Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis

BMC Genomics

Table 5 Classification of pseudogenes according to their possible origin.

Species	Species-specific duplication^a	Ancestral duplication^b	Function loss^c	duplicated pseudos ^d	duplicated segment ^e	retros ^f
S. cerevisiae	73	1	3	1	0	1, 6
C. glabrata	27	3	8	1	1	3, 0
Z. rouxii	71	20	14	6	41	1, 3
K. thermotolerans	39	11	18	0	17	0, 16
S. kluyveri	65	23	29	4	13	1, 12
K. lactis	35	12	14	5	7	0, 4
D. hansenii	153	14	8	2	62	1, 3
Y. lipolytica	213	11	6	6	19	2, 8

^a. number of pseudogenes originating from mutational inactivation of a duplicated gene copy formed after speciation.
^b. number of pseudogenes originating from mutational inactivation of a duplicated gene copy formed before speciation.
^c. number of pseudogenes originating from mutational inactivation of a single copy gene.
^d. number of duplicated pseudogenes among the first category (^a).
^e. number of pseudogenes being part of a duplicated segment involving other adjacent genes among the first category (^a).
^f. number of retro-processed pseudogenes, among the first category (^a), identified by: either the presence of a 3' poly(A)-tail (first number) or the proximity of retrotransposon-related sequence (second number). In each species, the candidates identified by these 2 criteria are different.

ISSN: 1471-2164