Bioinformatics Characterization and Annotation of the Mitochondrial Gene Space of the Palmyra Palm (Borassus flabellifer L.) From Whole-Genome Shotgun Sequences

Abstract

Background
Borassus flabellifer L. (Arecaceae), the Palmyra palm, is a drought-tolerant tree of ecological and
economic importance in South and Southeast Asia. Despite its resilience to abiotic stress, its
organellar genomic organization remains poorly characterized. A 2.41 Gb draft nuclear genome
assembly generated from whole-genome shotgun sequencing (NCBI BioProject: PRJNA1254180; Genome
accession: JBNPIT000000000) was analyzed using the BRAKER pipeline for coding sequence prediction. A
curated set of functionally annotated sequences was screened using GeSeq with BLAT-based homology
searches, HMMER profile searches, ARAGORN v1.2.38, and tRNAscan-
SE v2.0.7 to identify mitochondrial-associated loci. The mitochondrial gene space of B. flabellifer was
resolved into a concatenated coding framework spanning 17,559 bp. Annotation identified protein-
coding loci associated with oxidative phosphorylation, respiratory function, and organellar gene
expression, including rpl2 and orf135d. Multiple tRNA loci were recovered, including trnL-GAG, trnT-GGU,
trnR-CCG, trnT-CGU, trnP-GGG, trnS-UGA, and trnQ-UUG, with exon-intron organization resolved for
intron-containing loci. A putative rpoB-derived fragment was also detected, consistent with possible
intracellular plastid-to-mitochondrion sequence transfer. This study provides a curated annotation of the
mitochondrial gene space of B. flabellifer, offering a useful resource for comparative organellar genomics
in palms and a basis for future studies on mitochondrial evolution and organelle-linked breeding traits.