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 tuahiniensis

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 tuahiniensis
POC-48-S1-TP2	Pocillopora tuahiniensis
POC-50-S1-TP2	Pocillopora tuahiniensis
POC-53-S1-TP2	Pocillopora tuahiniensis
POC-57-S1-TP2	Pocillopora tuahiniensis
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 tuahiniensis
POC-48-S1-TP2	Pocillopora tuahiniensis
POC-50-S1-TP2	Pocillopora tuahiniensis
POC-53-S1-TP2	Pocillopora tuahiniensis
POC-57-S1-TP2	Pocillopora tuahiniensis
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.

---

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

Transcripts

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

• Apul_GCF_013753865.1_rna.fna - https://gannet.fish.washington.edu/acropora/E5-deep-dive/Transcripts/Apul_GCF_013753865.1_rna.fna

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

• Apul_mature.fasta - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Apul_ShortStack_31bp_fastp_merged_mature.fasta

• Apul_mature.gff3 - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Apul_ShortStack_31bp_fastp_merged_mature.gff3

• Apul_star.fasta - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Apul_ShortStack_31bp_fastp_merged_star.fasta

• Apul_star.gff3 - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Apul_ShortStack_31bp_fastp_merged_star.gff3

• Apul_precursor.fasta - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Apul_ShortStack_31bp_fastp_merged_precursor.fasta

• Apul_precursor.gff3 - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/D-Apul/output/13.2.1-Apul-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Apul_ShortStack_31bp_fastp_merged_precursor.gff3

lncRNA

• Apul_lncRNA.fasta - https://raw.githubusercontent.com/urol-e5/deep-dive/refs/heads/main/D-Apul/output/25-lncRNA-clean-up/Apul_lncRNA.fasta

• Apul_lncRNA.bed - https://raw.githubusercontent.com/urol-e5/deep-dive/refs/heads/main/D-Apul/output/25-lncRNA-clean-up/Apul_lncRNA.bed

---

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

Transcripts

• Porites_evermanni_CDS.fasta - https://gannet.fish.washington.edu/kdurkin1/deep-dive/E-Peve/data/Porites_evermanni_CDS.fasta

Constructed by extracting and aligning all CDS sequences from the gff Porites_evermanni_v1.annot.gff (https://gannet.fish.washington.edu/kdurkin1/deep-dive/E-Peve/data/Porites_evermanni_v1.annot.gff, downloaded from https://www.genoscope.cns.fr/corals/genomes.html March 11, 2022) with scaffold Porites_evermanni_v1.fa (https://gannet.fish.washington.edu/kdurkin1/deep-dive/E-Peve/data/Porites_evermanni_v1.fa, downloaded from https://www.genoscope.cns.fr/corals/genomes.html March 11, 2022). Code for transcripts fasta construction here: https://github.com/urol-e5/deep-dive/blob/main/E-Peve/code/12-Peve-RNAseq-kallisto.md

sRNA

• `Peve_mature.fasta' - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/E-Peve/output/08.2-Peve-sRNAseq-ShortStack-31bp-fastp-merged/named_Peve_ShortStack_31bp_fastp_merged_mature.fasta

• `Peve_mature.gff3' - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/E-Peve/output/08.2-Peve-sRNAseq-ShortStack-31bp-fastp-merged/named_Peve_ShortStack_31bp_fastp_merged_mature.gff3

• `Peve_star.fasta' - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/E-Peve/output/08.2-Peve-sRNAseq-ShortStack-31bp-fastp-merged/named_Peve_ShortStack_31bp_fastp_merged_star.fasta

• `Peve_star.gff3' - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/E-Peve/output/08.2-Peve-sRNAseq-ShortStack-31bp-fastp-merged/named_Peve_ShortStack_31bp_fastp_merged_star.gff3

• `Peve_precursor.fasta' - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/E-Peve/output/08.2-Peve-sRNAseq-ShortStack-31bp-fastp-merged/named_Peve_ShortStack_31bp_fastp_merged_precursor.fasta

• `Peve_precursor.gff3' - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/E-Peve/output/08.2-Peve-sRNAseq-ShortStack-31bp-fastp-merged/named_Peve_ShortStack_31bp_fastp_merged_precursor.gff3

lncRNA

• Peve_lncRNA.fasta - https://raw.githubusercontent.com/urol-e5/deep-dive/refs/heads/main/E-Peve/output/22-lncRNA-clean-up/Peve_lncRNA.fasta

• Peve_lncRNA.bed - https://raw.githubusercontent.com/urol-e5/deep-dive/refs/heads/main/E-Peve/output/22-lncRNA-clean-up/Peve_lncRNA.bed

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

---

Pocillopora tuahiniensis

Johnston et al 2023

Characters: The corallum is hemispherical and the branches are fairly evenly spaced, separated by ap- proximately 1–2 cm. Branches are straight and robust, and most branches ramify. Verrucae are evenly distributed and are equal in size and shape, approximately 1 mm. Verrucae are not verrucose at their tips, but rather are jagged and crown shaped.

Colour: Colonies may be brown, pink, or pale yellow, and like many Pocil- lopora species, have pigment concentrated in the oral opening of the polyps, forming a dark ring. .

Sister Species: Pocillopora verrucosa, which has relatively prominent verrucae.

Habitat: Shallow reef environments to deep forereef.

Abundance: Common on lagoon and forereef.

Genomic Resources from other Pocillopora species

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

Transcripts

• Pocillopora_meandrina_HIv1.genes.cds.fna - https://gannet.fish.washington.edu/acropora/E5-deep-dive/Transcripts/Pocillopora_meandrina_HIv1.genes.cds.fna; (http://cyanophora.rutgers.edu/Pocillopora_meandrina/)

sRNA

• Pmea_mature.fasta - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Pmea_ShortStack_31bp_fastp_merged_mature.fasta

• Pmea_mature.gff3 - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Pmea_ShortStack_31bp_fastp_merged_mature.gff3

• Pmea_star.fasta - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Pmea_ShortStack_31bp_fastp_merged_star.fasta

• Pmea_star.gff3 - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Pmea_ShortStack_31bp_fastp_merged_star.gff3

• Pmea_precursor.fasta - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Pmea_ShortStack_31bp_fastp_merged_precursor.fasta

• Pmea_precursor.gff3 - https://github.com/urol-e5/deep-dive/raw/refs/heads/main/F-Pmea/output/13.2.1-Pmea-sRNAseq-ShortStack-31bp-fastp-merged-cnidarian_miRBase/named_Pmea_ShortStack_31bp_fastp_merged_precursor.gff3

lncRNA

• Ptuh_lncRNAs.fasta - https://raw.githubusercontent.com/urol-e5/deep-dive/refs/heads/main/F-Pmea/output/22-lncRNA-clean-up/Ptuh_lncRNA.fasta

• Ptuh-lncRNA.bed - https://raw.githubusercontent.com/urol-e5/deep-dive/refs/heads/main/F-Pmea/output/22-lncRNA-clean-up/Ptuh_lncRNA.bed

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