| Parhyale hawaiensis | |
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| Adult male | |
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| Feeding on a slice of carrot | |
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| Species: | P. hawaiensis |
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| Parhyale hawaiensis Dana, 1853 | |
Parhyale hawaiensis is an amphipod crustacean species that is used in developmental and genetic analyses. It is categorized as an emerging model organism as the main biological techniques necessary for the study of an organism have been established.
P. hawaiensis is a detritovore that has a circumtropical, worldwide, intertidal, and shallow-water marine distribution, [1] [2] and it may occur as a species complex. [3] It has been reported to occur in large populations (more than 3,000 per square metre) on decaying mangrove leaf material in environments subjected to rapid changes in salinity. [4] The ability to tolerate rapid temperature and osmotic changes allows this species to thrive under typical laboratory conditions. It is a robust species and is being considered for aquaculture. [5]
Females produce embryos every 2 weeks once they reach sexual maturity. Embryogenesis is relatively short, lasting about 10 days at 26 °C (79 °F). Females normally brood the embryos in a ventral brood pouch. Close examination of the embryonic development of P. hawaiensis has produced the most detailed staging system for any crustacean. [7] Complete embryogenesis has been divided into 30 discrete stages, which are readily identifiable in living animals or by means of common molecular markers in fixed specimens. Hatchlings possess a complete complement of segments and appendages which are morphologically similar to those of adult animals.
P. hawaiensis is used in genetic research because eggs and embryos are easily manipulated. Embryos can be rapidly and easily removed from the brood pouch and maintained in seawater. Eggs can be collected and hatched individually, and the mature animals can subsequently be used in pairwise sister-brother or mother-son matings to generate inbred lines.
Fertilized eggs are sufficiently large to perform microinjections [8] and blastomere isolations [9] with relative ease. Developing P. hawaiensis embryos are clear, allowing for both detailed microscopic analyses in situ and the use of fluorescently tagged tracer molecules in live embryos. Early cleavage is holoblastic (total), allowing the fates of individual early cells to be explored through experimental manipulation. [7] [8] [9]
A transcriptome of P. hawaiensis was initially generated using the pyrosequencing technique. [10] This resource is freely available for download. Subsequent, more complete transcriptomes were generated using Illumina sequencing. The transcriptome data can be used for the creation of in situ probes and other experimental tools. The genome is available from NCBI
The genome of P. hawaiensis is available and was sequenced using Illumina short read sequencing. [11] This first version (V3.0) of the genome was recently superseded by a more contiguous version generated by Chicago sequencing through the Dovetail platform. The new version Phaw_5.0 is available on NCBI.
A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine). This is then reported as a text string, called a read. Some DNA sequencers can be also considered optical instruments as they analyze light signals originating from fluorochromes attached to nucleotides.
Amphipoda is an order of malacostracan crustaceans with no carapace and generally with laterally compressed bodies. Amphipods range in size from 1 to 340 millimetres and are mostly detritivores or scavengers. There are more than 9,900 amphipod species so far described. They are mostly marine animals, but are found in almost all aquatic environments. Some 1,900 species live in fresh water, and the order also includes the terrestrial sandhoppers such as Talitrus saltator and Arcitalitrus sylvaticus.
BGI Group, formerly Beijing Genomics Institute, is a Chinese genomics company with headquarters in Yantian, Shenzhen. The company was originally formed in 1999 as a genetics research center to participate in the Human Genome Project. It also sequences the genomes of other animals, plants and microorganisms.
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term transcriptome is a portmanteau of the words transcript and genome; it is associated with the process of transcript production during the biological process of transcription.
Gammarus roeselii is a species of freshwater amphipod native to Europe.
SOLiD (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation DNA sequencing technology developed by Life Technologies and has been commercially available since 2006. This next generation technology generates 108 - 109 small sequence reads at one time. It uses 2 base encoding to decode the raw data generated by the sequencing platform into sequence data.
Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.
RNA-Seq is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
The 1000 Plant Transcriptomes Initiative (1KP) was an international research effort to establish the most detailed catalogue of genetic variation in plants. It was announced in 2008 and headed by Gane Ka-Shu Wong and Michael Deyholos of the University of Alberta. The project successfully sequenced the transcriptomes of 1000 different plant species by 2014; its final capstone products were published in 2019.
Vasa is an RNA binding protein with an ATP-dependent RNA helicase that is a member of the DEAD box family of proteins. The vasa gene is essential for germ cell development and was first identified in Drosophila melanogaster, but has since been found to be conserved in a variety of vertebrates and invertebrates including humans. The Vasa protein is found primarily in germ cells in embryos and adults, where it is involved in germ cell determination and function, as well as in multipotent stem cells, where its exact function is unknown.
Hyalella azteca is a widespread and abundant species complex of amphipod crustacean in North America. It reaches 3–8 mm (0.12–0.31 in) long, and is found in a range of fresh and brackish waters. It feeds on algae and diatoms and is a major food of waterfowl.
De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome.
Illumina dye sequencing is a technique used to determine the series of base pairs in DNA, also known as DNA sequencing. The reversible terminated chemistry concept was invented by Bruno Canard and Simon Sarfati at the Pasteur Institute in Paris. It was developed by Shankar Balasubramanian and David Klenerman of Cambridge University, who subsequently founded Solexa, a company later acquired by Illumina. This sequencing method is based on reversible dye-terminators that enable the identification of single nucleotides as they are washed over DNA strands. It can also be used for whole-genome and region sequencing, transcriptome analysis, metagenomics, small RNA discovery, methylation profiling, and genome-wide protein-nucleic acid interaction analysis.
Embryo quality is the ability of an embryo to perform successfully in terms of conferring a high pregnancy rate and/or resulting in a healthy person. Embryo profiling is the estimation of embryo quality by qualification and/or quantification of various parameters. Estimations of embryo quality guides the choice in embryo selection in in vitro fertilization.
Single-cell sequencing examines the nucleic acid sequence information from individual cells with optimized next-generation sequencing technologies, providing a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment. For example, in cancer, sequencing the DNA of individual cells can give information about mutations carried by small populations of cells. In development, sequencing the RNAs expressed by individual cells can give insight into the existence and behavior of different cell types. In microbial systems, a population of the same species can appear genetically clonal. Still, single-cell sequencing of RNA or epigenetic modifications can reveal cell-to-cell variability that may help populations rapidly adapt to survive in changing environments.
In genetics, coverage is one of several measures of the depth or completeness of DNA sequencing, and is more specifically expressed in any of the following terms:
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated.
Pseudamphithoides incurvaria is a species of amphipod crustacean in the family Ampithoidae. It is native to shallow water in the tropical western Atlantic Ocean where it creates a home for itself from fragments of the algae on which it feeds. This seaweed contains certain chemicals that are distasteful and protect it from predatory fish.
Ampithoidae is a family of amphipod crustaceans. The family has a worldwide distribution as algal dwellers. They commonly create tube-shaped nests on their host plants or algae which serve as both shelter and food. Young ampithoids develop from eggs to a larval stage within their mother's brood-pouch, formed by the appendages of her abdomen.
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