Chromosomal-level genome of velvet bean (<i>Mucuna pruriens</i>) provides resources for L-DOPA synthetic research and development

Hao, Shijie; Ge, Qijin; Shao, Yunchang; Tang, Ben-Qin; Fan, Guangyi; Qiu, Canyu; Wang, Xue; Li, Liangwei; Liu, Xiaochuan; Shi, Chengcheng; Lee, Simon Ming‐Yuen

doi:10.1093/dnares/dsac031

Cited by 4 publications

(2 citation statements)

References 58 publications

(59 reference statements)

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“…While the nuclear and chloroplast genomes of M. pruriens have been previously documented (Yuan et al 2021;Hao et al 2022), The inclusion of the full mitochondrial genome allowed for detailed comparisons across various genomic compartments within an individual as well as with other lineages. This broader perspective enables a more comprehensive examination of evolutionary changes.…”

Section: Intergenomic Sequence Transfersmentioning

confidence: 99%

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

Satrio,

Nikmah,

Fendiyanto

et al. 2023

Preprint

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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.

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Section: Intergenomic Sequence Transfersmentioning

confidence: 99%

“…Mucuna pruriens was the rst Mucuna species whose entire nuclear genome was sequenced and used to study the L-DOPA biosynthesis-related genes (Hao et al 2022). On this plant, three genome assemblies were published.…”

Section: Introductionmentioning

confidence: 99%

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

Satrio,

Nikmah,

Fendiyanto

et al. 2023

Preprint

View full text Add to dashboard Cite

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An insight into dietetic and nutraceutical properties of underutilized legume: Mucuna pruriens (L.) DC.

Kumar,

Singh,

Lal

et al. 2024

Journal of Food Composition and Analysis

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The genomes of 5 underutilized Papilionoideae crops provide insights into root nodulation and disease resistance

Yuan,

Lei,

Jiang

et al. 2024

GigaScience

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Background The Papilionoideae subfamily contains a large amount of underutilized legume crops, which are important for food security and human sustainability. However, the lack of genomic resources has hindered the breeding and utilization of these crops. Results Here, we present chromosome-level reference genomes for 5 underutilized diploid Papilionoideae crops: sword bean (Canavalia gladiata), scarlet runner bean (Phaseolus coccineus), winged bean (Psophocarpus tetragonolobus), smooth rattlebox (Crotalaria pallida), and butterfly pea (Clitoria ternatea), with assembled genome sizes of 0.62 Gb, 0.59 Gb, 0.71 Gb, 1.22 Gb, and 1.72 Gb, respectively. We found that the long period of higher long terminal repeat retrotransposon activity is the major reason that the genome size of smooth rattlebox and butterfly pea is enlarged. Additionally, there have been no recent whole-genome duplication (WGD) events in these 5 species except for the shared papilionoid-specific WGD event (∼55 million years ago). Then, we identified 5,328 and 10,434 species-specific genes between scarlet runner bean and common bean, respectively, which may be responsible for their phenotypic and functional differences and species-specific functions. Furthermore, we identified the key genes involved in root-nodule symbiosis (RNS) in all 5 species and found that the NIN gene was duplicated in the early Papilionoideae ancestor, followed by the loss of 1 gene copy in smooth rattlebox and butterfly pea lineages. Last, we identified the resistance (R) genes for plant defenses in these 5 species and characterized their evolutionary history. Conclusions In summary, this study provides chromosome-scale reference genomes for 3 grain and vegetable beans (sword bean, scarlet runner bean, winged bean), along with genomes for a green manure crop (smooth rattlebox) and a food dyeing crop (butterfly pea). These genomes are crucial for studying phylogenetic history, unraveling nitrogen-fixing RNS evolution, and advancing plant defense research.

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Chromosomal-level genome of velvet bean (Mucuna pruriens) provides resources for L-DOPA synthetic research and development

Cited by 4 publications

References 58 publications

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

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

An insight into dietetic and nutraceutical properties of underutilized legume: Mucuna pruriens (L.) DC.

The genomes of 5 underutilized Papilionoideae crops provide insights into root nodulation and disease resistance

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