Transposable element distribution, abundance and role in genome size variation in the genus Oryza

Table 1 Description of genomes investigated and libraries used

Species	Genome type	Genome size (in Mbp)	Nr. of clones	Mean insert size (in Kb)	Genome fraction covered	Nr. of sequences	Mbp sequenced	% genome sequenced
O. nivara	AA	448	1920	3.4	0.015	3103	2.04	0.46
O. rufipogon	AA	439	1920	3.9	0.017	2555	1.92	0.44
O. glaberrima	AA	357	1920	2.8	0.015	3494	2.68	0.75
O. punctata	BB	425	1920	3.0	0.014	3144	1.93	0.45
O. officinalis	CC	651	2688	3.3	0.014	4848	3.84	0.59
O. minuta	BBCC	1124	5376	2.9	0.014	9459	7.19	0.64
O. alta	CCDD	1008	4032	3.4	0.014	7538	5.58	0.55
O. australiensis	EE	965	4224	2.5	0.011	7359	4.68	0.48
O. brachyantha	FF	362	1920	3.3	0.018	3377	2.38	0.66
O. granulata	GG	882	4224	3.1	0.015	6688	4.45	0.50
O. ridleyi	HHJJ	1283	6144	3.5	0.017	11091	8.16	0.64
O. coarctata	HHKK	1283*	6144	3.0	0.014	9524	6.86	0.53

All the genome size estimates are from Ammiraju et al (2006) [4] except those of O. glaberrima and O. minuta which are from Martinez et al (1994) [54] and of O. coarctata which is a rough estimate because the real genome size of this species is unknown. We therefore used the value estimated for O. ridleyi [HHJJ; 1283 Mbp], which is also an allotetraploid species and shares the HH genome type with O. coarctata.

ISSN: 2730-7182