The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA

BMC Genomics

Table 1 Amount of nuclear DNA in Volvox carteri that maps to the mitochondrial and plastid genomes.

		# of similarity regions^a	Avg. length of similarity region (nt)	Max similarity length (nt)	Cumulative lengths of similarity regions (nt)	Fraction of nuclear genome
Amount of nucDNA mapping to the mitochondrial genome (by mtDNA subcategory^b)	Protein-coding genes^c	114	64	291	7335	6.70 × 10^-5
	Sructural-RNA genes^d	73	40	207	2969	2.70 × 10^-5
	Intronic ORFs^e	278	30	233	278	0.25 × 10^-5
	Intergenic and non-ORF intronic regions^f	337	38	933	14782	13.53 × 10^-5
	Subtotal	802	39	933	33452	30.63 × 10^-5
Amount of nucDNA mapping to the plastid genome (by ptDNA subcategory^b)	Protein-coding genes^c	365	48	462	17440	15.90 × 10^-5
	Structural-RNA genes^d	127	31	170	4008	3.60 × 10^-5
	Intronic ORFs^e	31	34	154	1075	0.98 × 10^-5
	Intergenic and non-ORF intronic regions^f	927	22	3430	50631	46.36 × 10^-5
	Subtotal	1450	29	3430	73154	66.99 × 10^-5
Total nucDNA mapping to organelle DNA		2252	33	3430	106606	97.62 × 10^-5

Note: Nuclear DNA analyses are based on the V. carteri draft nuclear genome sequence (version 1) at the DOE JGI [18]. Only the first 75 scaffolds of the nuclear-genome assembly were analyzed; approximately 78% of the V. carteri nucDNA is contained in these 75 scaffolds and their cumulative length is 109.2 Mb.
^a The number of distinct regions in the V. carteri nucDNA that show >90% sequence identity and at least 25 nt of aligned length to organelle DNA.
^b Refers to the region of the organelle genome to which the nucDNA maps.
^c Includes all of the identified protein-coding genes.
^d Includes all of the identified tRNA- and rRNA-coding genes.
^e Includes all of the identified group I and II intronic-ORFs.
^f Includes all of the identified intergenic and non-ORF intronic regions.

ISSN: 1471-2164