Abstract
Here, we report the annotated draft genome sequences of two strains of Serratia spp., Ag1 and Ag2, isolated from the midgut of two different strains of Anopheles gambiae. The genomes of these two strains are almost identical.
GENOME ANNOUNCEMENT
The genus Serratia consists of Gram-negative rod-shaped facultative anaerobes. Members of this genus share a variety of habitats, such as freshwater, soil, plants, and the gut of invertebrates and vertebrates. The genus includes many human pathogenic strains (1). In addition, other strains have been investigated, for example, a strain from the gut of water flea Daphnia magna (2), and a strain that is associated with leaf-cutter ant fungus gardens (3). The mosquito gut ecosystem accommodates a dynamic microbiome (4, 5). Serratia odorifera could significantly enhance susceptibility to dengue virus DENV-2 in Aedes aegypti (6). In anopheline mosquitoes, Serratia marcescens has been found to be able to inhibit Plasmodium development in Anopheles gambiae (7, 8).
The Serratia sp. strain Ag1 was isolated from the Ngousso strain of A. gambiae that was originally collected in Cameroon in 2006, and maintained in the Vernick lab, the Institut Pasteur, Paris, France. The Serratia sp. strain Ag2 was isolated from the A. gambiae G3 strain in the Xu lab at New Mexico State University, Las Cruces, NM, USA. The G3 strain was derived from a collection originally in MacCarthy Island, the Gambia, and colonized in 1975. The genome was determined by Illumina paired-end technology at Genewiz, Inc. A total of 6.1 M reads for strain Ag1 and 4.5 M reads for strain Ag2 were generated. De novo assembly was performed using CLC genomic workbench (v7.0.4). The assembly of strain Ag1 contains 110 contigs totaling 5.35 Mbp. The assembly of strain Ag2 contains 109 contigs totaling 5.32 Mbp. The genomes were annotated by the NCBI Prokaryotic Genome Automatic Annotation Pipeline. The Ag1 genome includes 4,773 coding sequences (CDS) and 85 RNA genes. The Ag2 genome includes 4,706 CDS and 85 RNA genes. Genome comparison indicated the common origins of the isolates. Approximately 98.2% of the Ag1 genome has identical counterparts in Ag2, whereas 98.7% of the Ag2 genome has identical counterparts in Ag1. The differences between the two strains were minor. For example, contig 54 (9,245 bp) in Ag1 has no counterpart in Ag2, and contig 12 (18,403 bp) and contig 78 (15,537 bp) from Ag2 are not present in Ag1. Intriguingly, the two almost identical strains are associated with different mosquito colonies originally from different parts of Africa, and the two colonies were never maintained in the same insectary. This strongly suggests that the bacteria are persistently associated with the natural mosquito microbial flora in nature. As a member of the gut flora of Ngousso mosquitoes, strain Ag1 may be involved in the susceptibility to Plasmodium and O’nyong-nyong virus (9).
Recently, several genomes of mosquito associated bacteria have been sequenced, including Elizabethkingia anophelis (10, 11), Asaia spp. (12), Enterobacter spp. (13), Pseudomonas spp. (14), and Spiroplasma diminutum and S. taiwanense (15, 16). The available genomes will facilitate to characterize the structure and function of the mosquito microbiome.
Nucleotide sequence accession numbers.
The genome sequences have been deposited at GenBank under the accession numbers JQEI00000000 (Serratia sp. Ag1) and JQEJ00000000 (Serratia sp. Ag2).
ACKNOWLEDGMENTS
This work was supported by NIH grant SC1AI112786 and NSF grant DMS-1222592 to J.X. and European Research Council grant 323173 to K.D.V.
Footnotes
Citation Pei D, Hill-Clemons C, Carissimo G, Yu W, Vernick KD, Xu J. 2015. Draft genome sequences of two strains of Serratia spp. from the midgut of the malaria mosquito Anopheles gambiae. Genome Announc 3(2):e00090-15. doi:10.1128/genomeA.00090-15.
REFERENCES
- 1.Mahlen SD. 2011. Serratia infections: from military experiments to current practice. Clin Microbiol Rev 24:755–791. doi: 10.1128/CMR.00017-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Poehlein A, Freese HM, Daniel R, Simeonova DD. 2014. Draft genome sequence of Serratia sp. strain DD3, isolated from the guts of Daphnia magna. Genome Announc 2(5):e00903-14. doi: 10.1128/genomeA.00903-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Aylward FO, Tremmel DM, Starrett GJ, Bruce DC, Chain P, Chen A, Davenport KW, Detter C, Han CS, Han J, Huntemann M, Ivanova NN, Kyrpides NC, Markowitz V, Mavrommatis K, Nolan M, Pagani I, Pati A, Pitluck S, Teshima H, Deshpande S, Goodwin L, Woyke T, Currie CR. 2013. Complete genome of Serratia sp. strain FGI 94, a strain associated with leaf-cutter ant fungus gardens. Genome Announc 1(2):e00239-12. doi: 10.1128/genomeA.00239-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Boissière A, Tchioffo MT, Bachar D, Abate L, Marie A, Nsango SE, Shahbazkia HR, Awono-Ambene PH, Levashina EA, Christen R, Morlais I. 2012. Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection. PLoS Pathog 8:e1002742. doi: 10.1371/journal.ppat.1002742. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Wang Y, Gilbreath TM III, Kukutla P, Yan G, Xu J. 2011. Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya. PLoS One 6:e24767. doi: 10.1371/journal.pone.0024767. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Apte-Deshpande A, Paingankar M, Gokhale MD, Deobagkar DN. 2012. Serratia odorifera a midgut inhabitant of Aedes aegypti mosquito enhances its susceptibility to dengue-2 virus. PLoS One 7:e40401. doi: 10.1371/journal.pone.0040401. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Bahia AC, Dong Y, Blumberg BJ, Mlambo G, Tripathi A, Benmarzouk-Hidalgo OJ, Chandra R, Dimopoulos G. 2014. Exploring Anopheles gut bacteria for Plasmodium blocking activity. Environ Microbiol 16:2980–2994. doi: 10.1111/1462-2920.12381. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Bando H, Okado K, Guelbeogo WM, Badolo A, Aonuma H, Nelson B, Fukumoto S, Xuan X, Sagnon N, Kanuka H. 2013. Intra-specific diversity of Serratia marcescens in Anopheles mosquito midgut defines Plasmodium transmission capacity. Sci Rep 3:1641. doi: 10.1038/srep01641. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Carissimo G, Pondeville E, McFarlane M, Dietrich I, Mitri C, Bischoff E, Antoniewski C, Bourgouin C, Failloux A-B, Kohl A, Vernick KD. 2015. Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for RNA interference and gut microbiota. Proc Natl Acad Sci U S A 112:E176–E185. doi: 10.1073/pnas.1412984112. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Kukutla P, Lindberg BG, Pei D, Rayl M, Yu W, Steritz M, Faye I, Xu J. 2013. Draft genome sequences of Elizabethkingia anophelis strains R26T and Ag1 from the midgut of the malaria mosquito Anopheles gambiae. Genome Announc 1(6):e01030-13. doi: 10.1128/genomeA.01030-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Kukutla P, Lindberg BG, Pei D, Rayl M, Yu W, Steritz M, Faye I, Xu J. 2014. Insights from the genome annotation of Elizabethkingia anophelis from the malaria vector Anopheles gambiae. PLoS One 9:e97715. doi: 10.1371/journal.pone.0097715. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Shane JL, Bongio NJ, Favia G, Lampe DJ. 2014. Draft genome sequence of Asaia sp. strain SF2.1, an important member of the microbiome of Anopheles mosquitoes. Genome Announc 2(1):e01202-13. doi: 10.1128/genomeA.01202-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Jiang J, Alvarez C, Kukutla P, Yu W, Xu J. 2012. Draft genome sequences of Enterobacter sp. isolate Ag1 from the midgut of the malaria mosquito Anopheles gambiae. J Bacteriol 194:5481. doi: 10.1128/JB.01275-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Alvarez C, Kukutla P, Jiang J, Yu W, Xu J. 2012. Draft genome sequence of Pseudomonas sp. strain ag1, isolated from the midgut of the malaria mosquito Anopheles gambiae. J Bacteriol 194:5449. doi: 10.1128/JB.01173-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Chang TH, Lo WS, Ku C, Chen LL, Kuo CH. 2014. Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biol Evol 6:500–509. doi: 10.1093/gbe/evu033. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16.Lo WS, Ku C, Chen LL, Chang TH, Kuo CH. 2013. Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. Taiwanense. Genome Biol Evol 5:1512–1523. doi: 10.1093/gbe/evt108. [DOI] [PMC free article] [PubMed] [Google Scholar]