Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.

Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.tuna genome | visual system | animal opsin

We used reproductive success, rather than abundance or catch, to identify regimes because reproductive success responds faster to environmental changes. Peak abundance of Japanese sardine during 1951-1995 was about 1000 times higher than minimum abundance. A regime shift occurred in the early 1970s when carrying capacity (measured using spawner-recruit models) increased by about 75 times. We hypothesize that this was due to large-scale changes in the Kuroshio and Oyashio Current systems. Long-term environmental variation (regimes), interannual variability in recruitment success, and density-dependent recruitment and growth rates affected dynamics of Japanese sardine. We hypothesize that density-dependent effects on recruitment of Sardinops spp. are common but usually obscured in short data sets by environmental variability and measurement error. Virtual population analysis and forward-simulation modeling approaches gave similar biomass and recruitment estimates. The relationship between sardine biomass and catch per unit search time was nonlinear. Mass-at-age and biomass were correlated, and it may be possible to use mass-at-age as an abundance index. Current abundance is low, and we believe that the environment has shifted to a regime that is unfavorable for Japanese sardine.

We used fishery and survey data to calculate annual surplus production (ASP) and instantaneous surplus production rates (ISPR) for eight anchovy and nine sardine stocks. In addition, we calculated ASP per unit spawning area for six anchovy and six sardine stocks. Median ASP was highest for stocks with highest median biomass (mostly anchovies), and ASP was typically about 16% of stock biomass. ASP was often negative, more frequently for anchovies (36% of years) than for sardines (17% of years). ISPR was less variable for sardines and autocorrelated for longer-lived stocks (mostly sardines). Strong biomass increases tended to be preceded by short, abrupt increases in ISPR, and declines were pronounced when catches exceeded ASP for 5 years or more. The longest "runs" of positive and negative production were 21 and 4 years for sardine off Japan, 10 and 3 years for sardine off California, 8 and 2 years for anchovy off Peru, and 4 and 3 years for anchovy off California. ISPR is more sensitive to environmental changes than catch, biomass, or ASP and appear to be better for identifying environmentally induced regime shifts. Long time series show evidence of density-dependent effects on ASP in anchovies and sardines, but environmentally induced variation appears to dominate.Résumé : Des statistiques de pêche et des données d'inventaire nous ont servi à calculer la production excédentaire annuelle (ASP) et les taux instantanés de production excédentaire (ISPR) chez huit stocks d'anchois et neuf stocks de sardines. De plus, nous avons calculé l'ASP par unité de surface de frayère chez six stocks d'anchois et six stocks de sardines. L'ASP moyen est maximal chez les stocks qui possèdent la plus grande biomasse médiane (surtout des anchois) et correspond normalement à environ 16% de la biomasse du stock. L'ASP est souvent négative, plus souvent chez les anchois (36% des années) que chez les sardines (17% des années). L'ISPR est moins variable chez les sardines et est autocorrelé chez les stocks à longévité plus grande (surtout des sardines). Les augmentations importantes de biomasse sont normalement précédées d'une croissance abrupte de l'ISPR; lorsque les prises dépassent l'ASP pour

We used fishery and survey data to calculate annual surplus production (ASP) and instantaneous surplus production rates (ISPR) for eight anchovy and nine sardine stocks. In addition, we calculated ASP per unit spawning area for six anchovy and six sardine stocks. Median ASP was highest for stocks with highest median biomass (mostly anchovies), and ASP was typically about 16% of stock biomass. ASP was often negative, more frequently for anchovies (36% of years) than for sardines (17% of years). ISPR was less variable for sardines and autocorrelated for longer-lived stocks (mostly sardines). Strong biomass increases tended to be preceded by short, abrupt increases in ISPR, and declines were pronounced when catches exceeded ASP for 5 years or more. The longest "runs" of positive and negative production were 21 and 4 years for sardine off Japan, 10 and 3 years for sardine off California, 8 and 2 years for anchovy off Peru, and 4 and 3 years for anchovy off California. ISPR is more sensitive to environmental changes than catch, biomass, or ASP and appear to be better for identifying environmentally induced regime shifts. Long time series show evidence of density-dependent effects on ASP in anchovies and sardines, but environmentally induced variation appears to dominate.