Data Supporting the Analysis of Arctic Submesoscale Frontolysis/Frontogenesis and Vertical Transport

Data Supporting the Analysis of Arctic Submesoscale Frontolysis/Frontogenesis and Vertical Transport

This repository contains the code and data for the study of "Meso- and Submesoscale Variability of Arctic Ocean Mixed and Barrier Layers” By Wang et al.Specifically, this repository contains the following items:(1) The code for computing the mixed and barrier layers. Seawater properties are evaluated using the Gibbs-Seawater (GSW) Oceanographic Toolbox (https://www.teos-10.org/software.htm).(2) The code needed for wavenumber spectral analysis. The original package is available at https://phuybers.sites.fas.harvard.edu/Mfiles/index.html(3) Data to produce the figures of the study.

This repository contains the code and data for the study of "Meso- and Submesoscale Variability of Arctic Ocean Mixed and Barrier Layers” By Wang et al.Specifically, this repository contains the following items:(1) The code for computing the mixed and barrier layers. Seawater properties are evaluated using the Gibbs-Seawater (GSW) Oceanographic Toolbox (https://www.teos-10.org/software.htm).(2) The code needed for wavenumber spectral analysis. The original package is available at https://phuybers.sites.fas.harvard.edu/Mfiles/index.html(3) Data to produce the figures of the study.

How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood.
P. xylostella has become the most destructive pest of economically important food crops, including rapeseed, cauliflower and cabbage. This insect is the first species to have evolved resistance to dichlorodiphenyltrichloroethane (DDT) in the 1950s and to Bacillus thuringiensis (Bt) toxins in the 1990s and has developed resistance to all classes of insecticide, making it increasingly difficult to control.
A strain of the diamondback moth (DBM) (Fuzhou-S), P. xylostella, was reared on radish seedlings without exposure to insecticides for 5 years, spanning at least 100 generations. An inbred line was developed by successive single-pair sibling matings. Male pupae were used for genome sequencing.
DNA from the diamondback moth was collected in Fuzhou, China. We sequenced the 0.34 Gb genome to a depth of approximately 131.2 X with short reads from a series of libraries with various insert sizes ( 250bp and 500bp libraries per fosmid clone) on a HiSeq 2000 sequencer.
The assembled scaffolds have an N50 of 0.7 Mb. We identified 18,071 protein-coding genes.

Watermelon (Citrullus lanatus is an important cucurbit crop grown throughout the world. The annual world production of watermelon is about 90 million tons, making it among the top five most consumed fresh fruits (http://faostat.fao.org/).
We sequenced the 0.425 Gb genome to a depth of approximately 108.6 x with short reads from a series of libraries with various insert sizes ( 100-200 bp, 400 bp, 2 kb, 5 kb, 10 kb and 20 kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 46.18 Gb, with the contig and scaffold N50 values of 26.38 kb and 2.38 Mb respectively. We identified 23,440 protein-coding genes.

Green turtles are long-lived and may take up to 59 years to reach sexual maturity. Undertaking tremendous feats of navigation, adults return to the same beach to breed each season.
DNA from the green sea turtle was collected in Hong Kong. We sequenced the 2.24 Gb genome to a depth of approximately 82.3 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb,20kb and 40kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 180.94 Gb, with the contig and scaffold N50 values of 20.4 kb and 3.78 Mb respectively. We identified 19,633 protein-coding genes with an mean length of 1456 bp.Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).

The soft shell turtle can reach a carapace length of 1 ft (0.30 m). It has webbed feet for swimming. They are called "softshell" because their carapace lacks horny scutes (scales). The carapace is leathery and pliable, particularly at the sides. It is commercially farmed in vast numbers for the food trade.
DNA from the soft shell turtle was collected in Japan. We sequenced the 2.21 Gb genome to a depth of approximately 105.6 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb,20kb and 40kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 221.7 Gb, with the contig and scaffold N50 values of 21.9 kb and 3.33 Mb respectively. We identified 19,327 protein-coding genes with an mean length of ~1500bp. Experimental procedures and animal care were conducted in strict accordance with guidelines approved by the RIKEN Animal Experiments Committee (Approval IDs H14-23 and H16-10).

The Plum (Prunus mume), was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae to be sequenced.
DNA from the plum was collected in Tongmai town, Tibet, China. We sequenced the genome to a depth of approximately 101.4 X with short reads from a series of libraries with various insert sizes ( 180bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and 40kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 28.4 Gb with the contig and scaffold N50 values of 31.8 kb and 577.8 kb respectively.

Pear, the third most important temperate fruit species after grape and apple, belongs to the subfamily Pomoideae in the family Rosaceae. The majority of cultivated pears are functional diploids (2n = 34). The Pyrus genus is genetically diverse with thousands of cultivars, but it can be divided into two major groups, Occidental pears (European pears) and Oriental pears (Asiatic pears).
We sequenced the genome to a depth of approximately 107 X with short reads from a series of libraries with various insert sizes ( 170bp, 500bp, 800bp, 2kb, 5kb, 10kb, 20kb and 40kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 57 Gb. We identified 42,812 protein-coding genes.