Whole genome sequencing of a natural recombinant Toxoplasma gondiistrain reveals chromosome sorting and local allelic variants

Table 6 Calculation of the MRCA of Ugandan type II and III isolates and reference strains based on their relationship to the divergence between Me49 and VEG

Chromosome	Length* (bp)	Minor SNPs	Major SNPs	MRCA Me49/UgII (years)	MRCA VEG/UgIII (years)
Type II
II	2,302,931	125	4,370	4,291
IV	2,576,468	236	4,731	7,483
VI > 2.6 Mb	1,000,655	70	1,913	5,489
VIIa	4,502,211	135	8,663	2,338
IX 0.5-4 Mb	3,500,000	205	6,349	4,843
X	7,418,475	445	13,459	4,960
Total II	21,300,740	1,216	39,845	4,578
Type III
Ib > 1.2 Mb	756,324	6	1,375		655
III < 1.9 Mb	1,900,000	33	3,953		1,252
V	3,147,601	80	5,725		2,096
VIIb < 2.5 Mb	2,500,000	43	5,069		1,272
VIII > 4 Mb	2,923,375	49	6,268		1,173
XII < 1.5 Mb	1,500,000	69	3,259		3,176
Total III	12,727,300	280	25,648		1,638

The divergence between Ugandan and reference strains were calculated based on their relationship to the divergence between Me49 and VEG, with the MRCA estimated to be at 150,000 years ago [27]. A more comprehensive version is provided in Additional data file 4. *Length of regions with a major SNP type. MRCA, most recent common ancestor.

ISSN: 1474-760X