A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

Kim, Yunsoo; Cullis, Christopher A.

doi:10.1093/jxb/erw500

Cited by 30 publications

(44 citation statements)

References 18 publications

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“…Several inversions including a 421-bp inversion in the mimosoid species (Wang et al, 2017), a 7.5-kb inversion in the Cercioideae (Kim and Cullis, 2017), and a large inversion of 50-kb in the subfamily Papilionoideae (Guo et al, 2007;Cai et al, 2008;Keller et al, 2017) occur in legumes. A few studies have documented the presence of inversions in species of the MP clade, such as V. radiata (Jansen et al, 2007), L. luteus (Martin et al, 2014), and P. vulgaris (Bruneau et al, 1990).…”

Section: Inversionsmentioning

confidence: 99%

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

et al. 2020

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The Millettioid/Phaseoloid (MP) clade from the subfamily Papilionoideae (Leguminosae) consists of six tribes and ca. 3,000 species. Previous studies have revealed some plastome structural variations (PSVs) within this clade. However, many deep evolutionary relationships within the clade remain unresolved. Due to limited taxon sampling and few genetic markers in previous studies, our understanding of the evolutionary history of this clade is limited. To address this issue, we sampled 43 plastomes (35 newly sequenced) representing all the six tribes of the MP clade to examine genomic structural variations and phylogenetic relationships. Plastomes of the species from the MP clade were typically quadripartite (size ranged from 140,029 to 160,040 bp) and contained 109-111 unique genes. We revealed four independent gene losses (ndhF, psbI, rps16, and trnS-GCU), multiple IR-SC boundary shifts, and six inversions in the tribes Desmodieae, Millettieae, and Phaseoleae. Plastomes of the species from the MP clade have experienced significant variations which provide valuable information on the evolution of the clade. Plastid phylogenomic analyses using Maximum Likelihood and Bayesian methods yielded a well-resolved phylogeny at the tribal and generic levels within the MP clade. This result indicates that plastome data is useful and reliable data for resolving the evolutionary relationships of the MP clade. This study provides new insights into the phylogenetic relationships and PSVs within this clade.

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Section: Inversionsmentioning

confidence: 99%

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

et al. 2020

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“…This genomic region has undergone numerous rearrangements not only in the IRLC legumes (as mentioned above) but also in different lineages. For example; within Jasminum and Menodora, both of them are belonging Oleaceae, accD have been lost and the ycf4-psaI region in Jasminum section Primulina was relocated [31], the accD was found as a pseudogene in some species of Primula (Primulaceae) [32] and chloroplast genome of Tylosema esculentum as one of the basal legumes in the Caesalpinioideae, has an unique inverted region which is including six genes rbcL, accD, psaI, ycf4, cemA and petA [33].…”

Section: Introductionmentioning

confidence: 99%

Extensive survey of the ycf4 plastid gene throughout the IRLC legumes: Robust evidence of its locus and lineage specific accelerated rate of evolution, pseudogenization and gene loss in the tribe Fabeae

Moghaddam

Osaloo

2020

PLoS ONE

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The genome organization and gene content of plastome (plastid genome) are highly conserved among most flowering plant species. Plastome variation (in size and gene order) is rare in photosynthetic species but size variation, rearrangements and gene/intron losses is attributed to groups of seed plants. Fabaceae (legume family), in particular the subfamily Papilionoideae and the inverted repeat lacking clade (IRLC), a largest legume lineage, display the most dramatic and structural change which providing an excellent model for understanding of mechanisms of genomic evolution. The IRLC comprises 52 genera and ca 4000 species divided into seven tribes. In present study, we have sampled several representatives from each tribe across the IRLC from various herbaria and field. The ycf4 gene, which plays a role in regulating and assembly of photosystem I, is more variable in the tribe Fabeae than in other tribes. In certain species of Lathyrus, Pisum and Vavilovia, all belonging to Fabeae, the gene is either absent or a pseudogene. Our study suggests that ycf4 gene has undergone positive selection. Furthermore, the rapid evolution of the gene is locus and lineage specific and is not a shared character of the IRLC in legumes.

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“…Marama bean, through activities including course based undergraduate research at Case Western Reserve University, has a preliminary genome assembly and whole‐genome Illumina sequence data for 58 diverse individuals (Cullis et al., ). These data have been used to compile the chloroplast genome and identify diversity in this segment of the overall genome (Kim & Cullis, ). This genomic resource will be the basis of developing genetic maps and useful DNA markers for eventually applying MAS to marama.…”

Section: Environment Phenotype and Lifecycle Molecular Geneticsmentioning

confidence: 99%

“…The molecular genetic diversity among some populations in Namibia has been determined both by SSR variation (Nepolo, Chimwamurombe, Cullis, & Kandawa‐Schulz, ; Nepolo et al., ; Takundwa, Chimwamurombe, Kunert, et al., ) and chloroplast variation (Kim & Cullis, ) from the whole‐genome sequence data from 58 different individuals across the Namibian germplasm (Cullis et al., ). These data and the SSR data confirm earlier studies (Lawlor, ) showing that there is a great deal of variability within a population.…”

Section: Environment Phenotype and Lifecycle Molecular Geneticsmentioning

confidence: 99%

Development of marama bean, an orphan legume, as a crop

Cullis

Lawlor

Chimwamurombe

et al. 2019

Food and Energy Security

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Advances have been recently made in the breeding and characterization of three major legume crops of the semiarid tropics, chickpea, pigeon pea, and groundnut. However, other wild‐growing legumes, called “orphan legumes,” with potential as crops, but are not yet cultivated would benefit from further attention. This review considers the domestication of one such plant, marama bean (Tylosema esculentum). Marama has long been recognized as a potential crop particularly for southern Africa, but coordinated, long‐term research and development has been lacking. Marama is a perennial, outcrossing hexaploid, growing under extreme conditions in a restricted geographic range; only natural stands exist that are likely to be overexploited. Marama has two potential units of economic yield, seed and tuber. The seed is protein‐ and oil‐rich, with potential in the pharmaceutical and cosmetic industries while the tuber is high in carbohydrates. In this review, the different aspects of bringing a wild plant into cultivation are considered, together with the additional socioeconomic benefits of developing a breeding program. An international collaboration is analyzing aspects of the plant structure and physiology, molecular biology, and its interactions with environment with a view to developing marama as a crop, with a role in food security, that could be harvested by local communities. Molecular topics considered include next‐generation sequencing for developing molecular maps, genotyping by sequencing, identification of quantitative trait loci for important agronomic traits, protein quality, and incompatibility mechanisms. To achieve domestication requires seed gardens and fields, and the phenotyping of marama material from different locations. Community engagement will also ensure agronomic sustainability and farmer participation. This review describes an approach for a successful outcome of a breeding program to introduce improved marama and highlights the challenges in achieving this, which is a paradigm for the difficulties in the cultivation of “orphan species.”

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A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

Abstract: HighlightThe chloroplast genome of a basal legume has been assembled from next-generation sequence information. This genome, which has a unique inversion, an additional copy of the ycf1 gene, and sequence variation among individuals, has been characterized.

Cited by 30 publications

References 18 publications

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

New Insights Into the Plastome Evolution of the Millettioid/Phaseoloid Clade (Papilionoideae, Leguminosae)

Extensive survey of the ycf4 plastid gene throughout the IRLC legumes: Robust evidence of its locus and lineage specific accelerated rate of evolution, pseudogenization and gene loss in the tribe Fabeae

Development of marama bean, an orphan legume, as a crop

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