Draft Genome Sequence of Rickettsia sp. Strain MEAM1, Isolated from the Whitefly Bemisia tabaci

Abstract

We report the draft genome sequence of the Rickettsia sp. strain MEAM1, which is a facultative symbiont from an invasive species of the whitefly Bemisia tabaci. The total length of the assembled genome is approximately 1.24 Mb, with 335 scaffolds and 1,247 coding sequences predicted within the genome.

GENOME ANNOUNCEMENT

Rickettsia, an alphaproteobacterium, is a genus of intracellular bacteria that occur commonly in arthropods (1, 19, 20). In the whitefly Bemisia tabaci species complex, Rickettsia sp. is considered a facultative symbiont (2, 7, 12, 14, 15), and horizontal transmission of Rickettsia sp. between conspecific whiteflies or across trophic levels has been reported (5, 6). Rickettsia sp. can increase the heat tolerance of whiteflies by inducing the expression of heat shock genes (3) and affect the life parameters of the whitefly to produce more offspring (16). Here, we isolated a Rickettsia sp. strain from the Middle East-Asia Minor 1 (MEAM1) species of the whitefly B. tabaci complex (Rickettsia sp. strain MEAM1) (3, 4, 7), which is one of the most important invasive agricultural pests worldwide (8, 17, 18).

Rickettsia sp. strain MEAM1 was isolated from the bacteriocytes of whiteflies, and the total DNA of purified bacteria was amplified by multiple-displacement amplification using the Repli-g UltraFast minikit (Qiagen) (21). Two libraries with average insert sizes of 200 bp and 2 kb were constructed and sequenced using the Illumina HiSeq 2000 at BGI-Shenzhen (Shenzhen, China). We obtained 107 Mb and 64 Mb of high-quality, useful data from these two libraries, respectively. The individual reads were de novo assembled using SOAPdenovo v1.05. The protein-coding genes (CDSs) were predicted by Glimmer v3.0 and used to search the NCBI nonredundant database for function annotation.

The genus Rickettsia is classified into four groups: the ancestral group (AG), typhus group (TG), spotted fever group (SFG), and transitional group (TRG) (9, 10). The smallest genome of Rickettsia prowazekii (TG) has a size of 1,109,051 bp, encoding 839 open reading frames (GenBank accession number NC_017051), whereas the largest Rickettsia genome (the Rickettsia endosymbiont of Ixodes scapularis of SFG) is >2 Mb and contains 2,309 genes (11). The draft genome of Rickettsia sp. strain MEAM1 has approximately 1.24 Mb (G+C, 32.1%) and comprises 607 contigs (N₅₀, 3.0 kb) with an average depth of 138×. The high number of contigs in this draft genome is probably due to the loss of DNA fragments during multiple-displacement amplification and de novo assembly using short reads (90 bp) of Illumina sequencing. These contigs were further assembled into 335 scaffolds (N₅₀, 11.9 kb) based on the paired-end information, and a total of 1,247 genes were predicted within the genome. Phylogeny analyses of orthologous genes suggest that Rickettsia sp. strain MEAM1 belongs to AG, grouped together with Rickettsia bellii, which has a moderate reduced genome (e.g., for R. bellii RML369-C, size of 1.5 Mb, G+C of 31.7%, 1,429 CDSs) (20). Blast2GO was used to assign gene ontology (GO) terms for the Rickettsia sp. strain MEAM1 sequences against the Swiss-Prot database (E value < 1e−5) (13), and a number of proteins were involved in ATP binding and metal ion binding or have acyltransferase activity and oxidoreductase activity.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AJWD00000000. The version described in this paper is the first version, AJWD01000000.