Draft Genome Sequence of Endophytic Herbaspirillum sp. Strain WT00C, a Tea Plant Growth-Promoting Bacterium.

Endophytic Herbaspirillum sp. strain WT00C was isolated from tea plant (Camellia sinensis L.). Here, we report the 6.08 Mb draft genome sequence of this strain, providing bioinformation about its agronomic benefits and capability to reduce selenate/selenite into red elemental selenium.

GENOME ANNOUNCEMENT

Herbaspirillum sp. strain WT00C is an endophytic bacterium isolated from Camellia sinensis L. and is classified as a novel member in the genus Herbaspirillum (1). It does not exhibit any nitrogen-fixing activity but can produce indole-3-acetic acid (IAA), ammonia, and siderophores (1), similar to endophytic Herbaspirillum strains (2–4) and certain plant growth-promoting rhizobacteria (5–7). Inoculating the bacterium into tea plants markedly stimulates plant growth without any disease symptom (8). The strain WT00C enters plants only via plant vulnus, and colonizes specifically in tea plants (8). In addition, this bacterium can effectively reduce selenate/selenite into red elemental selenium. Here, we report the whole-genome draft sequence and annotation of the strain WT00C.

The genome of Herbaspirillum sp. strain WT00C was sequenced with an Illumina HiSeq 2000 instrument according to the manufacturer’s instructions. High molecular mass-genomic DNA prepared from the strain WT00C was used to construct small (500 bp) and large (6 kb) random sequencing libraries. In both the 500 bp and 6 kb libraries, the mean read length was 90 bp. The reads were filtered and assembled into contigs using SOAPdenovo v1.05 (http://soap.genomics.org.cn). The resulting sequences were assembled into four scaffolds consisting of 11 contigs based on all the paired-end information of reads. Repeat sequences and gene islands (Gis) were predicted using Tandem Repeat Finder (TRF) (9), IslandPath-DIOMB, and SIGI-HMM software (10). Potential protein-coding regions were identified by an integrated automatic annotation platform with Glimmer 3.0 (11) and BLAST softwares (12). Probable functions of translation products of open reading frames (ORFs) were inferred using the BLAST package to search the public databases nonredundant (nr) NCBI, UniProtKB/Swiss-Port (EMBL-EBI), Inter Pro (13), GO (Gene Ontology) (14), and Kyoto Encyclopedia of Genes and Genomes (KEGG) (15). The draft genome of the strain WT00C consists of 6,079,821 bp with a G+C content of 62.36% and 5,537 ORFs. Protein-coding regions cover 87.1% of the genome sequence. The predicted draft genome contains 57 tRNA genes and nine rRNA genes coding 5S, 16S, and 23S rRNA. The total tandem repeat length is 21,508 bp with 263 tandem repeats, which covers 0.354% genomic DNA. 140 minisatellite and 61 microsatellite DNAs were also predicted, and no plasmid or prophage sequence was found.

The genomic annotation reveales that the strain WT00C holds an ACC deaminase gene and genes related to pathways of indole-3-accetic acid (IAA), siderophore, urea biosynthesis, and selenocompound metabolism, but lacks nitrogen-fixation genes and glycohydrolase genes involved in plant cell wall degradation. This strain also contains genes encoding an intact type IV secretion system (T4SS), which is deficient in other Herbaspirillum strains. The genomic information suggests that tea plant-growth promotion by the strain WT00C is achieved by direct and indirect interactions between the bacterium and its host plant.

Accession number(s).

The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession number MIJG00000000. The version described in this paper is the first version.