Coral/Symbiont Genomes and Transcriptomes

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q
1		family	genus	species	strain	partner_type	tissue_source	resource_type	methods	research_group	contact	publication_status	anticipated_release_date	data_link	publication_link	publication_reference	notes

2	Suessiales	Symbiodiniaceae	Effrenium	voratum	CCMP421	free-living	culture	genome	10X Genomics linked reads	Rodriguez-Lanetty/Chan	c.chan1@uq.edu.au	unpublished				Chan et al. (unpublished)
3	Suessiales	Symbiodiniaceae	Effrenium	voratum	RCC1521	free-living	culture	genome	short reads + long reads	Chan	c.chan1@uq.edu.au	unpublished
4	Suessiales	Symbiodiniaceae	Effrenium	voratum	rt-383	free-living	culture	genome	short reads + long reads	Chan	c.chan1@uq.edu.au	unpublished
5	Scleractinia	Acroporidae	Acropora	millepora	NA	host	holobiont	genome	PacBio / 10x genomics / Illumina	Matz, Przeworski	matz@utexas.edu, mp3284@columbia.edu	published	released	https://www.dropbox.com/s/hezqx79m3fk1l8e/Amil_v2.01_annotated.zip?dl=0	https://doi.org/10.1126/science.aba4674
6	Scleractinia	Acroporidae	Acropora	cervicornis	NA	host	holobiont/sperm	genome	short read/ long read	Baums	baums@psu.edu	unpublished	Mid 2021	N/A	N/A
7	Scleractinia	Acroporidae	Acropora	palmata	NA	host	holobiont/sperm	genome	short read/ long read/ HiC	Baums	baums@psu.edu	unpublished	Mid 2021	N/A	N/A
8	Scleractinia	Euphylliidae	Galaxea	acrhelia	NA	host	holobiont	transcriptome	short read	Kenkel	ckenkel@usc.edu	published	released	https://dornsife.usc.edu/labs/carlslab/data/	https://academic.oup.com/gigascience/article/6/9/gix074/4091589
9	Scleractinia	Euphylliidae	Galaxea	astreata	NA	host	holobiont	transcriptome	short read	Kenkel	ckenkel@usc.edu	published	released	https://dornsife.usc.edu/labs/carlslab/data/	https://academic.oup.com/gigascience/article/6/9/gix074/4091589
10	Scleractinia	Poritidae	Goniopora	columna	NA	host	holobiont	transcriptome	short read	Kenkel	ckenkel@usc.edu	published	released	https://dornsife.usc.edu/labs/carlslab/data/	https://academic.oup.com/gigascience/article/6/9/gix074/4091589
11	Scleractinia	Acroporidae	Acropora	clathrata		host		genome	short read	Allen Chen' Lab/Parisa Alidoost Salimi	P_Alidoostsalimi@yahoo.com	unpublished				Alidoost Salimi et al. (unpublished)
12	Scleractinia	Acroporidae	Acropora	downingi		host		genome	short read	Allen Chen' Lab/Parisa Alidoost Salimi	P_Alidoostsalimi@yahoo.com	unpublished				Alidoost Salimi et al. (unpublished)
13	Scleractinia		Acropora	cervicornis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Lopez	joslo@nova.edu	unpublished	2021
14	Scleractinia	Acroporidae	Montipora	aequituberculata	NA	host	holobiont	transcriptome	short read	Kenkel	ckenkel@usc.edu	published	released	https://dornsife.usc.edu/labs/carlslab/data/	https://royalsocietypublishing.org/doi/10.1098/rspb.2019.0111
15	Scleractinia	Acroporidae	Montipora	aequituberculata	NA	host	holobiont	transcriptome	Illumina	Matz, van Oppen	matz@utexas.edu	published	released	https://www.dropbox.com/s/mnkqwz7oi3l226c/maequituberculata_transcriptome_july2014.zip?dl=0	https://doi.org/10.1111/mec.14489
16	Scleractinia		Acropora	cervicornis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Lopez	joslo@nova.edu	unpublished	2021
17	Scleractinia	Acroporidae	Montipora	capitata		host	holobiont	transcriptome	Illumina	Bhattacharya, Putnam	hputnam@uri.edu	published	released	http://cyanophora.rutgers.edu/montipora/	https://www.nature.com/articles/s41598-019-39274-3	Shumaker et al 2019
18	Scleractinia		Oculina	patagonica		host	holobiont	transcriptome	Illumina	Tali Mass	tmass@univ.haifa.ac.il	published	released
19	Scleractinia		Acropora	cytherea		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
20	Scleractinia		Acropora	hyacinthus		host	sperm	genome	PacBio/Illumina/Omni-C	Palumbi+Albright	elopez-nandam@calacademy.org	biorxiv	2021	https://www.ncbi.nlm.nih.gov/assembly/GCA_020536085.1/ (You can download the associated gff3, proteins fasta, and other annotation files for this assembly here: https://drive.google.com/drive/u/1/folders/15dh6eE8q850frTRVtglndXtzxSwj673g)	https://www.biorxiv.org/content/10.1101/2021.07.20.453148v1	López-Nandam et al. (preprint)
21	Scleractinia		Acropora	intermedia		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
22	Scleractinia		Acropora	muricata		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
23	Scleractinia	Poritidae	Porites	lobata	NA	host	holobiont	transcriptome	short read	Kenkel	ckenkel@usc.edu	published	released	https://dornsife.usc.edu/labs/carlslab/data/	https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15608
24	Scleractinia	Poritidae	Porites	astreoides	NA	host	holobiont	transcriptome	454 (gosh)	Matz	matz@utexas.edu	published	released	https://www.dropbox.com/s/dzvr219crsbgt0n/pastreoides_2014.zip?dl=0	doi: 10.1111/mec.12390
25	Scleractinia	Siderastreidae	Siderastrea	siderea	NA	host	holobiont	transcriptome	short read	Davies	daviessw@gmail.com	published	released	http://sites.bu.edu/davieslab/files/2017/11/Siderastrea_siderea_transcriptome.zip	https://www.frontiersin.org/articles/10.3389/fmars.2016.00112/full
26	Scleractinia		Acropora	palmata		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
27	Scleractinia		Acropora	pulchra		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
28	Scleractinia		Acropora	spathulata		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
29	Scleractinia		Acropora	valida		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
30	Scleractinia		Agaricia	agaricites		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
31	Scleractinia		Alveopora	japonica		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
32	Scleractinia	Rhizangiidae	Astrangia	poculata	NA	host	holobiont	genome	short read/ long read/ HiC	Baums	baums@psu.edu	unpublished	2021	N/A	N/A
33	Scleractinia		Balanophyllia	europaea		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
34	Scleractinia	Pocilloporidae	Pocillopora	meandrina		host	holobiont	transcriptome	Illumina	Bhattacharya, Putnam	hputnam@uri.edu	unpublished	2021
35	Scleractinia		Blastomussa	merleti		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
36	Scleractinia		Blastomussa	wellsi		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
37	Scleractinia		Colpophyllia	natans		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
38	Scleractinia	Poritidae	Porites	astreoides		host	holobiont	transcriptome	Illumina	Putnam	hputnam@uri.edu	unpublished	2021
39	Scleractinia	Poritidae	Porites	compressa		host	sperm	transcriptome	Illumina	Bhattacharya, Putnam	hputnam@uri.edu	unpublished	2021
40	Scleractinia	Poritidae	Porites	lobata		host	holobiont	transcriptome	Illumina	Bhattacharya, Putnam	hputnam@uri.edu	unpublished	2021
41	Scleractinia	Pocilloporidae	Pocillopora	acuta		host and symbiont	holobiont	transcriptome	short read	Mayfield	abm64@miami.edu	published	released	http://symbiont.iis.sinica.edu.tw/coral_pdltte/static/html/index.html#home	https://onlinelibrary.wiley.com/doi/full/10.1111/mec.12982	Mayfield et al. 2014, Molecular Ecology	check out the website for interactive querying features
42	Scleractinia	Pocilloporidae	Pocillopora	acuta + damicornis		host and symbiont	holobiont	transcriptome	short read	Traylor-Knowles	mconnelly@rsmas.miami.edu	published	2021	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA587509/	https://doi.org/10.1016/j.dci.2020.103717
43	Scleractinia	Pocilloporidae	Seriatopora	hystrix		host and symbiont	holobiont	transcriptome	short read	Mayfield	abm64@miami.edu	published	released	http://symbiont.iis.sinica.edu.tw/s_hystrix/static/html/	https://onlinelibrary.wiley.com/doi/full/10.1111/mec.13896	Mayfield et al. 2016, Molecular Ecology	the website may be temporarily down for maintenance
44	Scleractinia	Merulinidae	Cyphastrea	microphthalma		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
45	Scleractinia		Diploria	labyrinthiformis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
46	Scleractinia		Echinopora	lamellosa		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
47	Scleractinia	Merulinidae	Favites	pentagona		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
48	Scleractinia		Galaxea	fascicularis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
49	Scleractinia		Goniastrea	retiformis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
50	Scleractinia	Poritidae	Goniopora	columna		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
51	Scleractinia	Poritidae	Goniopora	djiboutiensis		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
52	Scleractinia		Dendrogyra	cylindrus		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
53	Scleractinia		Isopora	brueggemanni		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
54	Scleractinia		Meandrina	meandrites		host and symbiont	holobiont	genome	short read / long read / Hi-C	Lopez	joslo@nova.edu	unpublished	2021
55	Scleractinia		Meandrina	meandrites		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
56	Scleractinia		Micromussa	lordhowensis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
57	Scleractinia	Faviidae	Montastraea	cavernosa	NA	host	holobiont	genome	PacBio / 10x genomics	Matz	matz@utexas.edu	published	released	https://www.dropbox.com/s/yfqefzntt896xfz/Mcavernosa_genome.tgz	https://doi.org/10.1111/mec.15931	Rippe et al 2021, Molecular Ecology
58	Scleractinia		Montastraea	cavernosa		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
59	Scleractinia	Acroporidae	Montipora	capitata		host	sperm	genome	PacBio, hybrid	Bhattacharya, Putnam	hputnam@uri.edu	published	released	http://cyanophora.rutgers.edu/montipora/	https://www.nature.com/articles/s41598-019-39274-3	Shumaker et al 2019
60	Scleractinia		Montipora	capitata		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
61	Scleractinia		Montipora	digitata		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
62	Scleractinia		Mussismilia	brasiliensis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
63	Scleractinia		Mussismilia	hispida		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
64	Scleractinia		Oculina	arbuscula		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
65	Scleractinia		Oculina	patagonia		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
66	Scleractinia		Oculina	varicosa		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021	https://www.ncbi.nlm.nih.gov/sra/SRX6096996[accn]	https://doi.org/10.3389/fmars.2019.00662
67	Scleractinia		Oculina	patagonica		host and symbiont	holobiont	genome	short read Illumina	Tali Mass	tmass@univ.haifa.ac.il	unpublished	2021				From Israel
68	Scleractinia		Orbicella	annularis		host	sperm	genome	short read / long read / Hi-C	Lopez	joslo@nova.edu	unpublished	2021
69	Scleractinia		Orbicella	faveolata		host	sperm	genome	short read / long read / Hi-C	Lopez	joslo@nova.edu	unpublished	2021
70	Scleractinia		Orbicella	arbuscula		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
71	Scleractinia		Orbicella	franksi		host	sperm	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
72	Scleractinia		Orbicella	radians		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
73	Scleractinia	Agariciidae	Pavona	cactus		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
74	Scleractinia	Agariciidae	Pavona	decussata		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
75	Scleractinia	Merulinidae	Platygyra	daedalea		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
76	Scleractinia	Pocilloporidae	Pocillopora	damicornis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
77	Scleractinia	Pocilloporidae	Pocillopora	grandis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
78	Scleractinia	Pocilloporidae	Pocillopora	meandrina		host	holobiont	genome	PacBio, hybrid	Bhattacharya, Putnam	hputnam@uri.edu	unpublished	2021
79	Scleractinia	Pocilloporidae	Pocillopora	acuta		host	holobiont	genome	PacBio, hybrid	Bhattacharya, Putnam	hputnam@uri.edu	unpublished
80	Scleractinia	Poritidae	Porites	astreoides		host	holobiont	genome	PacBio, hybrid	Putnam	hputnam@uri.edu	unpublished	2021
81	Scleractinia	Poritidae	Porites	compressa		host	sperm	genome	PacBio, hybrid	Bhattacharya, Putnam	hputnam@uri.edu	unpublished	released
82	Scleractinia	Poritidae	Porites	harrisoni		host		genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	unpublished
83	Scleractinia		Porites	cylindrica		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
84	Scleractinia		Porites	rus		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
85	Scleractinia		Pseudodiploria	strigosa		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
86	Scleractinia	Pocilloporidae	Seriatopora	hystrix		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
87	Scleractinia	Siderastreidae	Siderastrea	savignyana		host	holobiont	genome	short read	Parisa Alidoost Salimi/Pargol Ghavam Mostafavi	P_Alidoostsalimi@yahoo.com	published		https://link.springer.com/article/10.1007/s11033-021-06251-x		Alidoost Salimi et al. 2021, Mol Biol Rep.
88	Scleractinia		Siderastrea	siderea		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
89	Scleractinia		Siderastrea	stellata		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
90	Scleractinia		Stephanocoenia	intersepta		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
91	Scleractinia		Stylophora	subseriata		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
92	Scleractinia		Turbinaria	reniformis		host and symbiont	holobiont	genome	short read / long read / Hi-C	Sweet / Coral Genome Project	M.Sweet@derby.ac.uk	unpublished	2021
93	Suessiales	Symbiodiniaceae	Breviolum	minutum	SSB01	symbiont	culture	transcriptome		Grossman	agrossman@carnegiescience.edu	published	released			Xiang et al. 2015, The Plant Journal
94	Suessiales	Symbiodiniaceae	Breviolum	aenigmaticum	mac04-487	symbiont	culture	transcriptome		Parkinson	jparkinson@usf.edu	published	released			Parkinson et al. 2016, Genome Biology and Evolution
95	Suessiales	Symbiodiniaceae	Breviolum	minutum	mac703, Mf1.05b, rt002, rt351	symbiont	culture	transcriptome		Parkinson	jparkinson@usf.edu	published	released			Parkinson et al. 2016, Genome Biology and Evolution
96	Suessiales	Symbiodiniaceae	Breviolum	pseudominutum	rt146	symbiont	culture	transcriptome		Parkinson	jparkinson@usf.edu	published	released			Parkinson et al. 2016, Genome Biology and Evolution
97	Suessiales	Symbiodiniaceae	Breviolum	psygmophilum	HIAp, Mf10.14b.02, PurPFlex, rt141	symbiont	culture	transcriptome		Parkinson	jparkinson@usf.edu	published	released			Parkinson et al. 2016, Genome Biology and Evolution
98	Suessiales	Symbiodiniaceae	Breviolum	minutum	Mf1.05b	symbiont	culture	genome		Satoh	norisky@oist.jp	published	released			Shoguchi et al. 2013, Current Biology
99	Suessiales	Symbiodiniaceae	Breviolum	minutum	Mf1.05b	symbiont	culture	transcriptome		Voolstra	christian.voolstra@uni-konstanz.de	published	released			Bayer et al. 2012, PLoS One
100	Suessiales	Symbiodiniaceae	Cladocopium	sp.		symbiont		transcriptome		Chan	c.chan1@uq.edu.au	published	released			Gonzalez-Pech et al. 2016, Frontiers in Marine Science