Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus)

Abstract

We present the first annotated genome assembly of the allopolyploid okra (Abelmoschus esculentus). Analysis of telomeric repeats and gene rich regions suggested we obtained whole chromosome and chromosomal arm scaffolds. Besides long distal blocks we also detected short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation upon polyploidization of okra. Ribosomal RNA genes are organized in 5S clusters separated from the 18S-5.8S-28S units, clearly indicating an S-type rRNA gene arrangement. The assembly is consistent with cytogenetic and cytometry observations, identifying 65 chromosomes and 1.45Gb of expected genome size in a haploid sibling. Approximately 57% of the genome consists of repetitive sequence. BUSCO scores and A50 plot statistics indicated a nearly complete genome. Kmer distribution analysis suggests that approximately 75% has a diploid nature, and at least 15% of the genome is heterozygous. We did not observe aberrant meiotic configurations, suggesting there is no recombination among the sub-genomes. BUSCO configurations pointed to the presence of at least 3 sub-genomes. These observations are indicative for an allopolyploid nature of the okra genome. Structural annotation using gene models derived from mapped transcriptome data, generated over 130,000 putative genes. The discovered genes appeared to be located predominantly at the distal ends of scaffolds, gradually decreasing in abundance toward more centrally positioned scaffold domains. In contrast, LTR retrotransposons were more abundant in centrally located scaffold domains, while less frequently represented in the distal ends. This gene and LTR-retrotransposon distribution is consistent with the observed heterochromatin organization of pericentromeric heterochromatin and distal euchromatin. The derived amino acid queries of putative genes were subsequently used for phenol biosynthesis pathway annotation in okra. Comparison against manually curated reference KEGG pathways from related Malvaceae species revealed the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.

The genome of okra (Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content

“…Previously, there have been controversies about the chromosome number in the okra genome, and the reported okra chromosome number has ranged from 2n = 72 to 2n = 130, based on karyotype analysis [ 21 , 29 ]. In our study, the chromosome number of okra was determined as 2n = 130 by FISH-based karyotype analysis and Hi-C data-assisted chromosome anchoring, which was consistent with previous reports [ 30 , 31 ]. Additionally, a previous study indicated that okra might be a polyploid species [ 30 ], which was validated by our genome assembly and subgenome phasing.…”

Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta

“…KB has united a variety of interactions, such as those between genes and proteins, elements and reactions, medications and illnesses, and organisms and cells (Kanehisa et al 2019 ). Parallel studies were reported in Vatica mangachapoi (Tang et al 2022 ), Hopea hainanensis (Huang et al 2022 ), Neesia altissima (Pratiwi et al 2022 ), C. capsularis (Satya et al 2017 ), Hibiscus hamabo siebold & zuccarini (Wang et al 2021 ), Abelmoschus esculentus (Nieuwenhuis et al 2021 ), Helicoverpa armigera (de la Paz Celorio-Mancera et al 2011 ), Gasterophilus nasalis (Zhang et al 2021 ), and Operculina turpethum (Biswal et al 2021 ). Additionally, GAEV was used to annotate the KO (Iacobas et al 2019 ; Emami-Khoyi et al 2020 ; Nand et al 2020 ; Shah et al 2021 ).…”