The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes

Table 2 Non-LTR retrotransposons in Ciona

	Deuterostomes		Protostomes	Other organisms^‡
Non-LTR clade	Ciona copy number*	Vertebrates (copy number in Fugu [15])	Copy number in D. melanogaster [30] and A. gambiae [31]^†
CR1		+ (NF^§)	+ (NF, 152)
CRE			+ (NF, NF)
I	+ (6-9)		+ (67, 19)
Jockey			+ (392, 28)
L1	+ (4-22)	+ (500)	+^¶	+
L2	+ (4-24)	+ (6,500)	+ (NF, NF)
LOA	+ (7-69)		+ (18, 19)
NeSL1			+ (NF, NF)
R1			+ (130, 3^¥)
R2	+ (3-13)		+ (0, NF)
R4		+ (1,000)	+ (NF, 2)
Rex1		+ (2,000)		+
RTE		+ (2,300)	+ (NF, 167)
Tad1				+
Total copy number	24-137	12,300	607, 390
Clade complexity**	Five in Ciona	Five in Fugu	Five in D. melanogaster and seven in A. gambiae

*Detailed in Table 1. ^†The first number in parentheses refers to D. melanogaster, the second to Aedes aegypti. ^‡See Figure 3. ^§NF, not found. ^¶Probably present in A. gambiae [31]. ^¥Underestimated in Holt et al. [31]. **Number of different clades.

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