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Species Characteristics and Genomic Resources

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Steven Roberts edited this page Jun 30, 2023 · 43 revisions

Here we will try to list out key species (corresponding to sub-efforts), describe the briefly and provide links to cononical genomic resources to use for analysis.

A) Pocillopora verrocosa / meadrina?

D) Acropora pulchra

E) Porites evermanni

F) Pocillopora meandrina

Table denoted samples for D, E, and F

Sample Name* Species/Strain*
POR-71-S1-TP2 Porites evermanni
POR-73-S1-TP2 Porites evermanni
POR-76-S1-TP2 Porites evermanni
POR-79-S1-TP2 Porites evermanni
POR-82-S1-TP2 Porites evermanni
POC-47-S1-TP2 Pocillopora meandrina
POC-48-S1-TP2 Pocillopora meandrina
POC-50-S1-TP2 Pocillopora meandrina
POC-53-S1-TP2 Pocillopora meandrina
POC-57-S1-TP2 Pocillopora meandrina
ACR-140-S1-TP2 Acropora pulchra
ACR-145-S1-TP2 Acropora pulchra
ACR-150-S1-TP2 Acropora pulchra
ACR-173-S1-TP2 Acropora pulchra
ACR-178-S1-TP2 Acropora pulchra

Pocillopora verrocosa

???? sub-effort A

Genomic Resources

lncRNA gtf:

lncRNA fasta:

  • TBD

Acropora pulchra

from CORALS of the World

Characters: Colonies are arborescent with cylindrical branches but may be corymbose, with horizontally fused basal branches which have upturned ends. They may form stands more than 5 metres across. Branches are smaller than those of the large staghorn Acropora species. Radial corallites are of mixed sizes, with projecting lower lips.

Colour: Pale to dark brown or blue, often with pale blue tips.

Similar Species: May superficially resemble Acropora muricata and A. yongei, but radial corallites are distinctive. Acropora aspera has similar radial corallites but these are much larger and more scale-like. See also A. loisetteae.

Habitat: Usually restricted to shallow back-reef margins.

Abundance: Usually uncommon but may be a dominant species.

Genomic Resources

see also:

https://github.com/urol-e5/deep-dive/issues/20

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_013753865.1/

https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Acropora_millepora/101/

Genome

GCF_013753865.1_Amil_v2.1_genomic.fna - http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1_genomic.fna

  • md5: e4491d2710f86311e53680c5ca23c232

GCF_013753865.1_Amil_v2.1_genomic.gff - http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1_genomic.gff

  • md5: eca0bae84f91c3264287f76afbe86189

Porites evermanni

from CORALS of the World

Characters: Colonies are massive with a tendency to form columns. Tentacles are usually extended during the day.

Colour: Usually mustard, sometimes brown.

Similar Species: Readily distinguished by extended polyps giving colonies a distinctive colour and a furry appearance. Corallites are similar to those of Porites australiensis and P. columnaris.

Habitat: Shallow protected reef environments, especially lagoons.

Abundance: Usually uncommon.

Genomic Resources

see also:

https://github.com/urol-e5/deep-dive/issues/21

Genome:

GFF:

Pocillopora meandrina

from CORALS of the World

Characters: Colonies are small upright bushes. Branches radiate from the initial point of growth. They are flattened, those in shallow water being curved when viewed from above. Verrucae are neat and uniform.

Colour: Usually cream, green or pink.

Similar Species: Pocillopora kelleheri. See also P. verrucosa, which has relatively prominent verrucae.

Habitat: Shallow reef environments.

Abundance: Common on exposed reef fronts, uncommon elsewhere.

Genomic Resources

Genome

GFFs

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