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Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish

Overview of attention for article published in BMC Genomics, May 2015
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Title
Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish
Published in
BMC Genomics, May 2015
DOI 10.1186/s12864-015-1600-7
Pubmed ID
Authors

Jun-ya Aoki, Wataru Kai, Yumi Kawabata, Akiyuki Ozaki, Kazunori Yoshida, Takashi Koyama, Takashi Sakamoto, Kazuo Araki

Abstract

Physical and linkage maps are important aids for the assembly of genome sequences, comparative analyses of synteny, and to search for candidate genes by quantitative trait locus analysis. Yellowtail, Seriola quinqueradiata, is an economically important species in Japanese aquaculture, and genetic information will be useful for DNA-assisted breeding. We report the construction of a second generation radiation hybrid map, its synteny analysis, and a second generation linkage map containing SNPs (single nucleotide polymorphisms) in yellowtail. Approximately 1.4 million reads were obtained from transcriptome sequence analysis derived from 11 tissues of one individual. To identify SNPs, cDNA libraries were generated from a pool of 500 whole juveniles, and the gills and kidneys of 100 adults. 9,356 putative SNPs were detected in 6,025 contigs, with a minor allele frequency ≥25%. The linkage and radiation hybrid maps were constructed based on these contig sequences. 2,081 markers, including 601 SNPs markers, were mapped onto the linkage map, and 1,532 markers were mapped in the radiation hybrid map. The second generation linkage and physical maps were constructed using 6,025 contigs having SNP markers. These maps will aid the de novo assembly of sequencing reads, linkage studies and the identification of candidate genes related to important traits. The comparison of marker contigs in the radiation hybrid map indicated that yellowtail is evolutionarily closer to medaka than to green-spotted pufferfish, three-spined stickleback or zebrafish. The synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 29 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Spain 1 3%
Unknown 28 97%

Demographic breakdown

Readers by professional status Count As %
Researcher 8 28%
Student > Master 4 14%
Student > Postgraduate 3 10%
Other 2 7%
Lecturer 1 3%
Other 3 10%
Unknown 8 28%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 41%
Biochemistry, Genetics and Molecular Biology 1 3%
Environmental Science 1 3%
Medicine and Dentistry 1 3%
Engineering 1 3%
Other 0 0%
Unknown 13 45%
Attention Score in Context

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 26 May 2015.
All research outputs
#13,944,553
of 22,807,037 outputs
Outputs from BMC Genomics
#5,345
of 10,650 outputs
Outputs of similar age
#134,021
of 267,399 outputs
Outputs of similar age from BMC Genomics
#139
of 258 outputs
Altmetric has tracked 22,807,037 research outputs across all sources so far. This one is in the 37th percentile – i.e., 37% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,650 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 46th percentile – i.e., 46% 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 267,399 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 258 others from the same source and published within six weeks on either side of this one. This one is in the 40th percentile – i.e., 40% of its contemporaries scored the same or lower than it.