Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization

Table 1 Distribution of genes associated with hotspot regions, minimum of 5 candidates on the arrays

Gene Name	# Genome Occurrences¹	#Array Occurrences²	# Array Candidates³	# Sig CNV⁴	% Sig of Candidates
mucin TcMUCII	728	506	164	121	73.7
serine carboxypeptidase	7	7	6	4	66.6
tryptophanyl-tRNA synthetase	23	8	6	4	66.6
mucin-associated surface	1377	948	437	243	55.6
retrotransposon hot	753	419	82	41	50
ATP-dependent chaperone	5	5	5	2	40
beta galactofuranosyl	66	47	10	4	40
mitogen-activated protein kinase	11	11	10	4	40
Sialidase	3209	789	135	51	37.7
clathrin coat	7	7	7	2	28.5
surface protease	425	258	88	25	28.4
myosin heavy	19	19	17	3	17.6
PIF1 helicase-like	12	12	12	2	16.6
mismatch repair	13	13	13	2	15.3
ATP-dependent DEAD/H	106	88	66	10	15.1
leucine-rich repeat	17	16	16	2	12.5
DNA topoisomerase	9	9	9	1	11.1
protein tyrosine	10	10	9	1	11.1
cytochrome c	20	18	13	1	7.6
protein transport	16	16	14	1	7.1
elongation factor	203	65	15	1	6.6
ABC transporter	33	33	33	2	6
ubiquitin-conjugating enzyme	24	24	23	1	4.3
serine/threonine protein	80	78	78	3	3.8
60S ribosomal	106	106	93	3	3.2
DNA repair	37	36	35	1	2.8
RNA-binding protein	80	72	71	2	2.8
hypothetical protein	11812	10489	9735	122	1.2
protein kinase	311	277	270	1	0.3

1. # genome occurrences = number of instances for the annotation in the genome.
2. # array occurrences = number of annotated genes with probes on the arrays.
3. # array candidates = number of annotated genes represented by probes on the arrays and which had probe density of 5 unique probes per 500 bp. Genes could have insufficient probe density due to repeat regions or they could have too few probes due to length of the gene (minimum of 5 probes).
4. # sig CNV = CNV with a minimum log2 ratio difference of +/- 0.5, for a minimum of 5 probes over a segment size of 500 bp in at least 5 test strains.

ISSN: 1471-2164