GENOMES - Cyanobacteria - page 95

Synechococcus sp. strain RCC307 which has one rRNA gene. However, the number of tRNA genes
is variable from 42 (BL107) to 46 (RS9917) or 48 (WH7805 and WH5701).
After a comparison of Synechococcus genomes, Dufresne et al . (2008) identifi ed 1572 gene
families that constitute a core genome in this genus. This represents 52% of the total genome of
Synechococcus sp. strain WH5701 and 67% of the total genome of Synechococcus sp. strain CC9902.
When a comparison is made with Prochlorococcus , the number of gene families in the core genome is
further reduced to 1228 gene families. However, Palenik et al . (2003) identifi ed 1314 genes common
to Synechococcus sp. strain WH8102 and Prochlorococcus strain MED4 and MIT9313 and 736 genes
specifi c to Synechococcus sp. strain WH8102.
There is fairly a constant number of genes (748±85) shared by 2-10 Synechococcus genomes.
Signifi cantly, four Synechococcus genomes (BL107, CC9311, CC9605 and CC9902) are characteristic
in possessing isiA and isiB genes that encode PSI antenna protein CP43 and fl avodoxin, respectively
that are separated while in other freshwater cyanobacteria these two genes are present in the same
operon. Additionally, the genomes of these four strains also showed a ferredoxin gene existing in
four to fi ve copies that makes them versatile in switching over from iron-depleted (fl avodoxin) to
iron-enriched habitats (ferredoxin). There is a considerable degree of variation in the presence of
unique genes (from 91 to 845) depending on genome size. These are distributed in a region called
as 'genomic islands' that are characterized by (i) a deviation in tetranucleotide frequency, (ii) longer
intergenic sequences (~105 bp) than shorter intergenic regions (~50 bp) outside these islands, (iii) a
correlation between the size of genomic islands and the length of the genome in general, (iv) a high
degree of similarity in genes that are shared by 11 genomes and (v) the acquisition of these genes
through LGT. Similarly, in the genome of Synechococcus sp. strain WH 8102 the genes governing
utilization of broad range of nitrogenous substances, some having transport potential, cell envelope
genes, genes governing sialic acid synthesis in regions of low G+C content point out to the group of
recently acquired genes through LGT. The existence of 16 probable phage integrases (that encode
site-specifi c recombinases) in the regions of low G+C of the genome of Synechococcus sp. strain WH
8102 prompted Palenik et al. (2003) to conclude that these are akin to pathogenicity islands transferred
between strains of pathogenic bacteria.
vii) Genome of S. elongatus PCC 6301 (formerly Anacystis nidulans Berkeley strain 6301) : The
complete nucleotide sequence of this freshwater cyanobacterium was determined by Sugita et al .
(2006) and is available at web database, CYORF (http://www.cyano.genome.jp/). The genome of
this organism consists of a single circular chromosome of 2,696,255 bp long with a G+C content of
55.5%. The number of protein-coding genes assigned on the chromosome is 2,525. The potential
protein-coding genes (56%) showed sequence similarities to known function. 35% of the genes
showed sequence similarities to the hypothetical genes. The rest of the 9% genes have no signifi cant
similarities to any of the predicted proteins in the public DNA databases. Two copies of rRNA gene
cluster (rrnA and rrnB) have been assigned on the chromosome at 1,050 kb and 1,650 kb positions in
the order of 16S-23S-5S. These two operons are separated at a distance of 6,05,653 bp measured from
5'-ends of the clusters. A total of 42 tRNA genes representing 42 tRNA species have been identifi ed
on the chromosome.
viii) Genome of Synechocystis sp . strain PCC 6803: Kaneko et al . (1995, 1996) determined the
sequences of the entire genome and assigned the essential protein-coding regions. Synechocystis
sp. strain PCC 6803 has a circular chromosome with a total of 3,573,470 bp and G+C content of
47.7%. The length of the genome closely corresponded to the estimation of genome size (3.6 Mb)
determined on the basis of restriction and linking analysis performed earlier by Kotani et al . (1994). A