Year: 2015
Type: article
Abstract: Initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a Monte Carlo method to estimate the conservation of gene order. The method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. The raw distances were then corrected for gene order convergence using an adaptation of the Jukes-Cantor model, as well as using the common distance correction D' = -ln(1-D). First, we compared the distances found via the order of six orthologs to distances found based on ortholog gene content and small subunit rRNA sequences. The Jukes-Cantor gene order distances are reasonably well correlated with the divergence of rRNA (R (2) = 0.24), especially at rRNA Jukes-Cantor distances of less than 0.2 (R (2) = 0.52). Gene content is only weakly correlated with rRNA divergence (R (2) = 0.04) over all distances, however, it is especially strongly correlated at rRNA Jukes-Cantor distances of less than 0.1 (R (2) = 0.67). This initial work suggests that gene order may be useful in conjunction with other methods to help understand the relatedness of genomes. Using the gene order distances in 143 genomes, the relations of prokaryotes were studied using neighbor joining and agreement subtrees. We then repeated our study of the relations of prokaryotes using gene order in 172 complete genomes better representing a wider-diversity of prokaryotes. Consistently, our trees show the Actinobacteria as a sister group to the bulk of the Firmicutes. In fact, the robustness of gene order support was found to be considerably greater for uniting these two phyla than for uniting any of the proteobacterial classes together. The results are supportive of the idea that Actinobacteria and Firmicutes are closely related, which in turn implies a single origin for the gram-positive cell.
Source: Frontiers in Microbiology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,801
Awards: TITLE: SIGNATURES OF LIFE FROM EARTH AND BEYOND IS IN RESPONSE TO CAN #NNH08ZDA002C NASA ASTROBIOLOGY INSTITUTE - CYCLE 5 BASIC AWARD FOR CYCLE FIVE OF NAI TO PENN STATE.1260.51 COOPERATIVE AGREEMENT SPECIAL CONDITION. (OCTOBER 2000) (A) THIS AWARD IS A COOPERATIVE AGREEMENT AS IT IS ANTICIPATED THERE WILL BE SUBSTANTIAL NASA INVOLVEMENT DURING PERFORMANCE OF THE EFFORT. NASA AND THE RECIPIENT MUTUALLY AGREE TO THE FOLLOWING STATEMENT OF ANTICIPATED COOPERATIVE INTERACTIONS WHICH MAY OCCUR DURING THE PERFORMANCE OF THIS EFFORT: NAI CENTRAL IS RESPONSIBLE FOR COORDINATING INSTITUTE ACTIVITIES ADVOCATING THE NEEDS & SCIENTIFIC INTERESTS OF THE MEMBERS OF THIS COOPERATIVE AGREEMENT DISBURSING FUNDS (INCLUDING A STRATEGIC DIRECTOR S DISCRETIONARY FUND FOR HIGH-RISK/HIGH-PAYOFF RESEARCH PROJECTS AND FOR FOSTERING COLLABORATION BETWEEN MEMBERS) SPONSORING THE NAI POSTDOCTORAL FELLOWSHIP PROGRAM COLLECTING AND ARCHIVING INFORMATION ON RESEARCH ACCOMPLISHMENTS & PUBLICATIONS ORGANIZING FOCUS GROUP MEETINGS & WORKSHOPS & EXPEDITING NETWORK CONNECTIVITY WHILE ENGINEERING THE INTERFACES BETWEEN THE SCIENTISTS & THE NETWORK. NAI CENTRAL IS ALSO RESPONSIBLE FOR ORGANIZING GENERAL MEETINGS WORKSHOPS & STRATEGIC RETREATS TO ENGAGE MEMBERS OF THE INSTITUTE IN INTEGRATED RESEARCH. NAI CENTRAL WILL IN ADDITION COORDINATE INSTITUTE-WIDE ACTIVITIES IN EDUCATION & PUBLIC OUTREACH & IN THE TRAINING OF STUDENTS & OTHER YOUNG INVESTIGATORS.AT THE CORE OF ASTROBIOLOGY IS THE CONSTRUCTION OF SCIENTIFIC KNOWLEDGE THAT ENABLES THE RECOGNITION OF SIGNATURES OF LIFE ON EARLY EARTH IN EXTREME ENVIRONMENTS AND IN EXTRATERRESTRIAL SETTINGS. TOGETHER WITH NEW CO-INVESTIGATORS FROM UNIVERSITY OF CALIFORNIA LOS ANGELES AND CALIFORNIA INSTITUTE OF TECHNOLOGY WE PROPOSE TO DEVELOP NOVEL APPROACHES TO DETECTING AND CHARACTERIZING LIFE INVESTIGATE BIOSIGNATURES IN MISSION-RELEVANT ECOSYSTEMS AND ANCIENT ROCKS AND EVALUATE THE POTENTIAL FOR BIOSIGNATURES IN EXTRATERRESTRIAL SETTINGS.(1) DEVELOPING NEW BIOSIGNATURES THE DEVELOPMENT AND TESTING OF POTENTIAL INDICATORS OF LIFE IS ESSENTIAL FOR PROVIDING A CRITICAL SCIENTIFIC BASIS FOR EXPLORATION OF LIFE IN THE COSMOS. OUR EFFORTS WILL FOCUS ON CREATING INNOVATIVE APPROACHES FOR THE ANALYSES OF CELLS AND OTHER ORGANIC MATERIAL FINDING WAYS IN WHICH METAL ABUNDANCES AND ISOTOPE SYSTEMS REFLECT LIFE AND DEVELOPING CREATIVE APPROACHES FOR USING ENVIRONMENTAL DNA TO STUDY PRESENT AND PAST LIFE.(2) BIOSIGNATURES IN RELEVANT MICROBIAL ECOSYSTEMS PSARC WILL INVESTIGATE MICROBIAL LIFE IN SOME OF EARTH S MOST MISSION-RELEVANT ECOSYSTEMS THE DEAD SEA THE CHESAPEAKE IMPACT STRUCTURE THE METHANE SEEPS OF THE EEL RIVER BASIN AND THE GREENLAND GLACIER ICE.(3) BIOSIGNATURES IN ANCIENT ROCKS THE EARTH S ARCHEAN AND PROTEROZOICEONS OFFER THE BEST OPPORTUNITY OF INVESTIGATING A MICROBIAL WORLD SUCH AS MIGHT BE FOUND ELSEWHERE IN THE COSMOS. THE ANCIENT RECORD ON EARTH PROVIDES ON OPPORTUNITY TO SEE WHAT GEOCHEMICAL SIGNATURES ARE PRODUCED BY MICROBIAL LIFE AND HOW THESE SIGNATURES ARE PRESERVED OVER GEOLOGIC TIME.(4) BIOSIGNATURES IN EXTRATERRESTRIAL SETTING. PSARC WILL INVESTIGATE THE ABUNDANCE OF SULFUR GASES AND ELUCIDATE HOW THESE GASES CAN BE EXPECTED TO EVOLVE WITH TIME ON YOUNG TERRESTRIAL PLANETS. WE WILL CONTINUE STUDIES OF PLANET FORMATION IN THE PRESENCE OF MIGRATION AND MODEL RADIAL TRANSPORT OF VOLATILES IN YOUNG PLANETARY SYSTEMS. FINAL PSARC WILL BE INVOLVED WITH SEARCHES FOR M STAR PLANETARY COMPANIONS AND PLANETS AROUND K-GIANT STARS.(B) THE TERMS ....(C) NASA S ABILITY TO PARTICIPATE ...., G4033973077, MEDIATION OF EARLY EVOLUTION & ECOLOGY BY CYANINDE INHIBITION?
OpenAlex ID: W2050456837