Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd

Abstract

An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.

Existence of Na+‐translocating NADH‐quinone reductase in Haemophilus influenzae

“…Very recently, Venter and his coworkers [10] reported the complete nucleotide sequence (1 830 137 bp) of the genome from the bacterium H. influenzae. We performed the homology search of nqr operon with the whole genome of H. influenzae and, surprisingly, a region homologous to the nqr operon was found in the genome of H. influenzae.…”

“…In combination with these results, the nqr operon was found to be constructed from six consecutive structural genes, where nqrl, nqr3 and nqr6 corresponded to ct-, y-, and 13-subunits, respectively, of the NQR complex. Very recently, Venter and his coworkers [10] reported the complete nucleotide sequence of the genome from the bacterium Haemophilus influenzae Rd, and the homology search of nqr operon was performed with the whole genome. Surprisingly, a gene cluster almost identical to the nqr operon was found to exist in the genome of H. influenzae.…”

Yeasties and beasties: 7 years of genome sequencing

“…Not least of these, J. Craig Venter's laboratory at the Institute of Genome Research (TIGR), completed the first bacterial genomes; Haemophilus influenzae and M. genitalium for which whole genome shotgun sequencing was employed [10][11][12]. As can be seen from Random sequencing using universal primers either using flourent or radioactive labelling assemble overlapping clones to form "contigs" directed finishing stage involving custom primers and modified chemistry genome projects use shotgun methodology, including that of C. elegans.…”

A genome alignment algorithm based on compression

“…Since 1995 when the first genome of a free-living organism was sequenced [5], a number of alignment tools capable of comparing genomes have been developed. Such examples are Gapped BLAST [6], Sim4 [7], SSAHA [8], Dialign [9], MGA [10], MUM-mer [11,12], Blastz [13], Chaos [14], and AVID [15].…”