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

Aoki JY, Kai W, Kawabata Y, Ozaki A, Yoshida K, Koyama T, Sakamoto T, Araki K - BMC Genomics (2015)

Bottom Line: 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 synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.

View Article: PubMed Central - PubMed

Affiliation: National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan. junaoki@affrc.go.jp.

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus

Gene Ontology assignment for assembled contigs. (A) Molecular function, (B) Biological process and (C) Cellular component assignment.
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Fig1: Gene Ontology assignment for assembled contigs. (A) Molecular function, (B) Biological process and (C) Cellular component assignment.

Mentions: Of 56,449 contigs, 24,035 (43%) had a significant hit and matched 15,280 unique protein records in the nr protein database. Gene ontology (GO) analysis was conducted on these 24,035 contigs. 17,076 sequences were assigned to at least one GO term describing three functional groups: biological process, molecular function and cellular component. Summaries of the level 2 GO assignments are shown in Figure 1. Among the 17,076 sequences, the molecular function ontology comprised the majority of GO assignments (83%), followed by biological processes (79%) and cellular components (74%). In the molecular function category, binding and catalytic activity represented about 80% of the total. For biological processes, sequences involved in cellular processes (19%), metabolic processes (18%), and biological regulation (13%) were highly represented. Finally, the cell and organelle term represented about 70% of the cellular component. Transcriptome assembly using next generation DNA sequencing and GO analysis has been reported in other fish species [33-35]. Our GO analysis of yellowtail transcriptome revealed similar results to those of other fishes.Figure 1


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

Aoki JY, Kai W, Kawabata Y, Ozaki A, Yoshida K, Koyama T, Sakamoto T, Araki K - BMC Genomics (2015)

Gene Ontology assignment for assembled contigs. (A) Molecular function, (B) Biological process and (C) Cellular component assignment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4493941&req=5

Fig1: Gene Ontology assignment for assembled contigs. (A) Molecular function, (B) Biological process and (C) Cellular component assignment.
Mentions: Of 56,449 contigs, 24,035 (43%) had a significant hit and matched 15,280 unique protein records in the nr protein database. Gene ontology (GO) analysis was conducted on these 24,035 contigs. 17,076 sequences were assigned to at least one GO term describing three functional groups: biological process, molecular function and cellular component. Summaries of the level 2 GO assignments are shown in Figure 1. Among the 17,076 sequences, the molecular function ontology comprised the majority of GO assignments (83%), followed by biological processes (79%) and cellular components (74%). In the molecular function category, binding and catalytic activity represented about 80% of the total. For biological processes, sequences involved in cellular processes (19%), metabolic processes (18%), and biological regulation (13%) were highly represented. Finally, the cell and organelle term represented about 70% of the cellular component. Transcriptome assembly using next generation DNA sequencing and GO analysis has been reported in other fish species [33-35]. Our GO analysis of yellowtail transcriptome revealed similar results to those of other fishes.Figure 1

Bottom Line: 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 synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.

View Article: PubMed Central - PubMed

Affiliation: National Research Institute of Aquaculture, Fisheries Research Agency, 224-1 Hiruta, Tamaki-cho, Watarai-gun, Mie, 519-0423, Japan. junaoki@affrc.go.jp.

ABSTRACT

Background: 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.

Results: 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus