scholarly journals Chromosome-Level Assembly of the Southern Rock Bream (Oplegnathus fasciatus) Genome Using PacBio and Hi-C Technologies

2021 ◽  
Vol 12 ◽  
Author(s):  
Yulin Bai ◽  
Jie Gong ◽  
Zhixiong Zhou ◽  
Bijun Li ◽  
Ji Zhao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Reference Genome ◽  
Rocky Reef ◽  
Northwest Pacific ◽  
Northwest Pacific Ocean ◽  
Oplegnathus Fasciatus ◽  
Marine Aquaculture ◽  
Total Length ◽  
Rock Bream ◽  
Chromosome Level

The Rock Bream (Oplegnathus fasciatus) is an economically important rocky reef fish of the Northwest Pacific Ocean. In recent years, it has been cultivated as an important edible fish in coastal areas of China. Despite its economic importance, genome-wide adaptions of domesticated O. fasciatus are largely unknown. Here we report a chromosome-level reference genome of female O. fasciatus (from the southern population in the subtropical region) using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 120 contigs with a total length of 732.95 Mb and a contig N50 length of 27.33 Mb. After chromosome-level scaffolding, 24 chromosomes with a total length of 723.22 Mb were constructed. Moreover, a total of 27,015 protein-coding genes and 5,880 ncRNAs were annotated in the reference genome. This reference genome of O. fasciatus will provide an important resource not only for basic ecological and population genetic studies but also for dissect artificial selection mechanisms in marine aquaculture.

scholarly journals The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Baohua Chen ◽  
Zhixiong Zhou ◽  
Qiaozhen Ke ◽  
Yidi Wu ◽  
Huaqiang Bai ◽  
...  
Keyword(s):  
Marine Fish ◽  
Single Molecule ◽  
Large Scale ◽  
Reference Genome ◽  
De Novo ◽  
Larimichthys Crocea ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Total Length ◽  
Chromosome Level

Abstract Larimichthys crocea is an endemic marine fish in East Asia that belongs to Sciaenidae in Perciformes. L. crocea has now been recognized as an “iconic” marine fish species in China because not only is it a popular food fish in China, it is a representative victim of overfishing and still provides high value fish products supported by the modern large-scale mariculture industry. Here, we report a chromosome-level reference genome of L. crocea generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The genome sequences were assembled into 1,591 contigs with a total length of 723.86 Mb and a contig N50 length of 2.83 Mb. After chromosome-level scaffolding, 24 scaffolds were constructed with a total length of 668.67 Mb (92.48% of the total length). Genome annotation identified 23,657 protein-coding genes and 7262 ncRNAs. This highly accurate, chromosome-level reference genome of L. crocea provides an essential genome resource to support the development of genome-scale selective breeding and restocking strategies of L. crocea.

scholarly journals The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Zhixiong Zhou ◽  
Bo Liu ◽  
Baohua Chen ◽  
Yue Shi ◽  
Fei Pu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Reference Genome ◽  
De Novo ◽  
Breeding Programs ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Single Molecule Sequencing ◽  
Total Length ◽  
Genome Scale ◽  
Chromosome Level

Abstract Takifugu bimaculatus is a native teleost species of the southeast coast of China where it has been cultivated as an important edible fish in the last decade. Genetic breeding programs, which have been recently initiated for improving the aquaculture performance of T. bimaculatus, urgently require a high-quality reference genome to facilitate genome selection and related genetic studies. To address this need, we produced a chromosome-level reference genome of T. bimaculatus using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 2,193 contigs with a total length of 404.21 Mb and a contig N50 length of 1.31 Mb. After chromosome-level scaffolding, 22 chromosomes with a total length of 371.68 Mb were constructed. Moreover, a total of 21,117 protein-coding genes and 3,471 ncRNAs were annotated in the reference genome. The highly accurate, chromosome-level reference genome of T. bimaculatus provides an essential genome resource for not only the genome-scale selective breeding of T. bimaculatus but also the exploration of the evolutionary basis of the speciation and local adaptation of the Takifugu genus.

scholarly journals Aerosol iron and aluminum solubility in the northwest Pacific Ocean: Results from the 2002 IOC cruise

2006 ◽  
Vol 7 (4) ◽  
pp. n/a-n/a ◽  
Author(s):  
Clifton S. Buck ◽  
William M. Landing ◽  
Joseph A. Resing ◽  
Geoffrey T. Lebon
Keyword(s):  
Pacific Ocean ◽  
Northwest Pacific ◽  
Northwest Pacific Ocean ◽  
The Northwest Pacific Ocean ◽  
Aluminum Solubility

scholarly journals Design of Wave Glider Optimal Parameters Suitable for the Northwest Pacific Ocean, the North Indian Ocean, and the South China Sea

2021 ◽  
Vol 9 (4) ◽  
pp. 408
Author(s):  
Xi Chen ◽  
Mei Hong ◽  
Shiqi Wu ◽  
Kefeng Liu ◽  
Kefeng Mao
Keyword(s):  
Indian Ocean ◽  
South China Sea ◽  
South China ◽  
North Indian Ocean ◽  
Northwest Pacific ◽  
Northwest Pacific Ocean ◽  
The North ◽  
Wave Element ◽  
Wave Glider ◽  
The Northwest Pacific Ocean

To study the optimal design of Wave Glider parameters in the wave environment of the Northwest Pacific Ocean, the North Indian Ocean, and the South China Sea, the average velocity of a Wave Glider was taken as the evaluation criterion. Wave reanalysis data from ERA5 were used to classify the mean wave height and period into five types by the K-means clustering method. In addition, a dynamic model was used to simulate the influence of umbilical length, airfoil, and maximum limited angle on the velocity of the Wave Glider under the five types of wave element. The force of the wings was simulated using FLUENT as the model input. The simulation results show that (1) 7 m is the most suitable umbilical length; (2) a smaller relative thickness should be selected in perfect conditions; and (3) for the first type of wave element, 15° is the best choice for the maximum limited angle, and 20° is preferred for the second, third, and fourth types, while 25° is preferred for the fifth type.

Protective immunity against Megalocytivirus infection in rock bream ( Oplegnathus fasciatus ) following CpG ODN administration

Vaccine ◽  
2017 ◽  
Vol 35 (30) ◽  
pp. 3691-3699 ◽  
Author(s):  
Myung-Hwa Jung ◽  
Jehee Lee ◽  
M. Ortega-Villaizan ◽  
Luis Perez ◽  
Sung-Ju Jung
Keyword(s):  
Protective Immunity ◽  
Cpg Odn ◽  
Oplegnathus Fasciatus ◽  
Rock Bream

scholarly journals Analysis of Atmospheric and Ionospheric Variations Due to Impacts of Super Typhoon Mangkhut (1822) in the Northwest Pacific Ocean

2021 ◽  
Vol 13 (4) ◽  
pp. 661
Author(s):  
Mohamed Freeshah ◽  
Xiaohong Zhang ◽  
Erman Şentürk ◽  
Muhammad Arqim Adil ◽  
B. G. Mousa ◽  
...  
Keyword(s):  
Wind Speed ◽  
Pacific Ocean ◽  
Tropical Cyclone ◽  
Sea Level ◽  
Northwest Pacific ◽  
Northwest Pacific Ocean ◽  
Sea Level Pressure ◽  
Level Pressure ◽  
Super Typhoon ◽  
The Northwest Pacific Ocean

The Northwest Pacific Ocean (NWP) is one of the most vulnerable regions that has been hit by typhoons. In September 2018, Mangkhut was the 22nd Tropical Cyclone (TC) over the NWP regions (so, the event was numbered as 1822). In this paper, we investigated the highest amplitude ionospheric variations, along with the atmospheric anomalies, such as the sea-level pressure, Mangkhut’s cloud system, and the meridional and zonal wind during the typhoon. Regional Ionosphere Maps (RIMs) were created through the Hong Kong Continuously Operating Reference Stations (HKCORS) and International GNSS Service (IGS) data around the area of Mangkhut typhoon. RIMs were utilized to analyze the ionospheric Total Electron Content (TEC) response over the maximum wind speed points (maximum spots) under the meticulous observations of the solar-terrestrial environment and geomagnetic storm indices. Ionospheric vertical TEC (VTEC) time sequences over the maximum spots are detected by three methods: interquartile range method (IQR), enhanced average difference (EAD), and range of ten days (RTD) during the super typhoon Mangkhut. The research findings indicated significant ionospheric variations over the maximum spots during this powerful tropical cyclone within a few hours before the extreme wind speed. Moreover, the ionosphere showed a positive response where the maximum VTEC amplitude variations coincided with the cyclone rainbands or typhoon edges rather than the center of the storm. The sea-level pressure tends to decrease around the typhoon periphery, and the highest ionospheric VTEC amplitude was observed when the low-pressure cell covers the largest area. The possible mechanism of the ionospheric response is based on strong convective cells that create the gravity waves over tropical cyclones. Moreover, the critical change state in the meridional wind happened on the same day of maximum ionospheric variations on the 256th day of the year (DOY 256). This comprehensive analysis suggests that the meridional winds and their resulting waves may contribute in one way or another to upper atmosphere-ionosphere coupling.

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