Genome Assemblies - Revision history

Ctelmer: /* Eucidaris tribuloides */

2024-04-10T18:17:20Z

Eucidaris tribuloides

← Older revision		Revision as of 18:17, 10 April 2024
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	The genome assembly is available on NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA63057 PRJNA63057].		The genome assembly is available on NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA63057 PRJNA63057].



	=='''''Allocentrotus fragilis'''''==		=='''''Allocentrotus fragilis'''''==

Ctelmer at 18:16, 10 April 2024

2024-04-10T18:16:03Z

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 =Future Species=
 =='''''Apostichopus parvimensis'''''==
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 The genome assembly is available on NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA63057 PRJNA63057].
 =='''''Allocentrotus fragilis'''''==

Ctelmer: /* Mesocentrotus franciscanus */

2024-04-10T18:10:38Z

Mesocentrotus franciscanus

← Older revision		Revision as of 18:10, 10 April 2024
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	=='''''Mesocentrotus franciscanus'''''==		=='''''Mesocentrotus franciscanus'''''==
	Red sea urchins, Mesocentrotus franciscanus (A. Agassiz, 1863) range from Alaska to Baja California at depths from just below the low tide line to 90 m. It prefers rocky shores that are sheltered from strong wave action. Although the red urchin has long been called ''Strongylocentrotus franciscanu''s, recent molecular phylogenies support the name to ''Mesocentrotus franciscanus'' (A. Agassiz, 1863) (Kober and Bernardi BMC Evolutionary Biology 2013, 13:88).		Red sea urchins, Mesocentrotus franciscanus (A. Agassiz, 1863) range from Alaska to Baja California at depths from just below the low tide line to 90 m. It prefers rocky shores that are sheltered from strong wave action. Although the red urchin has long been called ''Strongylocentrotus franciscanu''s, recent molecular phylogenies support the name to ''Mesocentrotus franciscanus'' (A. Agassiz, 1863) (Kober and Bernardi BMC Evolutionary Biology 2013, 13:88).

			The red sea urchin (''Mesocentrotus franciscanus'') is one of the earth’s longest living animals, reported to live more than 100 years with indeterminate growth, life-long reproduction, and no increase in mortality rate with age. To understand the genetic underpinnings of longevity and negligible aging, we constructed a chromosome-level assembly of the red sea urchin genome and compared it to that of short-lived sea urchin species. Genome-wide syntenic alignments identified chromosome rearrangements that distinguish short- and long-lived species. Expanded gene families in long-lived species play roles in innate immunity, sensory nervous system, and genome stability. An integrated network of genes under positive selection in the red sea urchin were involved in genomic regulation, mRNA fidelity, protein homeostasis, and mitochondrial function. Results implicate known longevity genes in sea urchin longevity, but also revealed novel molecular signatures that promote long-term maintenance of tissue homeostasis, disease resistance, and negligible aging [https://www.echinobase.org/echinobase/literature/article.do?method=display&articleId=53014 (Polinski et al. 2024)].

			Raw sequencing data and the genome assembly are deposited at NCBI with accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA914702 PRJNA914702]. Raw data include [https://www.ncbi.nlm.nih.gov/sra/SRX18805006 Illumina] paired end sequencing data, Oxford [https://www.ncbi.nlm.nih.gov/sra/SRX18805008 Nanopore] long-read data, and [https://www.ncbi.nlm.nih.gov/sra/SRX18805007 Hi-C] proximity ligation sequencing data in the Sequencing Read Archive (SRA): SRX18805006, SRX18805008, and SRX18805007. Additional data, including genome annotation fasta and GFF files, can be found on [https://doi.org/10.5281/zenodo.10038207 Zenodo].

			All code used to produce the assembly, analyses, results, and visualizations are available on [https://github.com/jmpolinski/Red-Sea-Urchin-Genome GitHub].

	A low coverage sequence of this species is available at NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA20313 PRJNA20313].		A low coverage sequence of this species is available at NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA20313 PRJNA20313].

Ctelmer at 17:55, 10 April 2024

2024-04-10T17:55:04Z

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 =Future Species=
 =='''''Apostichopus parvimensis'''''==
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 [[File:Lv_three_assemblies_vs_bac.png]]

Ctelmer: /* Lytechinus pictus */

2023-02-15T18:14:37Z

Lytechinus pictus

← Older revision		Revision as of 18:14, 15 February 2023
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	''L. pictus'' live between 7-9 years, and reach full size at approximately 4 cm in diameter in the lab. In the wild the average lifespan is estimated at approximately 3 years and average size is around 2 cm in diameter (Ebert, 1975). Their eggs are ~110 microns in diameter and are less pigmented than the eggs of ''S. purpuratus''. This species is best cultured between 20-24C and can reach competency to metamorphosis as quickly as 3 weeks post-fertilization. Newly settled animals are typically >1mm in diameter. Sexual maturity is reached as early as 4 months old, though more robust gamete production is typically reached at 6 months.		''L. pictus'' live between 7-9 years, and reach full size at approximately 4 cm in diameter in the lab. In the wild the average lifespan is estimated at approximately 3 years and average size is around 2 cm in diameter (Ebert, 1975). Their eggs are ~110 microns in diameter and are less pigmented than the eggs of ''S. purpuratus''. This species is best cultured between 20-24C and can reach competency to metamorphosis as quickly as 3 weeks post-fertilization. Newly settled animals are typically >1mm in diameter. Sexual maturity is reached as early as 4 months old, though more robust gamete production is typically reached at 6 months.

	The latest assembly is on NCBI with accession[https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA647794 PRJNA647794].		The latest assembly is on NCBI with accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA647794 PRJNA647794].

	=='''''Apostichopus parvimensis'''''==		=='''''Apostichopus parvimensis'''''==

Ctelmer at 18:14, 15 February 2023

2023-02-15T18:14:21Z

Show changes

Ctelmer: /* Future Species */

2023-02-03T20:17:28Z

Future Species

← Older revision		Revision as of 20:17, 3 February 2023
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	=Future Species=		=Future Species=
			=='''''Lytechinus pictus'''''==
			The painted white urchin, ''Lytechinus pictus'', is native to the East Pacific Ocean, with a geographic range spanning from Central California to Cedros Island, Mexico (Zigler and Lessios, 2004). ''L. pictus'' have been reported to live on sandy-bottoms and in sea grass bays, as well as in and around kelp beds at depths between 2-300m (Lawrence, 2006). It is the same species as ''Lytechinus anamesus'' (Cameron, 1984) (Zigler and Lessios, 2004).

			''L. pictus'' live between 7-9 years, and reach full size at approximately 4 cm in diameter in the lab. In the wild the average lifespan is estimated at approximately 3 years and average size is around 2 cm in diameter (Ebert, 1975). Their eggs are ~110 microns in diameter and are less pigmented than the eggs of ''S. purpuratus''. This species is best cultured between 20-24C and can reach competency to metamorphosis as quickly as 3 weeks post-fertilization. Newly settled animals are typically >1mm in diameter. Sexual maturity is reached as early as 4 months old, though more robust gamete production is typically reached at 6 months.

			The latest assembly is on NCBI with accession[https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA647794 PRJNA647794].

	=='''''Apostichopus parvimensis'''''==		=='''''Apostichopus parvimensis'''''==

Ctelmer: /* Future Species */

2023-02-03T19:55:12Z

Future Species

← Older revision		Revision as of 19:55, 3 February 2023
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	The genome assembly is available on NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA63057 PRJNA63057].		The genome assembly is available on NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA63057 PRJNA63057].

	==='''''Mesocentrotus franciscanus'''''===		=='''''Mesocentrotus franciscanus'''''==
	Red sea urchins, Mesocentrotus franciscanus (A. Agassiz, 1863) range from Alaska to Baja California at depths from just below the low tide line to 90 m. It prefers rocky shores that are sheltered from strong wave action. Although the red urchin has long been called ''Strongylocentrotus franciscanu''s, recent molecular phylogenies support the name to ''Mesocentrotus franciscanus'' (A. Agassiz, 1863) (Kober and Bernardi BMC Evolutionary Biology 2013, 13:88).		Red sea urchins, Mesocentrotus franciscanus (A. Agassiz, 1863) range from Alaska to Baja California at depths from just below the low tide line to 90 m. It prefers rocky shores that are sheltered from strong wave action. Although the red urchin has long been called ''Strongylocentrotus franciscanu''s, recent molecular phylogenies support the name to ''Mesocentrotus franciscanus'' (A. Agassiz, 1863) (Kober and Bernardi BMC Evolutionary Biology 2013, 13:88).

	A low coverage sequence of this species is available at NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA20313 PRJNA20313].		A low coverage sequence of this species is available at NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA20313 PRJNA20313].

	==='''''Allocentrotus fragilis'''''===		=='''''Allocentrotus fragilis'''''==
	''Allocentrotus fragilis'', the fragile sea urchin, lives on the sea floor at depths from 300 to 1600 ft. While ''Allocentrotus fragilis'' has long been the accepted name used for this species in the family Strongylocentrotidae, a more appropriate name might be ''Strongylocentrotus fragilis'' (Jackson, 1912). Indeed, the molecular evidence fully supports this change of name (Kober and Bernardi BMC Evolutionary Biology 2013, 13:88).		''Allocentrotus fragilis'', the fragile sea urchin, lives on the sea floor at depths from 300 to 1600 ft. While ''Allocentrotus fragilis'' has long been the accepted name used for this species in the family Strongylocentrotidae, a more appropriate name might be ''Strongylocentrotus fragilis'' (Jackson, 1912). Indeed, the molecular evidence fully supports this change of name (Kober and Bernardi BMC Evolutionary Biology 2013, 13:88).

	A low coverage sequence of this species is available at NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA20317 PRJNA20317].		A low coverage sequence of this species is available at NCBI at accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA20317 PRJNA20317].

	==='''''Amphiura filiformis'''''===		=='''''Amphiura filiformis'''''==
	''Amphiura filiformis'' (O. F. Muller, 1776) is a brittle star found on the seabed of the European coasts from Greece to Norway and Sweden including the Baltic Sea . It is an important member of soft bottom communities where it digs a shallow burrow and feeds on plankton. It serves as food for crayfish and finfish. Stemming from its remarkable ability to regenerate arms in a matter of weeks it has become an emerging model for regeneration and stem cell biology in biomedical research. Research targets include: 1) The cellular and molecular mechanisms underlying regeneration with links to neuroscience, stem cell biology and neuropeptide structure and function in the absence of a centralised nervous system. 2) Comparative developmental events involving the evolution of biomineralization in the echinoderm clade. 3) Support for phylogenomic analysis in an otherwise little studied group.		''Amphiura filiformis'' (O. F. Muller, 1776) is a brittle star found on the seabed of the European coasts from Greece to Norway and Sweden including the Baltic Sea . It is an important member of soft bottom communities where it digs a shallow burrow and feeds on plankton. It serves as food for crayfish and finfish. Stemming from its remarkable ability to regenerate arms in a matter of weeks it has become an emerging model for regeneration and stem cell biology in biomedical research. Research targets include: 1) The cellular and molecular mechanisms underlying regeneration with links to neuroscience, stem cell biology and neuropeptide structure and function in the absence of a centralised nervous system. 2) Comparative developmental events involving the evolution of biomineralization in the echinoderm clade. 3) Support for phylogenomic analysis in an otherwise little studied group.
	Development raw reads are available at NCBI accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA349786 PRJNA349786].		Development raw reads are available at NCBI accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA349786 PRJNA349786].

Ctelmer at 19:54, 3 February 2023

2023-02-03T19:54:03Z

← Older revision		Revision as of 19:54, 3 February 2023
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			__TOC__

	=Future Species=		=Future Species=

Ctelmer: /* Previous Echinoderm Genome Assemblies by Species */

2023-02-03T19:50:59Z

Previous Echinoderm Genome Assemblies by Species

← Older revision		Revision as of 19:50, 3 February 2023
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	Development raw reads are available at NCBI accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA349786 PRJNA349786].		Development raw reads are available at NCBI accession [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA349786 PRJNA349786].

	=Previous ~~Echinoderm Genome~~ Assemblies by Species=		=Previous Assemblies by Species=

	__TOC__		__TOC__