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Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis

Overview of attention for article published in BMC Genomics, October 2015
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Title
Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis
Published in
BMC Genomics, October 2015
DOI 10.1186/s12864-015-2094-z
Pubmed ID
Authors

Xiaolong Liu, Litao Zhang, Zhifeng Zhang, Xiaoyu Ma, Jianguo Liu

Abstract

Urechis unicinctus, an echiuran worm inhabiting the U-shaped burrows in the coastal mud flats, is an important commercial and ecological invertebrate in Northeast Asian countries, which has potential applications in the study of animal evolution, coastal sediment improvement and marine drug development. Furthermore, the worm can tolerate and utilize well-known toxicant-sulfide. However, knowledge is limited on the molecular mechanism of U. unicinctus responding to sulfide due to deficiency of its genetic information. In this study, we performed Illumina sequencing to obtain the first Urechis unicinctus transcriptome data. Sequenced reads were assembled and then annotated using blast searches against Nr, Nt, Swiss-Prot, KEGG and COG. The clean tags from four digital gene expression (DGE) libraries were mapped to the U. unicinctus transcriptome. DGE analysis and functional annotation were then performed to reveal its response to sulfide. The expressions of 12 candidate genes were validated using quantitative real-time PCR. The results of qRT-PCR were regressed against the DGE analysis, with a correlation coefficient and p-value reported for each of them. Here we first present a draft of U. unicinctus transcriptome using the Illumina HiSeq(TM) 2000 platform and 52,093 unique sequences were assembled with the average length of 738 bp and N50 of 1131 bp. About 51.6 % of the transcriptome were functionally annotated based on the databases of Nr, Nt, Swiss-Prot, KEGG and COG. Then based on the transcriptome, the digital gene expression analysis was conducted to examine the transcriptional response to sulfide during 6, 24 and 48 h exposure, and finally 1705, 1181 and 1494 tag-mapped genes were identified as differentially expressed genes in the 6-h, 24-h and 48-h libraries, then were further subjected to pathway analyses. In the DGE database of U. unicinctus, the alterations in certain known sulfide-related pathways indicate similar changes in response to sulfide. For more than 80 % of the identified pathway members, this is the first report on their association with sulfide stress, among which glycolysis pathway and PIDD involving pathways were unique and discussed in details, and were thought to play important roles in the sulfide tolerance of U. unicinctus. All the results are helpful to explain the mechanism of sulfide tolerance and detoxification.

Twitter Demographics

The data shown below were collected from the profiles of 2 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 11 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 9%
Unknown 10 91%

Demographic breakdown

Readers by professional status Count As %
Researcher 4 36%
Professor 2 18%
Student > Master 2 18%
Student > Ph. D. Student 1 9%
Student > Doctoral Student 1 9%
Other 1 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 4 36%
Biochemistry, Genetics and Molecular Biology 3 27%
Veterinary Science and Veterinary Medicine 1 9%
Business, Management and Accounting 1 9%
Environmental Science 1 9%
Other 1 9%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 22 October 2015.
All research outputs
#2,610,521
of 6,367,740 outputs
Outputs from BMC Genomics
#2,693
of 5,091 outputs
Outputs of similar age
#86,654
of 196,773 outputs
Outputs of similar age from BMC Genomics
#227
of 369 outputs
Altmetric has tracked 6,367,740 research outputs across all sources so far. This one has received more attention than most of these and is in the 56th percentile.
So far Altmetric has tracked 5,091 research outputs from this source. They receive a mean Attention Score of 3.9. This one is in the 42nd percentile – i.e., 42% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 196,773 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 52% of its contemporaries.
We're also able to compare this research output to 369 others from the same source and published within six weeks on either side of this one. This one is in the 31st percentile – i.e., 31% of its contemporaries scored the same or lower than it.