scholarly journals Chromosomal-level genome assembly of the painted sea urchin Lytechinus pictus, a genetically enabled model system for cell biology and embryonic development

2021 ◽  
Author(s):  
Jacob F Warner ◽  
James W Lord ◽  
Samantha A Schreiter ◽  
Katherine T Nesbit ◽  
Amro Hamdoun ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Genome Assembly ◽  
Related Species ◽  
Cell Biology ◽  
Laboratory Culture ◽  
Model System ◽  
Lytechinus Pictus ◽  
Long Read ◽  
Gene Models ◽  
Comparative Functional Genomics

Abstract The painted urchin Lytechinus pictus is a sea urchin in the family Toxopneustidae and one of several sea urchin species that are routinely used as an experimental research organism. Recently, L. pictus has emerged as a tractable model system for establishing transgenic sea urchin lines due to its amenability to long term laboratory culture. We present the first published genome of L. pictus. This chromosomal-level assembly was generated using Illumina sequencing in conjunction with Oxford Nanopore Technologies long read sequencing and HiC chromatin conformation capture sequencing. The 998.9 Mb assembly exhibits high contiguity and has a scaffold length N50 of 46.0 Mb with 97% of the sequence assembled into 19 chromosomal-length scaffolds. These 19 scaffolds exhibit a high degree of synteny compared to the 19 chromosomes of a related species Lytechinus variegatus. Ab initio and transcript evidence gene modeling, combined with sequence homology, identified 28,631 gene models that capture 92% of BUSCO orthologs. This annotation strategy was validated by manual curation of gene models for the ABC transporter superfamily, which confirmed the completeness and accuracy of the annotations. Thus, this genome assembly, in conjunction with recent high contiguity assemblies of related species, positions Lytechinus pictus as an exceptional model system for comparative functional genomics and it will be a key resource for the developmental, toxicological, and ecological biology scientific communities.

Terminal alpha-d-mannosides are critical during sea urchin gastrulation

Zygote ◽  
2016 ◽  
Vol 24 (5) ◽  
pp. 775-782 ◽  
Author(s):  
Heghush Aleksanyan ◽  
Jing Liang ◽  
Stan Metzenberg ◽  
Steven B. Oppenheimer
Keyword(s):  
Sea Urchin ◽  
Model System ◽  
National Institutes Of Health ◽  
Enzyme Treatment ◽  
Lytechinus Pictus ◽  
Sea Urchin Embryo ◽  
Health And Disease ◽  
High Mannose ◽  
Terminal Mannose

SummaryThe sea urchin embryo is a United States National Institutes of Health (NIH) designated model system to study mechanisms that may be involved in human health and disease. In order to examine the importance of high-mannose glycans and polysaccharides in gastrulation, Lytechinus pictus embryos were incubated with Jack bean α-mannosidase (EC 3.2.1.24), an enzyme that cleaves terminal mannose residues that have α1–2-, α1–3-, or α1–6-glycosidic linkages. The enzyme treatment caused a variety of morphological deformations in living embryos, even with α-mannosidase activities as low as 0.06 U/ml. Additionally, formaldehyde-fixed, 48-hour-old L. pictus embryos were microdissected and it was demonstrated that the adhesion of the tip of the archenteron to the roof of the blastocoel in vitro is abrogated by treatment with α-mannosidase. These results suggest that terminal mannose residues are involved in the adhesion between the archenteron and blastocoel roof, perhaps through a lectin-like activity that is not sensitive to fixation.

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

scholarly journals SYNTHESIS AND STORAGE OF MICROTUBULE PROTEINS BY SEA URCHIN EMBRYOS

1971 ◽  
Vol 50 (2) ◽  
pp. 516-528 ◽  
Author(s):  
Rudolf A. Raff ◽  
Gerald Greenhouse ◽  
Kenneth W. Gross ◽  
Paul R. Gross
Keyword(s):  
Amino Acids ◽  
Sea Urchin ◽  
Messenger Rna ◽  
Binding Activity ◽  
Total Soluble Protein ◽  
Cell Stage ◽  
Lytechinus Pictus ◽  
Sea Urchin Embryos ◽  
Tritiated Amino Acids ◽  
Vinblastine Sulfate

Studies employing colchicine binding, precipitation with vinblastine sulfate, and acrylamide gel electrophoresis confirm earlier proposals that Arbacia punctulata and Lytechinus pictus eggs and embryos contain a store of microtubule proteins. Treatment of 150,000 g supernatants from sea urchin homogenates with vinblastine sulfate precipitates about 5% of the total soluble protein, and 75% of the colchicine-binding activity. Electrophoretic examination of the precipitate reveals two very prominent bands. These have migration rates identical to those of the A and B microtubule proteins of cilia. These proteins can be made radioactive at the 16 cell stage and at hatching by pulse labeling with tritiated amino acids. By labeling for 1 hr with leucine-3H in early cleavage, then culturing embryos in the presence of unlabeled leucine, removal of newly synthesized microtubule proteins from the soluble pool can be demonstrated. Incorporation of labeled amino acids into microtubule proteins is not affected by culturing embryos continuously in 20 µg/ml of actinomycin D. Microtubule proteins appear, therefore, to be synthesized on "maternal" messenger RNA. This provides the first protein encoded by stored or "masked" mRNA in sea urchin embryos to be identified.

scholarly journals Exogenous hyalin and sea urchin gastrulation, Part II: hyalin, an interspecies cell adhesion molecule

Zygote ◽  
2008 ◽  
Vol 16 (1) ◽  
pp. 73-78 ◽  
Author(s):  
M. Alvarez ◽  
J. Nnoli ◽  
E.J. Carroll ◽  
V. Hutchins-Carroll ◽  
Z. Razinia ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Cell Adhesion Molecule ◽  
Cellular Interaction ◽  
Adhesive Interaction ◽  
Lytechinus Pictus ◽  
Developmental Effects ◽  
Sea Urchin Embryo ◽  
Repeat Domain ◽  
Precise Quantification ◽  
Main Component

SummaryThe 330 kDa fibrillar glycoprotein hyalin is a well known component of the sea urchin embryo extracellular hyaline layer. Only recently, the main component of hyalin, the hyalin repeat domain, has been identified in organisms as widely divergent as bacteria and humans using the GenBank database and therefore its possible function has garnered a great deal of interest. In the sea urchin, hyalin serves as an adhesive substrate in the developing embryo and we have recently shown that exogenously added purified hyalin from Strongylocentrotus purpuratus embryos blocks a model cellular interaction in these embryos, archenteron elongation/attachment to the blastocoel roof. It is important to demonstrate the generality of this result by observing if hyalin from one species of sea urchin blocks archenteron elongation/attachment in another species. Here we show in three repeated experiments, with 30 replicate samples for each condition, that the same concentration of S. purpuratus hyalin (57 μg/ml) that blocked the interaction in living S. purpuratus embryos blocked the same interaction in living Lytechinus pictus embryos. These results correspond with the known crossreactivity of antibody against S. purpuratus hyalin with L. pictus hyalin. We propose that hyalin–hyalin receptor binding may mediate this adhesive interaction. The use of a microplate assay that allows precise quantification of developmental effects should help facilitate identification of the function of hyalin in organisms as divergent as bacteria and humans.

Metabolic importance of Na+/K+-ATPase activity during sea urchin development.

1997 ◽  
Vol 200 (22) ◽  
pp. 2881-2892 ◽  
Author(s):  
P Leong ◽  
D Manahan
Keyword(s):  
Enzyme Activity ◽  
Atpase Activity ◽  
Sea Urchin ◽  
Sodium Pump ◽  
Sea Water ◽  
Strongylocentrotus Purpuratus ◽  
Lytechinus Pictus ◽  
Stimulation Of

Early stages of animal development have high mass-specific rates of metabolism. The biochemical processes that establish metabolic rate and how these processes change during development are not understood. In this study, changes in Na+/K+-ATPase activity (the sodium pump) and rate of oxygen consumption were measured during embryonic and early larval development for two species of sea urchin, Strongylocentrotus purpuratus and Lytechinus pictus. Total (in vitro) Na+/K+-ATPase activity increased during development and could potentially account for up to 77 % of larval oxygen consumption in Strongylocentrotus purpuratus (pluteus stage) and 80 % in Lytechinus pictus (prism stage). The critical issue was addressed of what percentage of total enzyme activity is physiologically active in living embryos and larvae and thus what percentage of metabolism is established by the activity of the sodium pump during development. Early developmental stages of sea urchins are ideal for understanding the in vivo metabolic importance of Na+/K+-ATPase because of their small size and high permeability to radioactive tracers (86Rb+) added to sea water. A comparison of total and in vivo Na+/K+-ATPase activities revealed that approximately half of the total activity was utilized in vivo. The remainder represented a functionally active reserve that was subject to regulation, as verified by stimulation of in vivo Na+/K+-ATPase activity in the presence of the ionophore monensin. In the presence of monensin, in vivo Na+/K+-ATPase activities in embryos of S. purpuratus increased to 94 % of the maximum enzyme activity measured in vitro. Stimulation of in vivo Na+/K+-ATPase activity was also observed in the presence of dissolved alanine, presumably due to the requirement to remove the additional intracellular Na+ that was cotransported with alanine from sea water. The metabolic cost of maintaining the ionic balance was found to be high, with this process alone accounting for 40 % of the metabolic rate of sea urchin larvae (based on the measured fraction of total Na+/K+-ATPase that is physiologically active in larvae of S. purpuratus). Ontogenetic changes in pump activity and environmentally induced regulation of reserve Na+/K+-ATPase activity are important factors that determine a major proportion of the metabolic costs of sea urchin development.

Autonomous and non-autonomous differentiation of ectoderm in different sea urchin species

Development ◽  
1995 ◽  
Vol 121 (5) ◽  
pp. 1497-1505 ◽  
Author(s):  
A.H. Wikramanayake ◽  
B.P. Brandhorst ◽  
W.H. Klein
Keyword(s):  
Sea Urchin ◽  
Strongylocentrotus Purpuratus ◽  
Protein A ◽  
Cellular Interactions ◽  
V Protein ◽  
Lytechinus Pictus ◽  
Sea Urchin Embryo ◽  
Oral Ectoderm ◽  
Temporal And Spatial

During early embryogenesis, the highly regulative sea urchin embryo relies extensively on cell-cell interactions for cellular specification. Here, the role of cellular interactions in the temporal and spatial expression of markers for oral and aboral ectoderm in Strongylocentrotus purpuratus and Lytechinus pictus was investigated. When pairs of mesomeres or animal caps, which are fated to give rise to ectoderm, were isolated and cultured they developed into ciliated embryoids that were morphologically polarized. In animal explants from S. purpuratus, the aboral ectoderm-specific Spec1 gene was activated at the same time as in control embryos and at relatively high levels. The Spec1 protein was restricted to the squamous epithelial cells in the embryoids suggesting that an oral-aboral axis formed and aboral ectoderm differentiation occurred correctly. However, the Ecto V protein, a marker for oral ectoderm differentiation, was detected throughout the embryoid and no stomodeum or ciliary band formed. These results indicated that animal explants from S. purpuratus were autonomous in their ability to form an oral-aboral axis and to differentiate aboral ectoderm, but other aspects of ectoderm differentiation require interaction with vegetal blastomeres. In contrast to S. purpuratus, aboral ectoderm-specific genes were not expressed in animal explants from L. pictus even though the resulting embryoids were morphologically very similar to those of S. purpuratus. Recombination of the explants with vegetal blastomeres or exposure to the vegetalizing agent LiCl restored activity of aboral ectoderm-specific genes, suggesting the requirement of a vegetal induction for differentiation of aboral ectoderm cells.(ABSTRACT TRUNCATED AT 250 WORDS)

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