Gap in synteny of plot but apparently syntenic genes in synHits

[Rowena-h]

Firstly, thanks for your fantastic tool!

I have a situation I'm not sure how to interpret. I have a big gap in synteny for one contig (circled in red).

Wanting to see what genes are in that gap region of Gt-23d, I dug into the syntenicBlock_coordinates file to figure out where the gap started and then looked at the corresponding synHits file to see what genes were there. However, I was a bit confused to see that the genes continued to blast to contiguous genes in the other genome and that were in the same orthogroup, and yet were being assigned to a different blkID per gene. Here's an extract of the synHits as it crosses the start of the gap (onwards from blkID Gt23d_vs_Gt8d: 390):

4_2011	Gt23d_EI_v1.1_ptg000002	181246	181905	Gt23d_EIv1_0020120.1	2012	Gt23d	TRUE	7_8271	Gt8d_EI_v1.1_ptg000005	4367039	4367628	Gt8d_EIv1_0082720.1	8272	Gt8d	TRUE	204	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 4	Gt23d_vs_Gt8d: 390
4_2012	Gt23d_EI_v1.1_ptg000002	182871	185010	Gt23d_EIv1_0020130.1	2013	Gt23d	TRUE	7_8270	Gt8d_EI_v1.1_ptg000005	4364087	4365842	Gt8d_EIv1_0082710.1	8271	Gt8d	TRUE	657	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 4	Gt23d_vs_Gt8d: 390
4_2013	Gt23d_EI_v1.1_ptg000002	185179	187531	Gt23d_EIv1_0020140.1	2014	Gt23d	TRUE	7_8269	Gt8d_EI_v1.1_ptg000005	4361507	4363805	Gt8d_EIv1_0082700.1	8270	Gt8d	TRUE	1090	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 4	Gt23d_vs_Gt8d: 390
4_2014	Gt23d_EI_v1.1_ptg000002	186839	192128	Gt23d_EIv1_0020150.1	2015	Gt23d	TRUE	7_8268	Gt8d_EI_v1.1_ptg000005	4356727	4361944	Gt8d_EIv1_0082690.1	8269	Gt8d	TRUE	2172	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 4	Gt23d_vs_Gt8d: 390
4_2015	Gt23d_EI_v1.1_ptg000002	192332	195143	Gt23d_EIv1_0020160.1	2016	Gt23d	TRUE	7_8267	Gt8d_EI_v1.1_ptg000005	4353859	4356407	Gt8d_EIv1_0082680.1	8268	Gt8d	TRUE	1092	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 4	Gt23d_vs_Gt8d: 390
4_2016	Gt23d_EI_v1.1_ptg000002	195401	198386	Gt23d_EIv1_0020170.1	2017	Gt23d	TRUE	7_8266	Gt8d_EI_v1.1_ptg000005	4351120	4353539	Gt8d_EIv1_0082670.1	8267	Gt8d	TRUE	1006	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 4	Gt23d_vs_Gt8d: 390
4_2017	Gt23d_EI_v1.1_ptg000002	197234	199515	Gt23d_EIv1_0020180.1	2018	Gt23d	TRUE	7_8265	Gt8d_EI_v1.1_ptg000005	4350099	4351593	Gt8d_EIv1_0082660.1	8266	Gt8d	TRUE	669	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 4	Gt23d_vs_Gt8d: 390
4_202	Gt23d_EI_v1.1_ptg000001	592941	596711	Gt23d_EIv1_0002030.1	203	Gt23d	TRUE	7_5223	Gt8d_EI_v1.1_ptg000004	652674	658015	Gt8d_EIv1_0052240.1	5224	Gt8d	TRUE	2012	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 3	Gt23d_vs_Gt8d: 40
4_2025	Gt23d_EI_v1.1_ptg000002	229428	235473	Gt23d_EIv1_0020260.1	2026	Gt23d	TRUE	7_8195	Gt8d_EI_v1.1_ptg000005	4109263	4115297	Gt8d_EIv1_0081960.1	8196	Gt8d	TRUE	2517	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 269
4_2026	Gt23d_EI_v1.1_ptg000002	229556	231195	Gt23d_EIv1_0020270.1	2027	Gt23d	TRUE	7_8196	Gt8d_EI_v1.1_ptg000005	4109392	4111031	Gt8d_EIv1_0081970.1	8197	Gt8d	TRUE	865	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 271
4_2027	Gt23d_EI_v1.1_ptg000002	235732	237511	Gt23d_EIv1_0020280.1	2028	Gt23d	TRUE	7_8197	Gt8d_EI_v1.1_ptg000005	4115538	4117357	Gt8d_EIv1_0081980.1	8198	Gt8d	TRUE	805	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 272
4_2028	Gt23d_EI_v1.1_ptg000002	237594	239740	Gt23d_EIv1_0020290.1	2029	Gt23d	TRUE	7_8198	Gt8d_EI_v1.1_ptg000005	4117423	4119502	Gt8d_EIv1_0081990.1	8199	Gt8d	TRUE	880	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 274
4_2029	Gt23d_EI_v1.1_ptg000002	240845	242189	Gt23d_EIv1_0020300.1	2030	Gt23d	TRUE	7_8199	Gt8d_EI_v1.1_ptg000005	4120696	4122068	Gt8d_EIv1_0082000.1	8200	Gt8d	TRUE	276	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 276
4_203	Gt23d_EI_v1.1_ptg000001	596922	598450	Gt23d_EIv1_0002040.1	204	Gt23d	TRUE	7_5225	Gt8d_EI_v1.1_ptg000004	658174	659619	Gt8d_EIv1_0052260.1	5226	Gt8d	TRUE	671	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 3	Gt23d_vs_Gt8d: 40
4_2030	Gt23d_EI_v1.1_ptg000002	244166	246375	Gt23d_EIv1_0020310.1	2031	Gt23d	TRUE	7_8201	Gt8d_EI_v1.1_ptg000005	4124099	4126327	Gt8d_EIv1_0082020.1	8202	Gt8d	TRUE	958	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 278
4_2031	Gt23d_EI_v1.1_ptg000002	246939	248975	Gt23d_EIv1_0020320.1	2032	Gt23d	TRUE	7_8202	Gt8d_EI_v1.1_ptg000005	4126375	4128747	Gt8d_EIv1_0082030.1	8203	Gt8d	TRUE	767	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 280
4_2032	Gt23d_EI_v1.1_ptg000002	249109	250735	Gt23d_EIv1_0020330.1	2033	Gt23d	TRUE	7_8203	Gt8d_EI_v1.1_ptg000005	4128798	4131667	Gt8d_EIv1_0082040.1	8204	Gt8d	TRUE	849	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 282
4_2033	Gt23d_EI_v1.1_ptg000002	251834	254192	Gt23d_EIv1_0020340.1	2034	Gt23d	TRUE	7_8204	Gt8d_EI_v1.1_ptg000005	4131621	4134003	Gt8d_EIv1_0082050.1	8205	Gt8d	TRUE	639	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 284
4_2034	Gt23d_EI_v1.1_ptg000002	257302	262684	Gt23d_EIv1_0020350.1	2035	Gt23d	TRUE	7_8205	Gt8d_EI_v1.1_ptg000005	4136525	4142519	Gt8d_EIv1_0082060.1	8206	Gt8d	TRUE	2293	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 285
4_2035	Gt23d_EI_v1.1_ptg000002	262734	263475	Gt23d_EIv1_0020360.1	2036	Gt23d	TRUE	7_8206	Gt8d_EI_v1.1_ptg000005	4142552	4143296	Gt8d_EIv1_0082070.1	8207	Gt8d	TRUE	203	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 287
4_2036	Gt23d_EI_v1.1_ptg000002	263585	265717	Gt23d_EIv1_0020370.1	2037	Gt23d	TRUE	7_8207	Gt8d_EI_v1.1_ptg000005	4143339	4145477	Gt8d_EIv1_0082080.1	8208	Gt8d	TRUE	832	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 289
4_2037	Gt23d_EI_v1.1_ptg000002	265005	267598	Gt23d_EIv1_0020380.1	2038	Gt23d	TRUE	7_8208	Gt8d_EI_v1.1_ptg000005	4144843	4147424	Gt8d_EIv1_0082090.1	8209	Gt8d	TRUE	858	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 291
4_2038	Gt23d_EI_v1.1_ptg000002	267727	272230	Gt23d_EIv1_0020390.1	2039	Gt23d	TRUE	7_8209	Gt8d_EI_v1.1_ptg000005	4147552	4152061	Gt8d_EIv1_0082100.1	8210	Gt8d	TRUE	1937	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 293
4_2039	Gt23d_EI_v1.1_ptg000002	271972	273444	Gt23d_EIv1_0020400.1	2040	Gt23d	TRUE	7_8210	Gt8d_EI_v1.1_ptg000005	4151767	4153412	Gt8d_EIv1_0082110.1	8211	Gt8d	TRUE	528	TRUE	FALSE	TRUE	Gt23d_vs_Gt8d: 5	Gt23d_vs_Gt8d: 295

I guess I'm either misunderstanding the output files or missing some idiosyncrasy in how GENESPACE defines synteny, but I was wondering why the plot ends up with a gap when to my eyes it looks like there are syntenic genes across the region.

I did notice that there seems to be a funny numerical sorting thing happening across rows in the synHits file e.g. going from 4_2017 to 4_202 before back to 4_2025, is that contributing to breaking up the blkIDs?

I've attached some full files in case that helps.

Thanks!

syntenicBlock_coordinates.csv

Gt23d_pangenes.txt

Gt23d_vs_Gt8d.synHits.txt