Complete plastome data of Saccharum hybrid cultivar VMC 76–16, a valuable genomic resource for investigating evolutionary relationships among modern sugarcane cultivars in Indonesia

Abstract

Sugarcane (Saccharum hybrid) is one of the world's most important sugar-producing crops and a valuable genomic resource for supporting molecular characterization and breeding programs. This article describes the complete chloroplast genome (plastome) dataset of the Indonesian sugarcane cultivar VMC 76–16, an introduced cultivar with desirable agronomic traits, including high sucrose content, early maturity, and tolerance to several major diseases. The plastome was assembled from paired-end DNBSEQ sequencing data comprising approximately 1.5 Gb of raw data generated from 5000,000 paired-end reads (2 × 150 bp). The assembled plastome is 141,181 bp in length with an overall GC content of 38.0% and exhibits the typical quadripartite structure, consisting of an 83,047 bp large single-copy (LSC) region, a 12,544 bp small single-copy (SSC) region, and two 22,795 bp inverted repeat (IR) regions. Genome annotation identified 135 genes, including 87 protein-coding genes, 40 transfer RNA genes, and eight ribosomal RNA genes. The dataset also includes comparative relative synonymous codon usage (RSCU) analysis of all available Saccharum plastomes retrieved from the NCBI database, simple sequence repeat (SSR) identification, and plastome-based phylogenetic analyses of Saccharum hybrid cultivar VMC 76–16 together with representative taxa of the tribe Andropogoneae. These data provide a genomic resource for comparative genomics, molecular characterization, phylogenetic analyses, plastome evolution studies, and future sugarcane breeding research.