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Comparative genomic analysis identifies structural features of CRISPR-Cas systems in Riemerella anatipestifer

Overview of attention for article published in BMC Genomics, August 2016
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Comparative genomic analysis identifies structural features of CRISPR-Cas systems in Riemerella anatipestifer
Published in
BMC Genomics, August 2016
DOI 10.1186/s12864-016-3040-4
Pubmed ID

De-Kang Zhu, Xue-Qin Yang, Yang He, Wang-Shu Zhou, Xiao-Heng Song, Jiang-Bo Wang, Yu Zhang, Ma-Feng Liu, Ming-Shu Wang, Ren-Yong Jia, Shun Chen, Kun-Feng Sun, Qiao Yang, Ying Wu, Xiao-Yue Chen, An-Chun Cheng


Riemerella anatipestifer infection is a contagious disease that has resulted in major economic losses in the duck industry worldwide. This study attempted to characterize CRISPR-Cas systems in the disease-causing agent, Riemerella anatipestifer (R. anatipestifer). The CRISPR-Cas system provides adaptive immunity against foreign genetic elements in prokaryotes and CRISPR-cas loci extensively exist in the genomes of archaea and bacteria. However, the structure characteristics of R. anatipestifer CRISPR-Cas systems remains to be elucidated due to the limited availability of genomic data. To identify the structure and components associated with CRISPR-Cas systems in R. anatipestifer, we performed comparative genomic analysis of CRISPR-Cas systems in 25 R. anatipestifer strains using high-throughput sequencing. The results showed that most of the R. anatipestifer strains (20/25) that were analyzed have two CRISPR loci (CRISPR1 and CRISPR2). CRISPR1 was shown to be flanked on one side by cas genes, while CRISPR2 was designated as an orphan. The other analyzed strains harbored only one locus, either CRISPR1 or CRISPR2. The length and content of consensus direct repeat sequences, as well as the length of spacer sequences associated with the two loci, differed from each other. Only three cas genes (cas1, cas2 and cas9) were located upstream of CRISPR1. CRISPR1 was also shown to be flanked by a 107 bp-long putative leader sequence and a 16 nt-long anti-repeat sequence. Combined with analysis of spacer organization similarity and phylogenetic tree of the R. anatipestifer strains, CRISPR arrays can be divided into different subgroups. The diversity of spacer organization was observed in the same subgroup. In general, spacer organization in CRISPR1 was more divergent than that in CRISPR2. Additionally, only 8 % of spacers (13/153) were homologous with phage or plasmid sequences. The cas operon flanking CRISPR1 was observed to be relatively conserved based on multiple sequence alignments of Cas amino acid sequences. The phylogenetic analysis associated with Cas9 showed Cas9 sequence from R. anatipestifer was closely related to that of Bacteroides fragilis and formed part of the subtype II-C subcluster. Our data revealed for the first time the structural features of R. anatipestifer CRISPR-Cas systems. The illumination of structural features of CRISPR-Cas system may assist in studying the specific mechanism associated with CRISPR-mediated adaptive immunity and other biological functions in R. anatipestifer.

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Mendeley readers

The data shown below were compiled from readership statistics for 31 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Portugal 1 3%
Unknown 30 97%

Demographic breakdown

Readers by professional status Count As %
Student > Master 6 19%
Student > Bachelor 4 13%
Researcher 4 13%
Student > Ph. D. Student 2 6%
Professor 2 6%
Other 3 10%
Unknown 10 32%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 9 29%
Agricultural and Biological Sciences 2 6%
Pharmacology, Toxicology and Pharmaceutical Science 1 3%
Environmental Science 1 3%
Veterinary Science and Veterinary Medicine 1 3%
Other 4 13%
Unknown 13 42%

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 July 2021.
All research outputs
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Outputs from BMC Genomics
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Outputs of similar age
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Outputs of similar age from BMC Genomics
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Altmetric has tracked 20,034,281 research outputs across all sources so far. This one has received more attention than most of these and is in the 72nd percentile.
So far Altmetric has tracked 9,932 research outputs from this source. They receive a mean Attention Score of 4.5. This one has gotten more attention than average, scoring higher than 74% 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 282,451 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 70% of its contemporaries.
We're also able to compare this research output to 52 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 75% of its contemporaries.