Nematostella vectensis

Overview
Full NameNematostella vectensis
GenusNematostella
Speciesvectensis
Common NameStarlet Sea Anemone
AbbreviationNvec

Cnidaria – the animal phylum that includes sea anemones, corals, jellyfish, and hydra – occupies a critical position in the tree of life. As the simplest Eumetazoans (animals with a tissue grade of organization) they are the most primitive animals with epithelial cells, neurons, stem cells, complex extra-cellular matrix, muscle fibers, and a fixed axis of symmetry. Ediacaran fossils with Cnidarian affinities are among the most ancient animal relics. As the principal architects and components of coral reefs, anthozoans (corals) are responsible for the maintenance of tremendous marine diversity. The sea anemone Nematostella vectensis, a member of the basal class Anthozoa within Cnidaria, is emerging a model system for the molecular dissection of Cnidarian development, providing key “evo-devo” studies to elucidate the emergence, elaboration, and deployment of the basic complement of genes that underlie the formation of animal body plans.

To help illuminate the evolutionary origins of animals we have sequenced the genome of Nematostella, discovering chromosome-scale macrosynteny shared between sea anemones, sponges, and amphioxus, as well as a lack of obvious TADs and extended HOX and NK gene clusters.







Publication:

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny (2020).
Bob Zimmermann, Sofia M.C. Robb, Grigory Genikhovich, Whitney J. Fropf, Lukas Weilguny, Shuonan He, Shiyuan Chen, Jessica Lovegrove-Walsh, Eric M. Hill, Katerina Ragkousi, Daniela Praher, David Fredman, Yehu Moran, Matthew C. Gibson*, and UlrichTechnau*

bioRxiv 2020.10.30.359448; doi: https://doi.org/10.1101/2020.10.30.359448

Feature Summary
The following features are currently present for this organism
Feature TypeCount
exon147,218
gene15,355
polypeptide15,355
CDS15,355
mRNA15,355
three_prime_UTR11,850
five_prime_UTR10,491
chromosome30
Data Analyses

All data loaded into SIMRbase has an "Analysis Page". These pages provide information about the methods and provide a link to download the files.

Name Programsort descending Source
Nematostella vectensis Nvec200 Gene Models BLASTX Celegans e!100 BLASTX Nvec200 gene models BLASTX celegan
Nematostella vectensis Nvec200 Gene Models BLASTX Lamprey e!100 BLASTX Nvec200 gene models BLASTX lamprey
Nematostella vectensis Nvec200 Gene Models BLASTX Schmidtea mediterranea smes_v2_hconf_SMESG BLASTX Nvec200 gene models BLASTX smed
Nematostella vectensis Nvec200 Gene Models BLASTX Refseq 100 Nematostella BLASTX Nvec200 gene models BLASTX refseq100_nvec
Nematostella vectensis Nvec200 Gene Models BLASTX Fly e!100 BLASTX Nvec200 gene models BLASTX fly
Nematostella vectensis Nvec200 Gene Models BLASTX Uniprot BLASTX Nvec200 gene models BLASTX uniprot
Nematostella vectensis Nvec200 Gene Models BLASTX Xenopus e!100 BLASTX Nvec200 gene models BLASTX xenopus
Nematostella vectensis Nvec200 Gene Models BLASTX Yeast e!100 BLASTX Nvec200 gene models BLASTX yeast
Nematostella vectensis Nvec200 Gene Models BLASTX Zebrafish e!100 BLASTX Nvec200 gene models BLASTX zebrafish
Nematostella vectensis Nvec200 Gene Models BLASTX Cavefish e!100 BLASTX Nvec200 gene models BLASTX cavefish
Nematostella vectensis Nvec200 Gene Models BLASTX Human e!100 BLASTX Nvec200 gene models BLASTX human
Nematostella vectensis Nvec200 Gene Models BLASTX Medaka e!100 BLASTX Nvec200 gene models BLASTX medaka
Nematostella vectensis Nvec200 Gene Models BLASTX Mouse e!100 BLASTX Nvec200 gene models BLASTX mouse
Nematostella vectensis Nvec200 Gene Models BLASTX Metazoa e!46 Nematostella BLASTX Nvec200 gene models BLASTX nematostella
Nematostella vectensis Nvec200 Gene Models BLASTX Branchiostoma floridae BLASTX Nvec200 gene models BLASTX bfl
Nematostella vectensis NVE (wien_nvec200_v1) Mapped to NVEC200 GFF gmap Wien_Nvec200.names.gff3
Nematostella vectensis Nvec200 Gene Models IPRSCAN IPRSCAN Nvec200 gene models IPRSCAN
Nematostella vectensis Nvec200 Gene Models Proteins FASTA MAKER Nvec200 Protein Model FASTA
Nematostella vectensis Nvec200 Gene Models Mapped GFF MAKER NVEC200.20200813.gff
Nematostella vectensis Nvec200 Gene Models Transcripts MAKER NVEC200 Transcript Models FASTA
Nematostella vectensis Genome Assembly (Nvec200) zimmerman Nvec200.fasta
Data & Downloads

Nematostella vectensis NV2 (wein_nvec200_tcsv2) transcriptome

This is our most recent trascriptome. It was created by Juan Daniel Montenegro Cabrera and Bob Zimmerman (2021). It is a combination of the KC Isoseq (kc_nvec200_v1) and a large collection of RNAseq data using Tama + Cupcake + Stringtie2 (TCS) to generate gene models.

Transcripts (NV2) NV2 (NV2t) transcript FASTA
Protein (NV2) NV2 (NV2t) protein FASTA
GFF3 (NV2) NV2 aligned to NVEC200 (NV2g,NV2t)
Gene Functional Annotations (EggNog) (NV2) Eggnog of NV2 genes (tab del)
Transcript Functional Annotations (Swissprot top hit) (NV2) Top Swissprot/uniprot hit for NV2 transcripts (tab del)
Transcript Ortholog Annotations (OMA) (NV2) Orthologs (OMA 2.4.2) for NV2 transcripts (tab del)

About the ID format

NV2g000001000.1
NV2 dataset identifier
g stands for gene
000001 gene number
000 transcript number: will always be 000 for a gene
.1 version 1
NV2t000001001.1
NV2 dataset identifier
t stands for transcript
000001 gene number
001 transcript number
.1 version 1



Nematostella vectensis Isoseq (kc_nvec200_v1) transcriptome

This is a transcriptome created by Shuonan He and Cynthia Shiyuan at SIMR using PacBio IsoSeq

Transcripts (NVE) KC Isoseq (kc_nvec200_v1) transcript FASTA
Protein (NVE) KC Isoseq (kc_nvec200_v1) protein FASTA
CDS (NVE) KC Isoseq (kc_nvec200_v1) CDS FASTA
GFF3 (NVE) KC Isoseq aligned to NVEC200 (kc_nvec200_v1)



Nematostella vectensis NVE (wien_nvec200_v1) transcriptome

This is the Vienna (nve) transcriptome.

Transcripts (NVE) NVE (Wien_Nvec200_v1) transcript FASTA
Protein (NVE) NVE (Wien_Nvec200_v1) protein FASTA
GFF3 (NVE) NVE aligned to NVEC200 (Wien_Nvec200_v1)



Gene Models for Nvec200 Genome assembly

These are gene model created by Carson Holt using MAKER seeded with KC Isoseq (kc_nvec200_v1)

Nvec200 Genome Assembly Nvec200
Transcripts (Nvec200_v1) NVEC200.20200813.transcripts.fasta
Proteins (Nvec200_v1) NVEC200.20200813.proteins.fasta
GFF3 (Nvec200_v1) NVEC200.20200813.gff






See Data Analysis page for a listing of the Analyses performed on Nvec200 genome assembly and gene models. The FASTAs and GFF are also there for download as well as other analysis.