconomic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multipurpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis. Data description: The RNA transcriptome data of D. aromatica's seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.

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Maser: one-stop platform for NGS big data from analysis to visualization

Cited by 49 publications

References 47 publications

Molecular basis of wax-based color change and UV reflection in dragonflies

Molecular basis of wax-based color change and UV reflection in dragonflies

Characterizing the Bioluminescence of the Humboldt Squid, Dosidicus gigas (d'Orbigny, 1835): One of the Largest Luminescent Animals in the World

De novo assembly of transcriptome dataset from leaves of Dryobalanops aromatica (Syn. Dryobalanops sumatrensis) seedlings grown in two contrasting potting media

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