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A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

Overview of attention for article published in BMC Genomics, May 2017
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (82nd percentile)
  • High Attention Score compared to outputs of the same age and source (85th percentile)

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Title
A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing
Published in
BMC Genomics, May 2017
DOI 10.1186/s12864-017-3757-8
Pubmed ID
Authors

Nam V. Hoang, Agnelo Furtado, Patrick J. Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P. Thirugnanasambandam, Frederik C. Botha, Robert J. Henry

Abstract

Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms. A total of 107,598 unique transcript isoforms were obtained, representing about 71% of the total number of predicted sugarcane genes. The majority of this dataset (92%) matched the plant protein database, while just over 2% was novel transcripts, and over 2% was putative long non-coding RNAs. About 56% and 23% of total sequences were annotated against the gene ontology and KEGG pathway databases, respectively. Comparison with de novo contigs from Illumina RNA-Sequencing (RNA-Seq) of the internode samples from the same experiment and public databases showed that the Iso-Seq method recovered more full-length transcript isoforms, had a higher N50 and average length of largest 1,000 proteins; whereas a greater representation of the gene content and RNA diversity was captured in RNA-Seq. Only 62% of PacBio transcript isoforms matched 67% of de novo contigs, while the non-matched proportions were attributed to the inclusion of leaf/root tissues and the normalization in PacBio, and the representation of more gene content and RNA classes in the de novo assembly, respectively. About 69% of PacBio transcript isoforms and 41% of de novo contigs aligned with the sorghum genome, indicating the high conservation of orthologs in the genic regions of the two genomes. The transcriptome dataset should contribute to improved sugarcane gene models and sugarcane protein predictions; and will serve as a reference database for analysis of transcript expression in sugarcane.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 180 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Netherlands 1 <1%
United States 1 <1%
Brazil 1 <1%
Unknown 177 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 41 23%
Student > Ph. D. Student 32 18%
Student > Master 21 12%
Student > Doctoral Student 13 7%
Student > Bachelor 11 6%
Other 23 13%
Unknown 39 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 80 44%
Biochemistry, Genetics and Molecular Biology 27 15%
Computer Science 3 2%
Environmental Science 3 2%
Unspecified 3 2%
Other 11 6%
Unknown 53 29%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 11. 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 28 September 2017.
All research outputs
#3,055,647
of 24,162,141 outputs
Outputs from BMC Genomics
#1,062
of 10,914 outputs
Outputs of similar age
#55,023
of 317,413 outputs
Outputs of similar age from BMC Genomics
#33
of 219 outputs
Altmetric has tracked 24,162,141 research outputs across all sources so far. Compared to these this one has done well and is in the 87th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 10,914 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done particularly well, scoring higher than 90% of its peers.
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 317,413 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 82% of its contemporaries.
We're also able to compare this research output to 219 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 85% of its contemporaries.