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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

Oxford grids showing conservation of synteny between yellowtail and four model fish. A: medaka, B: zebrafish, C: three-spined stickleback, D: green spotted pufferfish. Each box is highlighted as follows: 0–4: white square, 5–10: yellow square, 11–20: green square, 21–30: sky blue square, 31–40: blue square, more than 40: dark blue square.
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Fig4: Oxford grids showing conservation of synteny between yellowtail and four model fish. A: medaka, B: zebrafish, C: three-spined stickleback, D: green spotted pufferfish. Each box is highlighted as follows: 0–4: white square, 5–10: yellow square, 11–20: green square, 21–30: sky blue square, 31–40: blue square, more than 40: dark blue square.

Mentions: The 1,433 yellowtail EST marker sequences of the RH map were compared with the cDNA sequences of four fish species: medaka (Oryzias latipes), zebrafish (Danio rerio), three-spined stickleback (Gasterosteus aculeatus) and green-spotted pufferfish (Tetraodon nigroviridis) using the TBLASTX algorithm. Among the 1,433 yellowtail marker sequences, 1,036 genes (72.3%) had homologs in medaka, 1,064 genes (74.2%) had homologs in zebrafish, 1,073 genes (74.9%) had homologs in three-spined stickleback, and 1,032 genes (72.0%) had homologs in green-spotted pufferfish (Additional file 4). These values were not significantly different among the four fishes. Oxford grids between yellowtail and the four fish species are shown in Figure 4. The modal number of chromosomes in yellowtail is 48 [32]. This number is the same as that of medaka; all chromosomes could be paired one-to-one between yellowtail and medaka. The number of chromosomes in the two fishes is the same and their chromosomal structures are similar. These results suggested that we would observe conserved synteny between yellowtail and medaka, and that the syntenic relationship between yellowtail and zebrafish would be rather low. However, they might not be evolutionarily closer than the relationships between yellowtail and medaka. Medakas are a member of the order Beloniformes, which includes freshwater and marine fish, such as Pacific saury and flying fish. Zebrafish are a member of Cypriniformes, which consists exclusively of freshwater fish. Our synteny results reflected the known taxonomic relationships of these fishes. In Teleostei, it is thought that a whole genome duplication and eight subsequent major rearrangements occurred about 314–404 million years ago [39]. Moreover, medaka and zebrafish are thought to have diverged after the eight major rearrangement events, after which medaka and green-spotted pufferfish diverged. The chromosome number in three-spined sticklebacks is the same as that of green-spotted pufferfish. Furthermore, the Oxford grid between yellowtail and green-spotted pufferfish was similar to that between yellowtail and three-spined sticklebacks (Figure 4). However, in the Oxford grid between green-spotted pufferfish and three-spined sticklebacks, the chromosome groups were not paired one-to-one (Additional file 5). Yellowtail SQ11 and 14 correspond to linkage group 1 of three-spined sticklebacks, SQ5 and 18 correspond to linkage group 4, and SQ19 and 22 correspond to linkage group 7, respectively. Then, yellowtail SQ4 and 18 correspond to chromosome 1 of green-spotted pufferfish, SQ6 and 7 correspond to chromosome 2, and SQ11 and 12 correspond to chromosome 3, respectively. These chromosomes in three-spined sticklebacks and green-spotted pufferfish could be paired one-to-two with those of yellowtail. The number of chromosomes in three-spined sticklebacks and green-spotted pufferfish is N=21 and that of yellowtail is N=24. Thus, three-spined sticklebacks and green-spotted pufferfish have three fewer chromosomes than yellowtail; each chromosome is thought to have merged after the divergence from medaka about 191.8 M years ago. By analysis of the whole genome sequence, conserved segments and/or conserved segment orders will be distinguished using the RH map, and will aid studies of the dynamics of chromosome evolution between yellowtail and model fish species.Figure 4


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)

Oxford grids showing conservation of synteny between yellowtail and four model fish. A: medaka, B: zebrafish, C: three-spined stickleback, D: green spotted pufferfish. Each box is highlighted as follows: 0–4: white square, 5–10: yellow square, 11–20: green square, 21–30: sky blue square, 31–40: blue square, more than 40: dark blue square.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Oxford grids showing conservation of synteny between yellowtail and four model fish. A: medaka, B: zebrafish, C: three-spined stickleback, D: green spotted pufferfish. Each box is highlighted as follows: 0–4: white square, 5–10: yellow square, 11–20: green square, 21–30: sky blue square, 31–40: blue square, more than 40: dark blue square.
Mentions: The 1,433 yellowtail EST marker sequences of the RH map were compared with the cDNA sequences of four fish species: medaka (Oryzias latipes), zebrafish (Danio rerio), three-spined stickleback (Gasterosteus aculeatus) and green-spotted pufferfish (Tetraodon nigroviridis) using the TBLASTX algorithm. Among the 1,433 yellowtail marker sequences, 1,036 genes (72.3%) had homologs in medaka, 1,064 genes (74.2%) had homologs in zebrafish, 1,073 genes (74.9%) had homologs in three-spined stickleback, and 1,032 genes (72.0%) had homologs in green-spotted pufferfish (Additional file 4). These values were not significantly different among the four fishes. Oxford grids between yellowtail and the four fish species are shown in Figure 4. The modal number of chromosomes in yellowtail is 48 [32]. This number is the same as that of medaka; all chromosomes could be paired one-to-one between yellowtail and medaka. The number of chromosomes in the two fishes is the same and their chromosomal structures are similar. These results suggested that we would observe conserved synteny between yellowtail and medaka, and that the syntenic relationship between yellowtail and zebrafish would be rather low. However, they might not be evolutionarily closer than the relationships between yellowtail and medaka. Medakas are a member of the order Beloniformes, which includes freshwater and marine fish, such as Pacific saury and flying fish. Zebrafish are a member of Cypriniformes, which consists exclusively of freshwater fish. Our synteny results reflected the known taxonomic relationships of these fishes. In Teleostei, it is thought that a whole genome duplication and eight subsequent major rearrangements occurred about 314–404 million years ago [39]. Moreover, medaka and zebrafish are thought to have diverged after the eight major rearrangement events, after which medaka and green-spotted pufferfish diverged. The chromosome number in three-spined sticklebacks is the same as that of green-spotted pufferfish. Furthermore, the Oxford grid between yellowtail and green-spotted pufferfish was similar to that between yellowtail and three-spined sticklebacks (Figure 4). However, in the Oxford grid between green-spotted pufferfish and three-spined sticklebacks, the chromosome groups were not paired one-to-one (Additional file 5). Yellowtail SQ11 and 14 correspond to linkage group 1 of three-spined sticklebacks, SQ5 and 18 correspond to linkage group 4, and SQ19 and 22 correspond to linkage group 7, respectively. Then, yellowtail SQ4 and 18 correspond to chromosome 1 of green-spotted pufferfish, SQ6 and 7 correspond to chromosome 2, and SQ11 and 12 correspond to chromosome 3, respectively. These chromosomes in three-spined sticklebacks and green-spotted pufferfish could be paired one-to-two with those of yellowtail. The number of chromosomes in three-spined sticklebacks and green-spotted pufferfish is N=21 and that of yellowtail is N=24. Thus, three-spined sticklebacks and green-spotted pufferfish have three fewer chromosomes than yellowtail; each chromosome is thought to have merged after the divergence from medaka about 191.8 M years ago. By analysis of the whole genome sequence, conserved segments and/or conserved segment orders will be distinguished using the RH map, and will aid studies of the dynamics of chromosome evolution between yellowtail and model fish species.Figure 4

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