Gene duplication in an African cichlid adaptive radiation

Machado, Heather E; Jui, Ginger; Joyce, Domino A; Reilly, Christian RL; Lunt, David H; Renn, Suzy CP

doi:10.1186/1471-2164-15-161

BMC Genomics

Table 1 Genes duplicated relative to A. burtoni with informative BLAST hits

From: Gene duplication in an African cichlid adaptive radiation

GenBank	Homology	A.twe	M.est	P.sim	R.chi	BitScore
CN468828^2/2	Adenine nucleotide translocator s598	ns	ns	ns	0.60	567
CN468828^2/2	Adenine nucleotide translocator s598	ns	ns	ns	0.0019	567
DY630000	Alcohol dehydrogenase Class VI	ns	ns	0.73	ns	379
DY630000	Alcohol dehydrogenase Class VI	ns	ns	0.0015	ns	379
DY630424	Alkylated DNA repair protein alkB homolog 7	ns	0.43	ns	ns	304
DY630424	Alkylated DNA repair protein alkB homolog 7	ns	0.0002	ns	ns	304
DY629046	Arsenic (+3 oxidation state) methyltransferase	ns	ns	ns	1.06	150
DY629046	Arsenic (+3 oxidation state) methyltransferase	ns	ns	ns	0.0031	150
DY626788	ATPase, H + transporting, lysosomal V0 subunit E	ns	0.76	ns	ns	87.8
DY626788	ATPase, H + transporting, lysosomal V0 subunit E	ns	0.0028	ns	ns	87.8
DY628437	Claudin 29a (cldn29a) gene	ns	0.60	ns	ns	526
DY628437	Claudin 29a (cldn29a) gene	ns	0.005	ns	ns	526
DY632040	Coiled-coil domain containing protein 80	ns	ns	1.19	2.13	434
DY632040	Coiled-coil domain containing protein 80	ns	ns	3E-05	5E-07	434
DY629141	Crystallin gamma M2b	ns	ns	ns	0.43	829
DY629141	Crystallin gamma M2b	ns	ns	ns	0.0024	829
DY626204^1/2	C-type lectin domain family 4 member C	ns	0.38	ns	ns	246
DY626204^1/2	C-type lectin domain family 4 member C	ns	0.0039	ns	ns	246
DY631088	Cystatin-B	0.45	ns	ns	ns	150
DY631088	Cystatin-B	0.0016	ns	ns	ns	150
DY630353	Cytosolic sulfotransferase 3	ns	ns	0.62	0.64	713
DY630353	Cytosolic sulfotransferase 3	ns	ns	0.0015	0.0013	713
CN470675	Dazl gene	ns	ns	ns	0.57	89.7
CN470675	Dazl gene	ns	ns	ns	0.0040	89.7
DY629967^4/8	Ferritin heavy subunit	ns	ns	ns	0.82	1160
DY629967^4/8	Ferritin heavy subunit	ns	ns	ns	8E-05	1160
DY631817	Fish virus induced TRIM protein	ns	ns	0.590	ns	170
DY631817	Fish virus induced TRIM protein	ns	ns	0.0005	ns	170
DY626596	Fish virus induced TRIM protein	ns	ns	0.41	0.44	145
DY626596	Fish virus induced TRIM protein	ns	ns	0.0045	0.0030	145
DY628624	Gamma M7 crystallin	ns	ns	ns	0.42	169
DY628624	Gamma M7 crystallin	ns	ns	ns	0.0054	169
DY630388	Glutamyl-tRNA(Gln) amidotransferase	0.48	ns	ns	ns	347
DY630388	Glutamyl-tRNA(Gln) amidotransferase	0.0016	ns	ns	ns	347
DY626115^1/2	GTPase IMAP family member 7	ns	ns	1.14	ns	370
DY626115^1/2	GTPase IMAP family member 7	ns	ns	0.0016	ns	370
CN471284	High-mobility group 20B	0.60	ns	ns	ns	163
CN471284	High-mobility group 20B	0.0004	ns	ns	ns	163
CN469367	Hox gene cluster	1.34	1.16	0.86	1.11	183
CN469367	Hox gene cluster	3E-05	9E-05	0.0006	0.0002	183
DY627986	Hox gene cluster	1.81	1.12	0.80	1.22	95.1
DY627986	Hox gene cluster	3E-07	1E-05	0.0001	5E-06	95.1
DY629113	Immunoglobulin light chain	ns	ns	0.65	ns	482
DY629113	Immunoglobulin light chain	ns	ns	0.0025	ns	482
CN468953	Iron-sulfur cluster assembly enzyme ISCU	ns	ns	ns	0.86	610
CN468953	Iron-sulfur cluster assembly enzyme ISCU	ns	ns	ns	0.0022	610
DY628151	Kallikrein-8 precursor	1.02	ns	ns	ns	102
DY628151	Kallikrein-8 precursor	0.0015	ns	ns	ns	102
DY627800	Kinesin-like protein 2 (knsl2)	ns	0.86	1.84	1.14	398
DY627800	Kinesin-like protein 2 (knsl2)	ns	0.0013	9E-06	0.0003	398
CN469578	KLR1 gene	1.04	ns	ns	ns	154
CN469578	KLR1 gene	4E-05	ns	ns	ns	154
DY629760	LOC100150543, polyprotein	1.35	ns	0.65	0.79	141
DY629760	LOC100150543, polyprotein	8E-06	ns	0.001	0.0003	141
CN468718	LOC100151545, similar to Protein KIAA0284	0.72 0.0004	ns	ns	ns	145
DY629780	MHC class I	ns	0.84	1.26	1.05	161
DY629780	MHC class I	ns	0.0053	0.0005	0.0016	161
DY630620	MHC class IA antigen	ns	ns	0.42	ns	120
DY630620	MHC class IA antigen	ns	ns	0.0026	ns	120
DY630701	MHC class II alpha subunit	ns	ns	0.49	ns	764
DY630701	MHC class II alpha subunit	ns	ns	0.0053	ns	764
DY631898	MHC class II antigen alpha chain	ns	ns	0.94	ns	87.8
DY631898	MHC class II antigen alpha chain	ns	ns	0.0004	ns	87.8
DY631847	Mitotic spindle assembly checkpoint protein MAD2A	0.60	ns	ns	ns	374
DY631847	Mitotic spindle assembly checkpoint protein MAD2A	0.0008	ns	ns	ns	374
DY627079	Muscle-type creatine kinase CKM2	ns	0.41	ns	ns	787
DY627079	Muscle-type creatine kinase CKM2	ns	0.0049	ns	ns	787
CN469375^2/3	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	ns	0.69	ns	ns	663
CN469375^2/3	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	ns	0.0003	ns	ns	663
DY628779	Post-GPI attachment to proteins factor 2	ns	0.87	ns	ns	123
DY628779	Post-GPI attachment to proteins factor 2	ns	0.0002	ns	ns	123
DY626114^2/2	Ras association domain-containing protein 4	ns	0.82	ns	ns	1086
DY626114^2/2	Ras association domain-containing protein 4	ns	0.0001	ns	ns	1086
DY630104	Ras-related C3 botulinum toxin substrate 2	1.44	0.83	1.47	1.90	331
DY630104	Ras-related C3 botulinum toxin substrate 2	8E-06	0.0003	7E-06	1E-06	331
DY630508^1/3	Replication factor C subunit 5	1.04	ns	ns	ns	1234
DY630508^1/3	Replication factor C subunit 5	2E-05	ns	ns	ns	1234
DY628495	Ribosomal protein, large P2 (60S)	ns	ns	ns	1.01	161
DY628495	Ribosomal protein, large P2 (60S)	ns	ns	ns	0.0001	161
DY630832^2/3	Ribosomal protein S20 (40S)	ns	0.65	ns	ns	663
DY630832^2/3	Ribosomal protein S20 (40S)	ns	0.001	ns	ns	663
DY626643	Serine/threonine phosphatase gene	ns	0.57	0.57	0.54	87.8
DY626643	Serine/threonine phosphatase gene	ns	0.0004	0.0004	0.0063	87.8
CN470072	Sestrin 3	ns	1.30	1.61	1.70	116
CN470072	Sestrin 3	ns	0.0007	0.0002	0.0002	116
DY629126	Short coiled-coil protein	ns	ns	ns	0.59	242
DY629126	Short coiled-coil protein	ns	ns	ns	0.0025	242
DY630540	Small inducible cytokine SCYA102	ns	0.64	ns	ns	1204
DY630540	Small inducible cytokine SCYA102	ns	0.0019	ns	ns	1204
CN471492	Solute carrier family 9 (sodium/hydrogen exchanger)	ns	ns	0.63	ns	197
CN471492	Solute carrier family 9 (sodium/hydrogen exchanger)	ns	ns	0.0021	ns	197
CN471103^1/3	Ubiquitin	ns	ns	1.27	ns	985
CN471103^1/3	Ubiquitin	ns	ns	0.0042	ns	985
DY629776	UDP glycosyltransferase 2 family, polypeptide A1	ns	0.92	ns	ns	304
DY629776	UDP glycosyltransferase 2 family, polypeptide A1	ns	0.0006	ns	ns	304
CN469822	Vacuolar ATP synthase subunit G 1	0.79	ns	ns	ns	277
CN469822	Vacuolar ATP synthase subunit G 1	0.0007	ns	ns	ns	277
DY632057	Pituitary adenylate cyclase activating polypeptide receptor 1A	ns	1.73	1.98	1.79	170
DY626009	Non-LTR retrotransposon Rex1a	0.70	ns	ns	ns	82.4
DY626009	Non-LTR retrotransposon Rex1a	0.002	ns	ns	ns	82.4
DY629391	Non-LTR retrotransposon Rex3_Tet	0.94	ns	ns	ns	122
DY629391	Non-LTR retrotransposon Rex3_Tet	0.0028	ns	ns	ns	122
DY631649	SINE sequence	ns	0.78	ns	ns	138
DY631649	SINE sequence	ns	0.0002	ns	ns	138

Genomic Content Value: Log2 Hybridization coefficients for each species relative to A. burtoni as estimated by the linear model following background correction and normalization followed by the uncorrected p-value for those significantly different (P < FDR 0.1). BitScore: the quality of the alignment for the annotated homology. A.twe: A. tweddlei; M.est: M. estherae; P.sim: P. similis; R.chi: R. “chilingali”; “ns”: not significant; superscript numbers: when multiple array features represent a gene, these numbers indicate the number of significant array features and the total number of array features for that gene represented in the table by a single GenBank number and data row.

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ISSN: 1471-2164

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