Species Characteristics and Genomic Resources

Here we will list out key species (corresponding to sub-efforts), describing them briefly and provide links to canonical genomic resources to use for analysis.

TLDR: This is where we hope to have sequence files and genome feature files.

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

sRNA-seq Sample Name	Species/Strain
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
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
POR-73-S1-TP2	Porites evermanni
POR-79-S1-TP2	Porites evermanni
POR-82-S1-TP2	Porites evermanni

• Some samples failed QC and did not get sequenced for sRNA-seq.

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Acropora pulchra

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

Protein

• GCF_013753865.1_Amil_v2.1.protein.faa - http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1.protein.faa

• md5: 8125fbba63f60d12e2381c9d89caec94

sRNA

• known_miRNAs.gff3 - https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/known_miRNAs.gff3

  • md5: d9c407fde49dad766805eed720ef56b0

• known_miRNAs.fasta - https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/known_miRNAs.fasta

  • md5: bffabff46f25a8f6cf9b971f7d633fe5

lncRNA

GTF, FASTA

---

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:

• Porites_evermanni_v1.fa: https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.fa : downloaded https://www.genoscope.cns.fr/corals/genomes.html on 062923

• md5: 8e58bf0417bab85a2882f95fb2e8bb56

• Porites_evermanni_v1.annot.gff: https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.annot.gff : downloaded https://www.genoscope.cns.fr/corals/genomes.html on 062923

• md5: 9ef993fdb4ae01ea1a6c64c855dd8472

sRNA

• known_miRNAs.gff3 - https://gannet.fish.washington.edu/Atumefaciens/20230731-peve-E5_coral-ShortStack-sRNAseq/P_evermanni/ShortStack_out/known_miRNAs.gff3

  • md5: 5df2467b645659472bc23d041756e94e

• known_miRNAs.fasta - https://gannet.fish.washington.edu/Atumefaciens/20230731-peve-E5_coral-ShortStack-sRNAseq/P_evermanni/ShortStack_out/known_miRNAs.fasta

  • md5: 442af6be35fa6870a88db7908aaf25c2

Proteins

• Porites_evermanni_v1.annot.pep.fa: https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.annot.pep.fa : downloaded https://www.genoscope.cns.fr/corals/genomes.html on 062923

• md5: 3fce204309b6bd6fc03370512f1d81a9

lncRNA

GTF, FASTA

---

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

• https://owl.fish.washington.edu/halfshell/genomic-databank/Pocillopora_meandrina_HIv1.assembly.fasta

  • Downloaded 20230519: http://cyanophora.rutgers.edu/Pocillopora_meandrina/

• Genes

  • Pocillopora_meandrina_HIv1.genes.gff3 (55MB)

    • MD5 checksum: ace5c9a588321fada8e6771a1c758861

    • Downloaded 20230519: http://cyanophora.rutgers.edu/Pocillopora_meandrina/

    • NOTE: This is labelled as a GFF3, but in reality is a GTF file; as it only contains transcript/exon/CDS features. There are no gene features (e.g. 5'/3'UTR, mRNA, etc)

• Transposable Elements via Repeat Masker (https://github.com/urol-e5/deep-dive/issues/4)

  • https://gannet.fish.washington.edu/Atumefaciens/20230526-pmea-repeatmasker-Pocillopora_meandrina_HIv1.assembly/Pocillopora_meandrina_HIv1.assembly.fasta.out.gff

• sRNA

  • known_miRNAs.gff3 - https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/known_miRNAs.gff3

    • md5: 202a1cdd106eaa2a67181259ae4f0012

  • known_miRNAs.fasta - https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/known_miRNAs.fasta

    • md5: c1850de64682fea588fdec9e48715f0d

Protein

• Pocillopora_meandrina_HIv1.genes.pep.faa - https://gannet.fish.washington.edu/seashell/snaps/Pocillopora_meandrina_HIv1.genes.pep.faa Downloaded 20230623: http://cyanophora.rutgers.edu/Pocillopora_meandrina/

• md5 85109775369ecd9699bd2251e86ca630

lncRNA

GTF, FASTA