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The genome of the sea urchin Strongylocentrotus purpuratus.

ABSTRACT: We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

SUBMITTER: Sea Urchin Genome Sequencing Consortium

PROVIDER: S-EPMC3159423 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature

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The genome of the sea urchin Strongylocentrotus purpuratus.

Sodergren Erica E Weinstock George M GM Davidson Eric H EH Cameron R Andrew RA Gibbs Richard A RA Angerer Robert C RC Angerer Lynne M LM Arnone Maria Ina MI Burgess David R DR Burke Robert D RD Coffman James A JA Dean Michael M Elphick Maurice R MR Ettensohn Charles A CA Foltz Kathy R KR Hamdoun Amro A Hynes Richard O RO Klein William H WH Marzluff William W McClay David R DR Morris Robert L RL Mushegian Arcady A Rast Jonathan P JP Smith L Courtney LC Thorndyke Michael C MC Vacquier Victor D VD Wessel Gary M GM Wray Greg G Zhang Lan L Elsik Christine G CG Ermolaeva Olga O Hlavina Wratko W Hofmann Gretchen G Kitts Paul P Landrum Melissa J MJ Mackey Aaron J AJ Maglott Donna D Panopoulou Georgia G Poustka Albert J AJ Pruitt Kim K Sapojnikov Victor V Song Xingzhi X Souvorov Alexandre A Solovyev Victor V Wei Zheng Z Whittaker Charles A CA Worley Kim K Durbin K James KJ Shen Yufeng Y Fedrigo Olivier O Garfield David D Haygood Ralph R Primus Alexander A Satija Rahul R Severson Tonya T Gonzalez-Garay Manuel L ML Jackson Andrew R AR Milosavljevic Aleksandar A Tong Mark M Killian Christopher E CE Livingston Brian T BT Wilt Fred H FH Adams Nikki N Bellé Robert R Carbonneau Seth S Cheung Rocky R Cormier Patrick P Cosson Bertrand B Croce Jenifer J Fernandez-Guerra Antonio A Genevière Anne-Marie AM Goel Manisha M Kelkar Hemant H Morales Julia J Mulner-Lorillon Odile O Robertson Anthony J AJ Goldstone Jared V JV Cole Bryan B Epel David D Gold Bert B Hahn Mark E ME Howard-Ashby Meredith M Scally Mark M Stegeman John J JJ Allgood Erin L EL Cool Jonah J Judkins Kyle M KM McCafferty Shawn S SS Musante Ashlan M AM Obar Robert A RA Rawson Amanda P AP Rossetti Blair J BJ Gibbons Ian R IR Hoffman Matthew P MP Leone Andrew A Istrail Sorin S Materna Stefan C SC Samanta Manoj P MP Stolc Viktor V Tongprasit Waraporn W Tu Qiang Q Bergeron Karl-Frederik KF Brandhorst Bruce P BP Whittle James J Berney Kevin K Bottjer David J DJ Calestani Cristina C Peterson Kevin K Chow Elly E Yuan Qiu Autumn QA Elhaik Eran E Graur Dan D Reese Justin T JT Bosdet Ian I Heesun Shin S Marra Marco A MA Schein Jacqueline J Anderson Michele K MK Brockton Virginia V Buckley Katherine M KM Cohen Avis H AH Fugmann Sebastian D SD Hibino Taku T Loza-Coll Mariano M Majeske Audrey J AJ Messier Cynthia C Nair Sham V SV Pancer Zeev Z Terwilliger David P DP Agca Cavit C Arboleda Enrique E Chen Nansheng N Churcher Allison M AM Hallböök F F Humphrey Glen W GW Idris Mohammed M MM Kiyama Takae T Liang Shuguang S Mellott Dan D Mu Xiuqian X Murray Greg G Olinski Robert P RP Raible Florian F Rowe Matthew M Taylor John S JS Tessmar-Raible Kristin K Wang D D Wilson Karen H KH Yaguchi Shunsuke S Gaasterland Terry T Galindo Blanca E BE Gunaratne Herath J HJ Juliano Celina C Kinukawa Masashi M Moy Gary W GW Neill Anna T AT Nomura Mamoru M Raisch Michael M Reade Anna A Roux Michelle M MM Song Jia L JL Su Yi-Hsien YH Townley Ian K IK Voronina Ekaterina E Wong Julian L JL Amore Gabriele G Branno Margherita M Brown Euan R ER Cavalieri Vincenzo V Duboc Véronique V Duloquin Louise L Flytzanis Constantin C Gache Christian C Lapraz François F Lepage Thierry T Locascio Annamaria A Martinez Pedro P Matassi Giorgio G Matranga Valeria V Range Ryan R Rizzo Francesca F Röttinger Eric E Beane Wendy W Bradham Cynthia C Byrum Christine C Glenn Tom T Hussain Sofia S Manning Gerard G Miranda Esther E Thomason Rebecca R Walton Katherine K Wikramanayke Athula A Wu Shu-Yu SY Xu Ronghui R Brown C Titus CT Chen Lili L Gray Rachel F RF Lee Pei Yun PY Nam Jongmin J Oliveri Paola P Smith Joel J Muzny Donna D Bell Stephanie S Chacko Joseph J Cree Andrew A Curry Stacey S Davis Clay C Dinh Huyen H Dugan-Rocha Shannon S Fowler Jerry J Gill Rachel R Hamilton Cerrissa C Hernandez Judith J Hines Sandra S Hume Jennifer J Jackson Laronda L Jolivet Angela A Kovar Christie C Lee Sandra S Lewis Lora L Miner George G Morgan Margaret M Nazareth Lynne V LV Okwuonu Geoffrey G Parker David D Pu Ling-Ling LL Thorn Rachel R Wright Rita R

Science (New York, N.Y.) 20061101 5801

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or kno ...[more]

PMID: 17095691

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Project description:BackgroundThe organic matrix of biominerals plays an important role in biomineral formation and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin, which is an important model organism for developmental biology and biomineralization, only few matrix components have been identified and characterized at the protein level. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of possible matrix proteins at the gene level, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy, proteomic analysis.ResultsWe identified 110 proteins as components of sea urchin test and spine organic matrix. Fourty of these proteins occurred in both compartments while others were unique to their respective compartment. More than 95% of the proteins were detected in sea urchin skeletal matrices for the first time. The most abundant protein in both matrices was the previously characterized spicule matrix protein SM50, but at least eight other members of this group, many of them only known as conceptual translation products previously, were identified by mass spectrometric sequence analysis of peptides derived from in vitro matrix degradation. The matrices also contained proteins implicated in biomineralization processes previously by inhibition studies using antibodies or specific enzyme inhibitors, such as matrix metalloproteases and members of the mesenchyme-specific MSP130 family. Other components were carbonic anhydrase, collagens, echinonectin, a alpha2-macroglobulin-like protein and several proteins containing scavenger receptor cysteine-rich domains. A few possible signal transduction pathway components, such as GTP-binding proteins, a semaphorin and a possible tyrosine kinase were also identified.ConclusionThis report presents the most comprehensive list of sea urchin skeletal matrix proteins available at present. The complex mixture of proteins identified in matrices of the sea urchin skeleton may reflect many different aspects of the mineralization process. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Considering the many newly identified matrix proteins, this proteomic study may serve as a road map for the further exploration of biomineralization processes in an important model organism.

Project description:BackgroundThe sea urchin embryo has been an important model organism in developmental biology for more than a century. This is due to its relatively simple construction, translucent appearance, and the possibility to follow the fate of individual cells as development to the pluteus larva proceeds. Because the larvae contain tiny calcitic skeletal elements, the spicules, they are also important model organisms for biomineralization research. Similar to other biominerals the spicule contains an organic matrix, which is thought to play an important role in its formation. However, only few spicule matrix proteins were identified previously.ResultsUsing mass spectrometry-based methods we have identified 231 proteins in the matrix of the S. purpuratus spicule matrix. Approximately two thirds of the identified proteins are either known or predicted to be extracellular proteins or transmembrane proteins with large ectodomains. The ectodomains may have been solubilized by partial proteolysis and subsequently integrated into the growing spicule. The most abundant protein of the spicule matrix is SM50. SM50-related proteins, SM30-related proteins, MSP130 and related proteins, matrix metalloproteases and carbonic anhydrase are among the most abundant components.ConclusionsThe spicule matrix is a relatively complex mixture of proteins not only containing matrix-specific proteins with a function in matrix assembly or mineralization, but also: 1) proteins possibly important for the formation of the continuous membrane delineating the mineralization space; 2) proteins for secretory processes delivering proteinaceous or non-proteinaceous precursors; 3) or proteins reflecting signaling events at the cell/matrix interface. Comparison of the proteomes of different skeletal matrices allows prediction of proteins of general importance for mineralization in sea urchins, such as SM50, SM30-E, SM29 or MSP130. The comparisons also help point out putative tissue-specific proteins, such as tooth phosphodontin or specific spicule matrix metalloproteases of the MMP18/19 group. Furthermore, the direct sequence analysis of peptides by MS/MS validates many predicted genes and confirms the existence of the corresponding proteins.

Project description:Some sea urchins, including the purple sea urchin Strongylocentrotus purpuratus, have been successfully used in aquaculture, but their slow growth and late reproduction are challenging to overcome when developing efficient aquaculture production techniques. S. purpuratus develops via an indirect life history that is characterized by a drastic settlement process at the end of a larval period that lasts for several weeks. During this transition, the bilateral larva is transformed into a pentaradial juvenile, which will start feeding and growing in the benthic habitat. Due to predation and other ecological factors, settlement is typically associated with high mortality rates in juvenile populations. Additionally, juveniles require several days to develop a functional mouth and digestive system. During this perimetamorphic period, juveniles use up larval resources until they are capable to digest adult food. Mechanisms underlying the onset of juvenile feeding and metabolism have implications for the recruitment of natural populations as well as aquaculture and are relatively poorly understood in S. purpuratus. The insulin/insulin-like growth factor signalling (IIS)/Target of Rapamycin (TOR) pathway (IIS/TOR) is well conserved among animal phyla and regulates physiological and developmental functions, such as growth, reproduction, aging and nutritional status. We analyzed the expression of FoxO, TOR, and ILPs in post-settlement juveniles in conjunction with their early growth trajectories. We also tested how pre-settlement starvation affected post-settlement expression of IIS. We found that FoxO provides a useful molecular marker in early juveniles as its expression is strongly correlated with juvenile growth. We also found that pre-settlement starvation affects juvenile growth trajectories as well as IIS. Our findings provide preliminary insights into the mechanisms underlying post-settlement growth and metabolism in S. purpuratus. They also have important implications for sea urchin aquaculture, as they show that pre-settlement nutrient environment significantly affects both early growth trajectories and gene expression. This information can be used to develop new biomarkers for juvenile health in sea urchin population ecology and aquaculture aquaculture.

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The genome of the sea urchin Strongylocentrotus purpuratus.

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The genome of the sea urchin Strongylocentrotus purpuratus.

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