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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 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.
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
https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_013753865.1/
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Apul_GCF_013753865.1_rna.fna
- https://gannet.fish.washington.edu/acropora/E5-deep-dive/Transcripts/Apul_GCF_013753865.1_rna.fna
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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
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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:
-
known_miRNAs.fasta
- https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/A_pulchra/ShortStack_out/known_miRNAs.fasta- md5:
bffabff46f25a8f6cf9b971f7d633fe5
- md5:
-
Apul_lncRNAs.fasta
- https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/output/05.33-lncRNA-discovery/Apul_lncRNA.fasta -
Apul_lncRNA.bed
- https://github.com/urol-e5/deep-dive/blob/main/D-Apul/output/05.33-lncRNA-discovery/Apul_lncRNA.bed
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
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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
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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
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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:
-
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:
-
Peve_lncRNAs.fasta
- https://raw.githubusercontent.com/urol-e5/deep-dive/main/E-Peve/output/Peve_lncRNA.fasta -
Peve_lncRNA.bed
- https://github.com/urol-e5/deep-dive/blob/main/E-Peve/output/Peve_lncRNA.bed
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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
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.
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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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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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(https://github.com/urol-e5/deep-dive/issues/4)
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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/)
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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:
-
known_miRNAs.fasta
- https://gannet.fish.washington.edu/Atumefaciens/20230628-E5_coral-ShortStack-sRNAseq/P_meandrina/ShortStack_out/known_miRNAs.fasta- md5:
c1850de64682fea588fdec9e48715f0d
- md5:
-
Pmea_lncRNAs.fasta
- https://raw.githubusercontent.com/urol-e5/deep-dive/main/F-Pmea/output/02-lncRNA-discovery/Pmea_lncRNA.fasta -
Pmea-lncRNA.bed
- https://github.com/urol-e5/deep-dive/blob/main/F-Pmea/output/02-lncRNA-discovery/Pmea_lncRNA.bed
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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