NCBI BLAST + integrated into Galaxy

Cock, Peter; Chilton, John; Grüning, Björn; Johnson, James E.; Soranzo, Nicola

doi:10.1101/014043

Cited by 36 publications

(44 citation statements)

References 33 publications

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“…Transcript quantification was generated via Salmon (Patro, Duggal, Love, Irizarry, & Kingsford, ) as filtered trimmed reads were back aligned to the assembled transcriptome. Annotations were created by blasting the translated transcriptome against the UniProtKB (Swiss‐Prot) database by BLASTP (Camacho et al, ; Cock, Chilton, Grüning, Johnson, & Soranzo, ). Annotations were also created from the nr database using Diamond (version 0.9.18) in sensitive mode (Buchfink, Xie, & Huson, ).…”

Section: Methodsmentioning

confidence: 99%

Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae)

Maor-Landaw

Oppen

McFadden

2019

Ecology and Evolution

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Coral-dinoflagellate symbiosis underpins the evolutionary success of corals reefs. Successful exchange of molecules between the cnidarian host and the Symbiodiniaceae algae enables the mutualistic partnership. The algae translocate photosynthate to their host in exchange for nutrients and shelter. The photosynthate must traverse multiple membranes, most likely facilitated by transporters. Here, we compared gene expression profiles of cultured, free-living Breviolum minutum with those of the homologous symbionts freshly isolated from the sea anemone Exaiptasia diaphana, a widely used model for coral hosts. Additionally, we assessed expression levels of a list of candidate host transporters of interest in anemones with and without symbionts. Our transcriptome analyses highlight the distinctive nature of the two algal life stages, with many gene expression level changes correlating to the different morphologies, cell cycles, and metabolisms adopted in hospite versus free-living.Morphogenesis-related genes that likely underpin the metamorphosis process observed when symbionts enter a host cell were up-regulated. Conversely, many downregulated genes appear to be indicative of the protective and confined nature of the symbiosome. Our results emphasize the significance of transmembrane transport to the symbiosis, and in particular of ammonium and sugar transport. Further, we pinpoint and characterize candidate transporters-predicted to be localized variously to the algal plasma membrane, the host plasma membrane, and the symbiosome membrane-that likely serve pivotal roles in the interchange of material during symbiosis.Our study provides new insights that expand our understanding of the molecular exchanges that underpin the cnidarian-algal symbiotic relationship. K E Y W O R D S Breviolum minutum, Exaiptasia diaphana, free-living, in hospite, symbiosis, transporters S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Maor-Landaw K, van Oppen MJH, McFadden GI. Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae).

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Section: Methodsmentioning

confidence: 99%

Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae)

Maor-Landaw

Oppen

McFadden

2019

Ecology and Evolution

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“…Species‐specific primers for the CPD and 6‐4 PP photolyase genes and the β‐actin housekeeping gene were produced for quantitative PCR (Table ). CPD, 6‐4 PP B‐actin transcripts were identified from an in‐house reference larval L. peronii transcriptome (SRA bio‐sample accession number: PRJNA438838) using the BLASTN discontiguous megablast tool (Camacho et al, ; Cock, Chilton, Grüning, Johnson, & Soranzo, ) within the Galaxy Australia instance (http://usegalaxy.org.au) against homologous amphibian sequences (accession numbers: NM_001095658.1 CPD photolyase‐like L homolog [ Xenopus laevis ]; NM_001087952.2 Xenopus laevis 6‐4 photolyase; NM_213719 Xenopus tropicalis actin, beta). Primers were designed from the resulting L. peronii mRNA transcripts using PrimerQuest software (Integrated DNA Technologies) with acceptance of the default parameters.…”

Section: Methodsmentioning

confidence: 99%

Cooler temperatures slow the repair of DNA damage in tadpoles exposed to ultraviolet radiation: Implications for amphibian declines at high altitude

Morison

Cramp

Alton

et al. 2019

Global Change Biology

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Ultraviolet B radiation (UVBR) damages the DNA of exposed cells, causing dimers to form between adjacent pyrimidine nucleotides. These dimers block DNA replication, causing mutations and apoptosis. Most organisms utilize biochemical or biophysical DNA repair strategies to restore DNA structure; however, as with most biological reactions, these processes are likely to be thermally sensitive. Tadpoles exposed to elevated UVBR at low environmental temperatures have significantly higher rates of mortality and developmental deformities compared with tadpoles exposed to the same levels of UVBR at higher environmental temperatures. We hypothesized that low environmental temperatures impair the primary enzymatic (photolyase) DNA repair pathway in amphibians, leading to the accumulation of DNA damage. To test this hypothesis, we compared DNA repair rates and photolyase gene expression patterns in Limnodynastes peronii. Tadpoles were acutely exposed to UVBR for 1 hr at either 20 or 30°C, and we measured DNA damage and photolyase expression levels at intervals following this exposure. Temperature had a significant effect on the rate of DNA repair, with repair at 30°C occurring twice as fast as repair at 20°C. Photolyase gene expression (6‐4 PP and CPD) was significantly upregulated by UVBR exposure, with expression levels increasing within 6 hr of UVBR exposure. CPD expression levels were not significantly affected by temperature, but 6‐4 PP expression was significantly higher in tadpoles in the 30°C treatment within 12 hr of UVBR exposure. These data support the hypothesis that DNA repair rates are thermally sensitive in tadpoles and may explain why enigmatic amphibian declines are higher in montane regions where UVBR levels are naturally elevated and environmental temperatures are lower.

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“…Multiple alternatives to Sequenceserver similarly provide graphical user interfaces (GUIs) for BLAST (Tao, 2006; Deng et al ., 2007; O’Connor et al ., 2008; Cock et al ., 2015; NCBI, 2014). However, they have three broad levels of shortcomings (summarized in Supplementary Table S1).…”

Section: Discussionmentioning

confidence: 99%

“…Finally, the most appropriate solution for many laboratories would be to have access to a shared graphical user interface to run BLAST on private datasets. Several free and open source software packages make this possible, including ViroBLAST (Deng et al ., 2007), GMOD’s BlastGraphic (O’Connor et al ., 2008), NCBI’s wwwblast (Tao, 2006), NCBI’s Amazon Cloud BLAST (NCBI, 2014), and Galaxy BLAST (Cock et al ., 2015). Unfortunately, setting up such interfaces is challenging: they are either deprecated and no longer maintained, or have complex installation dependencies such as custom configuration of the Apache web server (Fielding & Kaiser, 1997) or CGI paths (Gundavaram, 1996).…”

Section: Introductionmentioning

confidence: 99%

“…Once set up, a further challenge is using the graphical user interface. For example, users typically must choose between multiple BLAST algorithms (TBLASTX, TBLASTN, BLASTX, BLASTN, BLASTP) before entering query data or choosing search databases (e.g., Tao, 2006; Deng et al ., 2007; O’Connor et al ., 2008; NCBI, 2014; Cock et al ., 2015; Johnson et al ., 2008). This implicitly requires detailed knowledge of BLAST algorithms and available databases - yet even experienced BLAST users make frequent mistakes and must revisit their decisions.…”

Section: Introductionmentioning

confidence: 99%

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Sequenceserver: a modern graphical user interface for custom BLAST databases

Priyam

Woodcroft

Rai

et al. 2015

Preprint

122

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28The dramatic drop in DNA sequencing costs has created many opportunities for novel biological research. These 29 opportunities largely rest upon the ability to effectively compare newly obtained and previously known sequences. 30This is commonly done with BLAST, yet using BLAST directly on new datasets requires substantial technical skills or 31 helpful colleagues. Furthermore, graphical interfaces for BLAST are challenging to install and largely mimic underlying 32 computational processes rather than work patterns of researchers. 33We combined a user-centric design philosophy with sustainable software development approaches to create Se-34 quenceserver (http://sequenceserver.com), a modern graphical user interface for BLAST. Sequenceserver sub-35 stantially increases the efficiency of researchers working with sequence data. This is due to innovations at three 36 levels. First, our software can be installed and used on custom datasets extremely rapidly for personal and shared

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NCBI BLAST + integrated into Galaxy

Cited by 36 publications

References 33 publications

Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae)

Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae)

Cooler temperatures slow the repair of DNA damage in tadpoles exposed to ultraviolet radiation: Implications for amphibian declines at high altitude

Sequenceserver: a modern graphical user interface for custom BLAST databases

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