Abstract

Gluconacetobacter diazotrophicus PAl 5 is of agricultural significance due to its ability to provide fixed nitrogen to plants. Consequently, its genome sequence has been eagerly anticipated to enhance understanding of endophytic nitrogen fixation. Two groups have sequenced the PAl 5 genome from the same source (ATCC 49037), though the resulting sequences contain a surprisingly high number of differences. Therefore, an optical map of PAl 5 was constructed in order to determine which genome assembly more closely resembles the chromosomal DNA by aligning each sequence against a physical map of the genome. While one sequence aligned very well, over 98% of the second sequence contained numerous rearrangements. The many differences observed between these two genome sequences could be owing to either assembly errors or rapid evolutionary divergence. The extent of the differences derived from sequence assembly errors could be assessed if the raw sequencing reads were provided by both genome centers at the time of genome sequence submission. Hence, a new genome sequence standard is proposed whereby the investigator supplies the raw reads along with the closed sequence so that the community can make more accurate judgments on whether differences observed in a single stain may be of biological origin or are simply caused by differences in genome assembly procedures.

Highlights

  • Gluconacetobacter diazotrophicus PAl 5 is a bacterial endophyte of sugarcane, originally isolated in Brazil [1] that provides fixed nitrogen to its plant host, in addition to increasing plant growth by mechanisms independent of nitrogen fixation [2,3]

  • Bacterial strain The bacterial strain used in this study is Gluconacetobacter diazotrophicus PAl 5 obtained from the American Type Culture Collection (ATCC 49037)

  • The two PAl 5 genome sequences to an optical map, the resulting analysis led to the determination that the sequence reported by Joint Genome Institute (JGI) is a more accurate representation of the PAl 5 strain (ATCC 49037) while the sequence reported by RioGene contained numerous rearrangements

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Summary

Introduction

Gluconacetobacter diazotrophicus PAl 5 is a bacterial endophyte of sugarcane, originally isolated in Brazil [1] that provides fixed nitrogen to its plant host, in addition to increasing plant growth by mechanisms independent of nitrogen fixation [2,3]. The ability of G. diazotrophicus to increase growth and reduce plant dependence on nitrogen fertilization makes it important to increasing the efficiency of biofuel production from sugarcane [4]. Since it was first isolated, additional strains of G. diazotrophicus have been isolated in several other countries and plant hosts [5,6,7,8,9,10]. The RioGene sequence has been published [11]

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