Comparative Genomics Studies Of Comamonas Testosteroni And Lysobacter And Anchoring Of The Maize B73 BIBAC Clones On The B73 Reference Sequence

Comparative genomics is a research field in which biological method is used to compare DNA sequences, genes, gene orders, regulatory sequences and other genome features at the full or partial genome level. At present, comparative genomics has been used as a powerful tool for studying biological evolution and mutation, gene functional prediction and even genome sequence assemblies. It is also used widely in the research fileds of agriculture and medicine. In this dissertation, comparative genomics was used for analyzing the Comamonas testosteroni and Lysobacter genomes and anchoring of the maize B73 BIBAC clones onto the B73 reference sequence.Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to multiple heavy metals and multiple drugs. However, comprehensive genomic analysis among C. testosteroni strains is lacked. To understand similarities and differences among the genomes of C. testosteroni, and to investigate the genome bases of the features of this species, we sequenced 10 strains of C. testosteroni and analyzed them together with other related published genome sequences. The results revealed that: 1) strains of C. testosteroni have genome sizes ranging from 5.1 to 6.0 Mb and G+C contents ranging from 61.1~61.8%. The pan-genome contained 10,165 gene families and the core genome contained 3,599 gene families. Heap’s law analysis indicated that the pan-genome of C. testosteroni may be open(α = 0.639); 2) From 31 phenotypes of 11 available C. testosteroni strains, 99.4% were found to be correlated to their corresponding genotype, indicating a high correlation between phenotypes and genotypes; 3) gene clusters for nitrate/nitrite reduction, steroids degradation and metal and multi-drug resistance were found and were highly conserved among all these genomes. These gene clusters can be used in molecular identification and MLST(Multi Locus Sequence Typing); 4) the genome similarity and nucleotide polymorphisms of C. testosteroni strains may be related to geographical distances and environmental heavy metal content. This work provided an overview on the genomes of C. testosteroni and new genome resources that would accelerate the further investigations of this species. Importantly, this work focused on the analysis of potential genetic determinants for the typical characters and found high correlation between the phenotypes and their corresponding genotypes.Members of Lysobacter are a kind of bacteria that could secretes extracellular enzyme to lyse cells of other microbe. We have sequenced the genomes of four Lysobacter strains and performed comparative genomic analysis among them before. In this study, we performed a new comparative analysis among these four genomes together with other four newly published genomes of Lysobacter strains on NCBI to understand the genomic differences between different species in this genus. The results revealed that: 1) these eight genomes have great differences; 2) there might be whole-genome expansion/contraction between the three large genomes and five small genomes; 3) the phylogenetic relationship among strain AZ78, HS124 and 13-6 is questionable. Although this study is a preliminary comparative analysis of Lysobacter genome, it provided basic data for future study on this bacteria genus, and most importantly, it pointed out the direction of the study on the genome variation of the genus Lysobacter.Our laboratory has constructed a maize B73 BIBAC library and performed Agrobacterium-mediated rice genetic transformation with randomly selected BIBAC clones. In order to obtain the sequence information of those selected BIBAC clones, we produced paired BIBAC end sequences for 1152 B73 BIBAC clones and fingerpints for 36 of them, and anchored the BIBAC clones onto the maize reference sequence using these BIBAC end sequences and fingerprints. The result revealed that: 1) due to the high component of repeat sequences, only 26.6% of clones could be anchored to single sites through paired end sequences; 2) 50% to 60% of the multi-sites anchored clones could be accurately refined to single sites by BIBAC clone fingerprints. This method could also be used in genome comparative analysis among closely related species.