Genome Sequence of Blattabacterium sp. Strain BGIGA ...

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May 10, 2012 - them into amino acids for the host (4, 8, 12, 15, 16). The genome ... in free-living relatives are absent, reflecting a substantial reduction of functional .... automatic genome annotation and pathway reconstruction server. Nu-.
GENOME ANNOUNCEMENT

Genome Sequence of Blattabacterium sp. Strain BGIGA, Endosymbiont of the Blaberus giganteus Cockroach Charlie Y. Huang, Zakee L. Sabree, and Nancy A. Moran Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA

Cockroaches harbor the obligate flavobacterial endosymbiont Blattabacterium sp., which resides within the host’s bacteriocytes and can recycle ammonia and urea nitrogenous wastes into amino acids for the host. We report the complete genome sequence of the Blattabacterium sp. associated with the giant roach Blaberus giganteus.

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lattabacterium sp., the obligate flavobacterial endosymbiont of cockroaches and the lower termite Mastotermes darwiniensis, is implicated in rescuing nitrogenous wastes and processing them into amino acids for the host (4, 8, 12, 15, 16). The genome of this beneficial insect endosymbiont is highly reduced (⬃590 to 640 kb) compared to closely related, free-living genera. Entire biosynthetic pathways involved in various metabolic functions found in free-living relatives are absent, reflecting a substantial reduction of functional capability. Nonetheless, the pathways that recycle nitrogenous waste compounds, like urea and ammonia, to produce various amino acids and vitamins have been selectively retained in all Blattabacterium genomes. Analysis of Blattabacterium genomes from multiple cockroach families will enhance our understanding of the stability and functional nature of this hostmicrobe relationship from the endosymbiont perspective. The tropical Blaberus giganteus (Blaberidae:Dictyoptera) grows to up to 6 inches long, making it one of the largest roaches (3), and it is primarily found in Central and South America. Its primary diet includes, but is not limited to, decaying plant material. Given the host’s typically nitrogen-poor, plant-based diet, Blattabacterium sp. strain BGIGA is expected to be under selective pressure to maintain key nitrogen recycling and nutrient biosynthesis pathways. Thirteen micrograms of DNA was prepared from fat bodies dissected from two lab-reared B. giganteus specimens and submitted to the Yale University Keck DNA Sequencing Lab for sequencing with an Illumina Genome Analyzer IIx. A 100-bp paired-end library was constructed from a multiplexed DNA sample that included B. giganteus fat body DNA. A total of 26,305,538 paired reads were quality filtered (adapter sequences removed and sequences of ⬍40 bp excluded) into 17,458,144 paired reads and 205,533 single reads. Most of the gaps between 12,684 Velvetgenerated (19) contigs were closed in silico by using ABACAS (2), IMAGE (17), and ICORN (13) in an iterative genome assembly strategy. PCR amplification and Sanger sequencing were used to bridge gaps between the 40 remaining contigs, yielding a circular chromosome and a single, circular plasmid. Artemis (14) and Projector 2 (18) were used to view assemblies. Putative protein-coding regions were identified using Glimmer (5), and functional prediction was done using searches based on Blastp (1) and HMMR (6) against the GenBank nr and Pfam databases, respectively. The Kegg KAAS database was consulted for metabolic reconstructions (11). RNAs were identified through Rfam database (7) searches and by using tRNAscan-SE (10). The Blaberus giganteus Blattabacterium sp. endosymbiont

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strain BGIGA has a 629,165-bp chromosome and a 3,423-bp plasmid. The G⫹C contents of the chromosome and plasmid are 25.7% and 30.9%, respectively. Over 95% of the BGIGA chromosome consists of open reading frames; there are 573 protein-coding genes and 38 RNA-coding genes, including tRNAs specifying all amino acids and a single complete rRNA operon. The BGIGA genome functionally overlaps with other completely sequenced Blattabacterium genomes in that it is capable of reclaiming nitrogen from urea and ammonia and produces all of the essential amino acids as well as various cofactors. Thus, these data provide further evidence that the general functional role of this endosymbiont as a nutrient provider is ubiquitous among cockroaches. Nucleotide sequence accession numbers. The complete chromosome and plasmid sequences have been deposited in the NCBI GenBank database under accession numbers CP003535 and CP003536, respectively. ACKNOWLEDGMENTS We acknowledge financial support for this work from the U.S. National Science Foundation (award 0626716 to N.A.M.), Yale University, and the Yale Science and Engineering Association (to C.Y.H.).

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Received 10 May 2012 Accepted 4 June 2012 Address correspondence to Zakee L. Sabree, [email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.00789-12

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8. Lopez-Sanchez MJ, et al. 2009. Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PLoS Genet. 5:e1000721. doi:10.1371/ journal.pgen.1000721. 9. Reference deleted. 10. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955–964. 11. Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35:W182–W185. 12. Neef A, et al. 2011. Genome economization in the endosymbiont of the wood roach Cryptocercus punctulatus due to drastic loss of amino acid synthesis capabilities. Genome Biol. Evol. 3:1437–1447. 13. Otto TD, Sanders M, Berriman M, Newbold C. 2010. Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 26:1704 –1707.

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