A complete chloroplast and mitochondrial genome for velvet bean (Mucuna pruriens, Fabaceae), with genome structure and intergenomic sequence transfers analyses

Abstract

Mucuna pruriens, commonly known as the velvet bean, holds considerable economic and cultural importance as a member of the Fabaceae family. The economic value of this plant is derived from its high protein content, medicinal properties, and potential applications in agriculture and industry. Although the entire nuclear genome consisting of 11 chromosomes of M. pruriens has been published, the comprehensive assembly of the organelle genome, specifically the mitochondria, has not been previously accomplished. The evaluation of sequence transfer from both the chloroplast and mitochondrial genomes to the nuclear genome has not been conducted. The complete chloroplast and mitochondrial genome of M. pruriens var. utilis was assembled and annotated through the utilization of a hybrid approach involving Illumina short-reads and Oxford Nanopore long-reads. The genome of chloroplasts was found to be arranged in a singular circular structure measuring 155,617 bp in length. This structure encompassed a total of 75 genes responsible for encoding proteins, along with 4 genes for ribosomal RNA and 28 genes for transfer RNA. The organization of the mitochondrial genome consisted of a singular circular structure measuring 410,745 bp in length, encompassing a total of 39 protein-coding genes, 4 ribosomal RNA genes, and 16 transfer RNA genes. Through the analysis of sequence transfer, it has been determined that a total of 154,498 bp and 158,285 bp of DNA, derived from the chloroplast and mitochondrial genome respectively, have been incorporated into the nuclear genome. These transfer events predominantly occurred in a relatively recent timeframe. The frequency of transfers of chloroplast to nuclear genome sequences was found to be similar to that of transfers of mitochondrial to nuclear genome sequences. This study presents the initial assembly of the entire organelle, specifically the mitochondrial genome of M. pruriens, which serves as a valuable tool for comprehending the genomic evolution within the diverse Fabaceae family.