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Table 2 Comparison of expected and observed numbers of GBS loci of selected hybrid Phytophthora species in clades 1, 6 and 7

From: Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Clade Parental species Number of parental loci Hybrid species Number of hybrid loci
Observed Uniquea Shared Expectedb Observed Shared with parental species
1a P. cactorum 15,565 3707 11,858 P. ×serendipita 19,621 19,181 15,231
P. hedraiandra 15,914 4056 15,444
1a P. cactorum 15,565 3827 11,738 P. cactorum ×
P. hedraiandra-related1
19,243 18,325 14,812
P. hedraiandra-related1 15,416 3678 14,639
1a P. hedraiandra 15,914 3055 12,859 P. hedraiandra ×
P. hedraiandra-related1
18,471 18,081 15,363
P. hedraiandra-related1 15,416 2557 14,961
1a P. cactorum 15,565 14,000 1565 P. ×pelgrandis 28,992 27,550 14,706
1 P. nicotianae 14,992 13,427 13,194
6b P. thermophila 21,405 13,904 7501 P. thermophila ×
P. amnicola
36,190 32,562 19,368
P. amnicola 22,286 14,785 19,083
6b P. amnicola 22,286 14,828 7458 P. amnicola ×
P. chlamydospora
35,077 32,010 17,966
P. chlamydospora 20,249 12,791 19,378
6b P. chlamydospora 20,249 15,356 4893 P. chlamydospora ×
P. lacustris
38,305 31,337 17,760
P. lacustris 22,949 18,056 16,028
7a P. uniformis 22,757 10,059 12,698 P. ×alni 46,703 45,128 21,957
P. ×multiformis 36,644 23,946 34,259
7b P. niederhauseric 15770c 14,183 1587 P. niederhauseri ×
P. asparagi-related
42,486 42,192 15,770
6 P. asparagid 28,303 26,716 24,851
  1. aNumber of unique loci calculated as the average number of loci for the species minus the average number of loci shared with the other parental species
  2. bExpected loci in the hybrid calculated as the sum of the number of unique loci for each parental species and the number of loci shared between the parental species
  3. cBecause P. niederhauseri is a hybrid itself, the theoretical number of loci for non-hybrid P. niederhauseri was estimated based on the number of shared loci of the P. niederhauseri × P. asparagi-related hybrid and the hybrid P. niederhauseri isolates that have an allele similarity = 93%
  4. dP. asparagi-related is not present in our set of isolates so P. asparagi was used instead, assuming it has a similar number of loci