Extended Data Table 1. Assembly and annotation statistics for the recently described assemblies compared to the present assemblies.

	PmUG01	Pmal	PmlGA01	PocGH01	Poc1	Poc2	PowCR01	Pow1	Pow2
Size (Kb)	33,618	31,925	23,693	33,485	34,519	38,010	33,579	35,285	35,192
Largest (kb)	3,564	56	3,177	2,946	94	491	3,061	569	657
Average (kb)	534	4	474	22	9	17	43	26	22
Gaps	0	2,236	3,697	894	1,224	2,049	1,264	62	79
Scaffolds	63	7,270	50	654	4,025	2,227	787	1,362	1,611
Scaffold N50 (kb)	2,312	6	2,076	1,039	18	46	990	174	137
Contigs	63	9,506	3,717	1,548	5,249	4,276	2,047	1,424	1,687
Contig N50 (kb)	2,312	5	14	39	12	17	30	140	114
Genes	6,591	6,343	4,764	7,198	7,776	8,625	7,052	8,421	8,646
1:1 Orthologs	4291	3783	3837	4296	3956	3874	4174	3950	3958
Core**
Short Genesa	102	104	109	99	69	63	88	89	85
Partial	2	551	90	18	252	201	7	4	4
Pseudo	20	0	245	10	0	0	322	0	0
Unknown functionb	1,753	1,886	1,508	1,761	1,833	1,804	1,562	1,780	1,778
>7 exon orthologs	281	204	190	280	241	251	260	252	253
Median length (>7 exon) (aa)	477	368	340	478	500	495	462	455	443
Subtelomeres**
Short Genesa	46	278	117	71	536	531	131	857	997
Partial	8	621	246	262	547	676	156	2	6
Pseudogenes	1236	3	21	978	4	6	393	11	10
Unknown functionb	765	1328	447	437	1176	1330	734	1824	2122

^aLess than 100 amino acids.

^bAnnotated as either ‘hypothetical protein’ or ‘conserved Plasmodium protein’.

^**Core defined as genes that have 1–1 orthologues between P. falciparum 3D7 and P. vivax P01.

Grey columns indicate genome assemblies from ref. 7.