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Species Characteristics and Genomic Resources
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.
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 |
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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.
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.
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/
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
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GCF_013753865.1_Amil_v2.1.protein.faa - http://gannet.fish.washington.edu/seashell/snaps/GCF_013753865.1_Amil_v2.1.protein.faa
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md5:
8125fbba63f60d12e2381c9d89caec94
sRNA
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known_miRNAs.gff3
- https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/known_miRNAs.gff3- md5:
d9c407fde49dad766805eed720ef56b0
- md5:
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known_miRNAs.fasta
- https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/known_miRNAs.fasta- md5:
bffabff46f25a8f6cf9b971f7d633fe5
- md5:
lncRNA
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.
see also:
https://github.com/urol-e5/deep-dive/issues/21
Genome:
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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
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md5:
8e58bf0417bab85a2882f95fb2e8bb56
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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
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md5:
9ef993fdb4ae01ea1a6c64c855dd8472
sRNA
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known_miRNAs.gff3
- https://gannet.fish.washington.edu/Atumefaciens/20230731-peve-E5_coral-ShortStack-sRNAseq/P_evermanni/ShortStack_out/known_miRNAs.gff3- md5:
5df2467b645659472bc23d041756e94e
- md5:
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known_miRNAs.fasta
- https://gannet.fish.washington.edu/Atumefaciens/20230731-peve-E5_coral-ShortStack-sRNAseq/P_evermanni/ShortStack_out/known_miRNAs.fasta- md5:
442af6be35fa6870a88db7908aaf25c2
- md5:
Proteins
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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
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md5:
3fce204309b6bd6fc03370512f1d81a9
lncRNA
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.
Genome
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https://owl.fish.washington.edu/halfshell/genomic-databank/Pocillopora_meandrina_HIv1.assembly.fasta
- Downloaded 20230519: http://cyanophora.rutgers.edu/Pocillopora_meandrina/
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Genes
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Pocillopora_meandrina_HIv1.genes.gff3 (55MB)
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MD5 checksum:
ace5c9a588321fada8e6771a1c758861
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Downloaded 20230519: http://cyanophora.rutgers.edu/Pocillopora_meandrina/
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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)
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Transposable Elements via Repeat Masker (https://github.com/urol-e5/deep-dive/issues/4)
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sRNA
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known_miRNAs.gff3
- https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/known_miRNAs.gff3- md5:
202a1cdd106eaa2a67181259ae4f0012
- md5:
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known_miRNAs.fasta
- https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/known_miRNAs.fasta- md5:
c1850de64682fea588fdec9e48715f0d
- md5:
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Protein
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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/
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md5
85109775369ecd9699bd2251e86ca630
lncRNA