Dataset Information

De novo Genome Assessment of Serratia marcescens SGT5.3, a Potential Plant Growth-Promoting Bacterium Isolated from the Surface of Capsicum annuum Fruit.

ABSTRACT: Serratia marcescens SGT5.3, a potential plant growth-promoting strain with a wide range of functions, was isolated from the surface of Capsicum annuum fruit. Here, we report the whole-genome sequence of this bacterium. Gene prediction revealed various functional genes potentially involved in plant growth promotion and development.

SUBMITTER: Mamphogoro TP

PROVIDER: S-EPMC9872702 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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<i>De novo</i> Genome Assessment of Serratia marcescens SGT5.3, a Potential Plant Growth-Promoting Bacterium Isolated from the Surface of Capsicum annuum Fruit.

Mamphogoro Tshifhiwa Paris TP Kamutando Casper Nyaradzai CN Maboko Martin Makgose MM Aiyegoro Olayinka Ayobami OA Babalola Olubukola Oluranti OO

Microbiology resource announcements 20230104 1

Serratia marcescens SGT5.3, a potential plant growth-promoting strain with a wide range of functions, was isolated from the surface of Capsicum annuum fruit. Here, we report the whole-genome sequence of this bacterium. Gene prediction revealed various functional genes potentially involved in plant growth promotion and development. ...[more]

PMID: 36598272

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Project description:BackgroundPepper, Capsicum annuum L., Solanaceae, is a major staple economically important vegetable crop worldwide. Limited functional genomics resources and whole genome association studies could be substantially improved through the application of molecular approach for the characterization of gene content and identification of molecular markers. The massive parallel pyrosequencing of two pepper varieties, the highly pungent, Saengryeg 211, and the non-pungent, Saengryeg 213, including de novo transcriptome assembly, functional annotation, and in silico discovery of potential molecular markers is described. We performed 454 GS-FLX Titanium sequencing of polyA-selected and normalized cDNA libraries generated from a single pool of transcripts obtained from mature fruits of two pepper varieties.ResultsA single 454 pyrosequencing run generated 361,671 and 274,269 reads totaling 164.49 and 124.60 Mb of sequence data (average read length of 454 nucleotides), which assembled into 23,821 and 17,813 isotigs and 18,147 and 15,129 singletons for both varieties, respectively. These reads were organized into 20,352 and 15,781 'isogroups' for both varieties. Assembled sequences were functionally annotated based on homology to genes in multiple public databases and assigned with Gene Ontology (GO) terms. Sequence variants analyses identified a total of 3,766 and 2,431 potential (Simple Sequence Repeat) SSR motifs for microsatellite analysis for both varieties, where trinucleotide was the most common repeat unit (84%), followed by di (9.9%), hexa (4.1%) and pentanucleotide repeats (2.1%). GAA repeat (8.6%) was the most frequent repeat motif, followed by TGG (7.2%), TTC (6.5%), and CAG (6.2%).ConclusionsHigh-throughput transcriptome assembly, annotation and large scale of SSR marker discovery has been achieved using next generation sequencing (NGS) of two pepper varieties. These valuable informations for functional genomics resource shall help to further improve the pepper breeding efforts with respect to genetic linkage maps, QTL mapping and marker-assisted trait selection.

Dataset Information

De novo Genome Assessment of Serratia marcescens SGT5.3, a Potential Plant Growth-Promoting Bacterium Isolated from the Surface of Capsicum annuum Fruit.

Publications

<i>De novo</i> Genome Assessment of Serratia marcescens SGT5.3, a Potential Plant Growth-Promoting Bacterium Isolated from the Surface of Capsicum annuum Fruit.

Similar Datasets

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