Genome architecture and genetic diversity of allopolyploid okra ( Abelmoschus esculentus )

作者：Ronald Nieuwenhuis, Thamara Hesselink, Hetty C. van den Broeck, Jan Cordewener, Elio Schijlen, Linda V. Bakker, Sara Diaz Trivino, D. Struss, Simon‐Jan de Hoop, Hans de Jong, Sander Peters · 发表于：The Plant Journal · 年份：2023 · DOI：10.1111/tpj.16602 · 被引用次数：9 · 研究领域：Agricultural Practices and Plant Genetics、Chromosomal and Genetic Variations、Plant Virus Research Studies

The allopolyploid okra (Abelmoschus esculentus) unveiled telomeric repeats flanking distal gene-rich regions and short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation. Ribosomal RNA (rRNA) genes organize into 5S clusters, distinct from the 18S-5.8S-28S units, indicating an S-type rRNA gene arrangement. The assembly, in line with cytogenetic and cytometry observations, identifies 65 chromosomes and a 1.45 Gb genome size estimate in a haploid sibling. The lack of aberrant meiotic configurations implies limited to no recombination among sub-genomes. k-mer distribution analysis reveals 75% has a diploid nature and 15% heterozygosity. The configurations of Benchmarking Universal Single-Copy Ortholog (BUSCO), k-mer, and repeat clustering point to the presence of at least two sub-genomes one with 30 and the other with 35 chromosomes, indicating the allopolyploid nature of the okra genome. Over 130 000 putative genes, derived from mapped IsoSeq data and transcriptome data from public okra accessions, exhibit a low genetic diversity of one single nucleotide polymorphisms per 2.1 kbp. The genes are predominantly located at the distal chromosome ends, declining toward central scaffold domains. Long terminal repeat retrotransposons prevail in central domains, consistent with the observed pericentromeric heterochromatin and distal euchromatin. Disparities in paralogous gene counts suggest potential sub-genome differentiation implying possi...