Complete Genome Sequence of “Candidatus Sulcia muelleri” ML, an Obligate Nutritional Symbiont of Maize Leafhopper (Dalbulus maidis)

Abstract

“Candidatus Sulcia muelleri” is a symbiont of sap-feeding insects in the suborder Auchenorrhyncha. The strain “Ca. Sulcia muelleri” ML is associated with the maize leafhopper (Dalbulus maidis), collected in Brazil, which is a disease vector that affects corn production. Here, we report the complete genome sequence of this bacterium.

GENOME ANNOUNCEMENT

The bacterium “Candidatus Sulcia muelleri” is a symbiont of sap-feeding insects in the suborder Auchenorrhyncha (1). This bacterium reaches high abundance inside specialized host cells (i.e., bacteriocytes) and provides its hosts with essential amino acids to supplement the nutritional deficiency of plant sap (2–7). The “Ca. Sulcia muelleri” genomes characterized to date have a size range of 191 to 277 kb and varied in their gene content for the biosynthesis of seven or eight essential amino acids. For the remaining two or three essential amino acids, their insect hosts have acquired lineage-specific secondary symbionts (4, 6).

To facilitate future comparative and evolutionary analyses, we determined the complete genome sequence of “Ca. Sulcia muelleri” strain ML from maize leafhopper (Dalbulus maidis). This insect is a vector for three important phytopathogens (i.e., maize bushy stunt phytoplasma, corn stunt spiroplasma, and maize rayado fino virus) that affect corn production in tropical/subtropical America (8). The colony of laboratory-reared insects used in this study was established using specimens collected in Jardinópolis (Sao Paulo State, Brazil; 20.912931 S and 47.896399 W) in 2009. The total DNA of individual insects was extracted using DNeasy blood and tissue kit (Qiagen); 39 samples were pooled for the preparation of Illumina sequencing library.

The procedure for genome sequencing, assembly, and annotation is based on that described in our previous studies (9–15). Briefly, the Illumina MiSeq platform was used to generate 251-bp reads from one paired-end library (~358 bp insert, 3,506,770 reads). The de novo assembly was performed using Velvet version 1.2.10 (16) with the following parameters; k, 141; scaffolding, no; exp_cov, auto; cov_cutoff, 10; max_coverage, 160; and min_contig_lgth, 2,000. The putative “Ca. Sulcia muelleri” ML contigs were identified by BLASTN (17) searches against the “Ca. Sulcia muelleri” ALF genome (6). The initial assembly was iteratively improved by mapping the raw reads to the contigs using the Burrows-Wheeler Aligner (BWA) version 0.6.2 (18), programmatically checked using the MPILEUP program in SAMTOOLS package version 0.1.18 (19), and visually inspected using IGV version 2.1.24 (20). All gaps were filled by using reads overhanging at the contig margins. The programs RNAmmer (21), tRNAscan-SE (22), and PRODIGAL (23) were used for gene prediction. For each protein-coding gene, the gene name and product description were initially annotated based on the homologous genes in “Ca. Sulcia muelleri” strains ALF (6) and GWSS (2) as identified by OrthoMCL (24). Subsequently, BLASTP (17) searches against the NCBI nonredundant (nr) protein database (25) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (26) were used to assist manual curation of the annotation.

The complete genome of “Ca. Sulcia muelleri” ML contains one circular chromosome that is 190,405 bp in size with a G+C content of 24.1%. The first version of annotation includes one set of 16S-23S-5S rRNA genes, 29 tRNA genes (covering all 20 amino acids), and 187 protein-coding genes.

Nucleotide sequence accession number.

The complete genome sequence of “Ca. Sulcia muelleri” ML has been deposited at DDBJ/EMBL/GenBank under the accession number CP010105.