High-Quality Draft Genome Sequence of Endophytic Kluyvera Ascorbata Strain PCL31 Isolated from Piper Crocatum (red betel).

Authors

Elizabeth Sidhartha, Rahadian Pratama, Ernst Richard Ng, Irene Nathania Christiawan, Yeshaya Valentine, Rio Hermantara, I Made Artika, Okti Nadia Poetri, Mega Safithri

Published in

F1000Research. Volume 15. Pages 1073. Epub Aug 21, 2026.

Abstract

Endophytic bacteria within medicinal plants are a largely untapped reservoir of bioactive compounds and adaptive genetic traits. Piper crocatum (red betel), a Southeast Asian medicinal herb rich in flavonoids, alkaloids, and phenolics, offers a chemically selective niche for endophytes, yet the genomes of its microbial associates remain poorly characterised. Kluyvera ascorbata occurs as a plant-associated endophyte and an opportunistic human pathogen, and its chromosomal blaKLUA gene is the recognised progenitor of the clinically important CTX-M-2 β-lactamase sublineage. We report a high-quality draft genome of endophytic strain PCL31, isolated from surface-sterilised Piper crocatum tissues collected in Bogor, Indonesia. Whole-genome sequencing used the Oxford Nanopore PromethION platform, with de novo assembly in Flye, polishing in Medaka, and quality assessment by QUAST and BUSCO. The assembly spans 4,978,299 bp across eight contigs (N50 1.45 Mbp; GC content 54.26%; 100% BUSCO completeness, enterobacterales_odb10, n = 440). Species identity was confirmed by digital DNA-DNA hybridisation (dDDH 88.6% against the type strain K. ascorbata ATCC 33433) and average nucleotide identity (ANI 98.6% against reference genome NZ_CP096201.1). Annotation identified 4,579 protein-coding sequences, 22 ribosomal RNA, 88 transfer RNA, and 81 non-coding RNA genes, and no CRISPR/Cas systems. antiSMASH 8.0 predicted four biosynthetic gene clusters (BGCs): a 53.8 kb non-ribosomal peptide synthetase (NRPS)-metallophore cluster matching the conserved enterobactin locus (MIBiG similarity 0.83), plus three low-similarity clusters (≤ 0.50) of uncertain novelty - a ribosomally synthesised and post-translationally modified peptide (RiPP)-like cluster, a terpene-precursor cluster, and an azole-containing RiPP. CARD-RGI profiling returned one Perfect hit ( blaCTX-M-2) and 25 Strict hits, the latter dominated by intrinsic Enterobacteriaceae efflux and target-modification genes; phenotypic confirmation was not performed. This genome provides a resource for bioprospecting secondary metabolites from medicinal-plant endophytes and underscores the value of plant-associated isolates for biosafety and antimicrobial-resistance surveillance in opportunistic pathogens.

PMID:
42920424
Bibliographic data and abstract were imported from PubMed on 24 Oct 2026.

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