Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

Patil, Shrikant; Moeys, Sara; von Dassow, Peter; Huysman, Marie J. J.; Mapleson, Daniel; De Veylder, Lieven; Sanges, Remo; Vyverman, Wim; Montresor, Marina; Ferrante, Maria Immacolata

doi:10.1186/s12864-015-1983-5

Table 2 Protein, gene model or transcript IDs for the genes involved in meiosis analyzed in this study

From: Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

Protein name	Accession numbers of proteins used as query	Thalassiosira pseudonana protein ID	Phaeodactylum tricornutum protein ID	Fragilariopsis cylindrus protein ID	Pseudo-nitzschia multiseries protein ID	Pseudo-nitzschia multistriata gene model ID	Seminavis robusta Transcript ID
DNA replication and chromosome maintenance
Mcm2	NP_001185154.1	29936	18622	204899	209470	0061270.1	Semro_comp78811_c0_seq1
Mcm3	Q9FL33.1	34975	51597	264318	318351	0004850.1	Semro_comp50104_c0_seq1
Mcm4	NP_179236.3	269123	51412	146869	203268	0078600.1^b	Semro_comp82592_c0_seq1
Mcm5	NP_001189521.1	31609	11490	224321	255529	0118810.1	Semro_comp83065_c1_seq1
Mcm6	AED95141.1	26545	468	193082	321321	0022580.1	Semro_comp61600_c0_seq1
Mcm7	P43299.2	262526	13243	184349	243980	0109820.1	Semro_comp70058_c0_seq2
Mcm8	NP_187577.1	261512	52561	189062	213178	0068370.1	Semro_comp79168_c0_seq3
Mcm9	NP_179021.3	37362	981	156569	183315	0056900.1	Semro_comp59174_c0_seq1
Smc1	AEE79265.1	35499	25506	212269	162817	0116990.1	Semro_comp83927_c0_seq1
Smc2	NP_201047.1	1393	30352	210755	191984	0096310.1	Semro_comp61213_c0_seq1
Smc3	NP_180285.4	259020	52607	208027	251818	0079810.1	Semro_comp78328_c0_seq1
Smc4	AED95695.1	42365	44165	212991	144962	0030660.1	Semro_comp76089_c0_seq1
Smc5	AED92224.1	9851	54192	193562	286374	0102810.1	Semro_comp64598_c0_seq1
Smc6	NP_196383.1	1743	36853	177172	165557	0090050.1	Semro_comp65344_c0_seq1
Pds5	NP_177883.5	5929	1590	136077	203285	0089060.1	Semro_comp82484_c0_seq6
Scc3	AEC10920.1	8747	51870	234878	38865	0079350.1	Semro_comp20575_c0_seq1
Rec8/Syn1^a	NP_196168.1	NF	NF	NF	NF	NF	NF
Rad21	NP_851110.1	8557	44595	245879	324402	0072170.1	Semro_comp80503_c0_seq6
Double-strand break formation
Spo11-1^a	AEE75304.1	NF	NF	NF	NF	NF	NF
Spo11-2^a	AEE34178.1	263510	36531	242364	156625	0108120.1^b	Semro_comp74200_c0_seq1
Spo11-3/Top VIA	NP_195902.1	42646	24838	239125	251788	0081370.1	Semro_comp59497_c0_seq2
DNA damage sensing and response
Rad50	AEC08614.1	9195	51876	243939	320939	0001820.1	Semro_comp61512_c0_seq1
Mre11	NP_200237.1	34332	54699	275781	233741	0086370.1	Semro_comp82091_c0_seq3
Xrs2/Nbs1	ABA54896.1	NF	NF	NF	NF	NF	NF
Crossover regulation
Mer3^a	AAX14498.1	11979	39994	239915	285411	0087420.1	Semro_comp60890_c0_seq1
Hop1/Asy1^a	AEE34638.1	NF	NF	NF	NF	NF	NF
Red1/Asy3^a	AEC10782.1	NF	NF	NF	NF	NF	NF
Zip1/Zyp1^a	AEE30217.1	NF	NF	NF	NF	NF	NF
Zip2^a	NP_011265.1	NF	NF	NF	NF	NF	NF
Zip3/Hei10^a	NP_175754.2	NF	NF	NF	NF	NF	NF
Zip4^a	ABO71664.1	NF	NF	NF	NF	NF	NF
Dmc1^a	AAC49617.1	NF	NF	NF	NF	NF	NF
Hop2^a	CAF28783.1	NF	NF	NF	NF	NF	NF
Mnd1^a	NP_194646.2	25513	54296	273989	295346	0080640.1	Semro_comp20014_c0_seq1
Msh4^a	AAT70180.1	261368	51916	144820	259109	0116300.1^b	Semro_comp57561_c0_seq2
Msh5^a	NP_188683.3	16039	52173	149505	183820	0023810.1	Semro_comp80580_c0_seq6
Double-strand break repair (recombinational repair)
Rad51-A	BAE99388.1	261303	51999	165795 (A1) 197408 (A2)	212272 (A1) 1352 (A2)	0056780.1 (A1) 0086180.1 (A2)	Semro_comp76648_c0_seq1
Rad51-B	NP_180423.3	261577	40092	241710	325273	0105810.1	Semro_comp71219_c0_seq1
Rad51-C	CAC14091.1	257784^b	54137	201530	29459	0104040.1	Semro_comp71710_c0_seq3
Rad51-D	NP_001077479.1	NF	NF	NF	NF	NF	NF
Xrcc2	NP_201257.2	NF	NF	NF	NF	NF	NF
Xrcc3	NP_200554.1	2081^c	31781	242664^c	292867^c	comp26486_c0_seq1^c	Semro_comp70556_c0_seq2^c
Rec-A	BAE99388.1	267595	51425	186275	166360	0063260.1	Semro_comp77000_c0_seq1
Rad52	CAA86623.1	25447	49083	238228	50181	0088620.1	Semro_comp79910_c0_seq1
Rad1	Q9LKI5.2	22869	30908	208467	230429	0074360.1^b	Semro_comp82187_c0_seq2
Msh2	AEE76112.1	32661	19604	159571	153636	0083140.1	Semro_comp80478_c0_seq1
Msh6	NP_001190656.1	261781	53969	212924	190397	0084190.1	Semro_comp80580_c0_seq6
Mlh1	NP_567345.2	263509	54331	136590	257081	0125040.1	Semro_comp75421_c0_seq1
Mlh2	NP 013135.1	NF	NF	NF	NF	NF	NF
Mlh3	NP_195277.5	NF	NF	NF	NF	NF	NF
Pms1	AAM00563.1	264783	14607	248102	242883	0117080.1	Semro_comp73186_c0_seq1
Mms4/Eme1	AAF06816.1	NF	NF	NF	NF	NF	NF
Mus81	NP_194816.2	NF	36625	241086	63674	0100930.1^b	Semro_comp84506_c0_seq2
Fancm	NP_001185141.1	11922	47619	248113	68428	0010100.1	Semro_comp74927_c0_seq1^c
Accessory proteins required during meiosis
Fen1	AED93576.1	269347	48638	206746	260195	0006800.1	Semro_comp51200_c0_seq1
Exo1	Q8L6Z7.2	4742	48206	261553	110816	0067080.1	Semro_comp61722_c0_seq1
Dna2	NP_001184943.1	10652	35426	241656	326992	0027070.1	Semro_comp83726_c0_seq1
Brca1	AAO39850.1	NF	NF	NF	NF	NF	NF
Brca2	AEE81814.1	6763	36784	253990	284242	0067160.1	Semro_comp82255_c0_seq4

Genes marked with ^a are genes that do not have known functions outside meiosis. Arabidopsis thaliana meiotic proteins were used as query sequence; whenever the specific query gene was not found/present in A. thaliana, Saccharomyces cerevisiae proteins were used (accession numbers in bold). Protein IDs are given for the diatom genomes available at the JGI portal, gene models IDs are given for the Pseudo-nitzschia multistriata genome and transcripts IDs for Seminavis robusta. Actual gene model IDs for P. multistriata include the prefix PSNMU-V1.4_AUG-EV-PASAV3
^bcorrected gene model, NF not found, ^cgene model might need validation

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