Table 1.

Pseudogenes Identified within V. canescens Genome Corresponding to Lost Nudiviral Core Genes

Function	Gene Name	Bracovirus	VcENV	Transcript Abundance in Venturia (RPKM)
DNA replication	dnapol	−	Pseudogene	4
	helicase	+	+	27
	helicase 2	Nd	nd	Nd
	Integrase	+	Pseudogene	0
	fen-1	+	Pseudogene	>1
Transcription	lef-4 (RNApol s.u.)	+	+	488
	lef-5 (RNApol s.u.)	+	+	245
	lef-8 (RNApol s.u.)	+	+	125
	lef-9 (RNApol s.u.)	+	+	724
	p47 (initiation factor)	+	+	916
Envelope component	p74	+	+	12,900
	pif-1	+	+a	5,196
	pif-2	+	+	1,980
	pif-3	+	+	2,655
	pif-4	+	+	7,731
	pif-5 (4 copiesb)	+	+	527; 863; 1,048; 2,286
	pif-6	+	+	3,011
	p33	+	+	5,553
	vp91	+	+	2,966
	Ac81 (3 copiesb)	−	+	272; 1,777; 1,080
	11K (5 copiesb)	+	+	40,978; 41,939; 980; 1,831; 4,225
Capsid component	38K (major component)	+	Pseudogene	0
	vp39 (major component)	+	Pseudogene	4
	vlf-1	+	Pseudogene	17
	OrNVorf22 (p6.9)	+	Pseudogene	9
Unknown	GbNVorf19 (3 copies)	+	+	4,555; 127; 1,032
	OrNVorf61 (PmNVorf62)	−	+	4,044
	OrNVorf18 (PmNVorf99)	+	+	6,319
	OrNVorf76 (HzNVorf143)	−	+	4,012
Nucleotid metabolism	tk1	Nd	nd	Nd
	tk2	Nd	nd	Nd
	tk3	Nd	nd	Nd

Note. —Table cells are highlighted in light or intense green depending on the presence of a functional gene or a detected pseudogene. Functions are those determined for homologous baculovirus proteins. Core genes of nudiviral origin conserved in braconid wasps associated with bracoviruses and VcENV are listed for comparison. The different values indicated in transcript abundance column correspond to the expression of the different gene copies.

^aPseudogene identified in addition to the functional core gene.

^bGene family.

−, no pseudogene detected; nd, not determined; s.u., subunit.