Evolutionary origins of taro (<i>Colocasia esculenta</i>) in Southeast Asia

Ahmed, Ibrar; Lockhart, P. J.; Agoo, Esperanza Maribel G.; Naing, Kyaw Wai; Nguyen, Dzu Van; Medhi, Dilip K; Matthews, Peter J.

doi:10.1002/ece3.6958

Cited by 53 publications

(42 citation statements)

References 66 publications

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“…No one single locus is good enough for evolutionary comparisons at all time scales; slow evolving regions should be preferred for deep divergences, while mutational hotspots for the closely related taxa and recently diverged species ( Ahmed et al, 2013 ; Ahmed, 2015 ; Li et al, 2020 ). A recent report of Ahmed et al (2020) on family Araceae showed the practical implication of the use of repeats in identification of suitable polymorphic loci for the study of phylogeography and population genetics. Their developed markers from the identified loci providing new insight about the origin of Colocasia esculenta in southeast Asia instead of Papua New Guinea ( Ahmed et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…A recent report of Ahmed et al (2020) on family Araceae showed the practical implication of the use of repeats in identification of suitable polymorphic loci for the study of phylogeography and population genetics. Their developed markers from the identified loci providing new insight about the origin of Colocasia esculenta in southeast Asia instead of Papua New Guinea ( Ahmed et al, 2020 ). Our current results support strong associations between repeats and substitutions and repeats and InDels in Araceae, which can be helpful for identifying species-specific suitable loci for the study of phylogeography, domestication, and population genetics of other species of Araceae.…”

Section: Discussionmentioning

confidence: 99%

“…Many mutational events occur in the cp genome, including InDels, SNPs, inversions, tandem repeats, and oligonucleotide repeats ( Poczai and Hyvönen, 2011 ; Jheng et al, 2012 ; Xu et al, 2015 ; Abdullah et al, 2019 ; Iram et al, 2019 ; Sablok et al, 2019 ). Sufficient polymorphism and uniparental inheritance make the chloroplast genome suitable for phylogenetic inference, resolution of taxonomic discrepancies, population genetics, barcoding, and estimation of time of lineage divergence ( Poczai et al, 2011 ; Ahmed, 2014 ; Poczai and Hyvönen, 2017 ; Mehmood et al, 2020c ; Shahzadi et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Mutational Dynamics of Aroid Chloroplast Genomes II

et al. 2021

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The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10–0.19), weak (0.20–0.29), moderate (0.30–0.39), strong (0.40–0.69), very strong (0.70–0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between “SNPs and InDels,” 0.50 between “InDels and repeats,” and 0.42 between “SNPs and repeats.” In qualitative analyses, 95–100% of the repeats at family and sub-family level, while 36–86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mutational Dynamics of Aroid Chloroplast Genomes II

et al. 2021

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“…It is mainly grown for its corm starch, which can be baked, fried, boiled, or made into fresh or fermented paste, flour, drink, crisps or chips. Additionally, its leaves are eaten in sauces, soups or stews due to the high content of vitamins, minerals, secondary metabolites and fiber [8,[14][15][16][17].…”

Section: The Energy and Nutritional Values Of Taromentioning

confidence: 99%

Cocoyam [Colocasia esculenta (L.) Schott]: Exploring the Production, Health and Trade Potentials in Sub-Saharan Africa

et al. 2021

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Cocoyam [Colocasia esculenta (L.) Schott] also known as taro is regarded as an important staple crop in the Pacific Islands, Asia and Africa. But, Africa has been unpopular in the taro international market though it accounted for the highest share of the global taro production level in the last two decades. Therefore, this study explores the global taro production outlook in two decades (2000–2019) with a special focus on African countries noting their challenges and limitations. Also, industrial, nutritional and health benefits of taro were discussed to showcase other viable potentials of the crop beyond its usefulness as a food security crop on the African continent.

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“…This is prokaryotic by the origin and shows uniparental inheritance paternal in some gymnosperm and maternal in most angiosperms [6][7][8]. The uniparental inheritance and differential mutation rate of different regions of the chloroplast genome makes it suitable for studies ranged from population genetics to phylogenetics [9,10]. Many mutational events occurred with chloroplast genomes, including InDels (insertions-deletions), substitutions, inversions, copy number variations, etc [11][12][13][14][15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Pseudogenization oftrnT-GGUin chloroplast genomes of the plant family Asteraceae

Abdullah

Mehmood

Heidari

et al. 2021

Preprint

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The chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the trnT-GGU gene was previously reported in the Cryptomeria japonica (Cupressaceae), Pelargonium x hortorum (Geraniaceae), and in the two species of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of twelve subfamilies of Asteraceae and found pseudogenization of this gene is not limited to the two species of Gnaphalieae or the tribe Gnaphalieae. We report for the first time that this gene is pseudo in the species of three subfamilies of Asteraceae, including Gymnarrhenoideae, Cichorioideae and Asteroideae. The analyses of the species of 78 genera of Asteroideae revealed that this pseudogenization event is linked to the insertion within the 5′ acceptor stem and not linked to the habit, habitat, and geographical distribution of the plant.

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Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia

Abstract: Before the Columbian exchange of crops between the Americas and the Old World, Colocasia esculenta (L.) Schott (taro, Araceae) was the world's most widespread food crop, grown in tropical to temperate

Cited by 53 publications

References 66 publications

Mutational Dynamics of Aroid Chloroplast Genomes II

Mutational Dynamics of Aroid Chloroplast Genomes II

Cocoyam [Colocasia esculenta (L.) Schott]: Exploring the Production, Health and Trade Potentials in Sub-Saharan Africa

Pseudogenization oftrnT-GGUin chloroplast genomes of the plant family Asteraceae

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