Congruence Between Morphological and Molecular Approach in Understanding Species Relationship in Ipomoea spp.: A Rare Event in Taxonomy

Das, Sabuj Kanti

doi:10.3923/ajps.2011.263.268

Cited by 8 publications

(3 citation statements)

References 11 publications

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“…Molecular markers, such as restriction fragment length polymorphisms (RFLPs) of genomic DNA, random amplified polymorphic DNAs (RAPDs), inter-simple sequence repeats (ISSRs), and some gene sequences have been used to investigate phylogenetic relationships of I. batatas and its wild relatives ( Gao et al, 2011 ; Rajapakse et al, 2004 ; Huang & Sun, 2000 ; Jarret & Austin, 1994 ; Jarret, Gawel & Whittemore, 1992 ). In Ipomoea , various studies including morphology of pollen, flower, and seed; systemic characteristics, and floral anthocyanin regulators have been conducted ( Jayeola & Oladunjoye, 2012 ; Das, 2011 ; Streisfeld & Rausher, 2007 ).…”

Section: Introductionmentioning

confidence: 99%

A systematic comparison of eight new plastome sequences from Ipomoea L

Sun

Dong

Cao

et al. 2019

PeerJ

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Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions (ndhA intron, ndhH-ndhF, ndhF-rpl32, rpl32-trnL, rps16-trnQ, and ndhF) in the Ipomoea genus, eight (trnG, rpl32-trnL, ndhA intron, ndhF-rpl32, ndhH-ndhF, ccsA-ndhD, trnG-trnR, and pasA-ycf3) in the Batatas group, and eight (ndhA intron, petN-psbM, rpl32-trnL, trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ, and trnG) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. Conclusions The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced Ipomoea species. Our comparative analysis included a broad range of Ipomoea chloroplast genomes, providing valuable information for Ipomoea species identification and enhancing the understanding of Ipomoea genetic resources.

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Section: Introductionmentioning

confidence: 99%

A systematic comparison of eight new plastome sequences from Ipomoea L

Sun

Dong

Cao

et al. 2019

PeerJ

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“…Although hundreds of studies on Ipomoea have been published since the genus was validly published (Linnaeus, 1753: 159), it had never been monographed. The only previous “global” taxonomic review, published by Choisy more than 170 years ago, included just 282 species (Choisy, 1834, 1838, 1845), and more recent studies focused on small parts of the genus (e.g., Marderosian, 1965; Austin, 1991; Staples & al., 2005; Ogunwenmo, 2008; Austin, 2013; Austin & McDonald, 2014; Swamy & Ramana, 2018; Rattanakrajang & al., 2022) or on small groups of species, frequently those related to sweet potato or other widespread species (McDonald & Austin, 1990; Austin & Staples, 1991; Austin, 1997; Das, 2011; Abdel Khalik & al., 2012; Abdel Khalik, 2013; Folorunso, 2013). A few authors also addressed the genus at a national or regional level, but several of these more extensive treatments date back to the 19th century or the first half of the 20th century (Grisebach, 1864; Gray, 1878; Hallier, 1894; House, 1908) and most of the more recent, with a few notable exceptions (e.g., Van Ooststroom, 1953; O'Donell, 1960; Verdcourt, 1963; Austin, 1975, 1982; Meeuse & Welman, 2000; Wood & al., 2015), are basic checklists of species or provide only limited information about the taxa included.…”

Section: Introductionmentioning

confidence: 99%

The challenges of classifying big genera such asIpomoea

Muñoz‐Rodríguez

Wood

Wells

et al. 2023

TAXON

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Big genera represent a significant proportion of the world's plants. However, comprehensive taxonomic and evolutionary studies of these genera are often complicated by their size and geographic spread. This paper explores the challenges faced in classifying these megadiverse plant groups consequent to the existing tension between diagnosability and increasing levels of resolution from molecular sequence data. We use recent examples from across angiosperms to illustrate how monophyly, diagnosability and completeness interplay with each other in attempts to classify several big genera and, specifically, the genus Ipomoea (Convolvulaceae). Ipomoea and the tribe Ipomoeeae have been the object of recent taxonomic and phylogenetic studies that highlight the limitations of previous attempts to classify the group, and show that the smaller segregate genera traditionally recognised in Ipomoeeae are nested within Ipomoea and are neither monophyletic nor diagnosable. We argue that existing classifications must be abandoned, and that recognising an expanded Ipomoea that incorporates all segregate genera of the Ipomoeeae is the most appropriate solution as it reconciles the properties of monophyly, diagnosability and completeness, and favours nomenclatural stability.

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“…Molecular markers, such as restriction fragment length polymorphisms (RFLPs) of genomic DNA, random amplified polymorphic DNAs (RAPDs), inter-simple sequence repeats (ISSRs), and some gene sequences have been used to investigate phylogenetic relationships of I. batatas and its wild relatives (Gao et al, 2011;Rajapakse et al, 2004;Huang & Sun, 2000;Jarret & Austin, 1994;Jarret & Gawel, 1992). In Ipomoea, various studies including morphology of pollen, flower, and seed; systemic characteristics, and floral anthocyanin regulators have been conducted (Jayeola & Oladunjoye, 2012;Das, 2011;Streisfeld & Rausher, 2007). With the development of next-generation sequencing, large amounts of genomic data have been obtained to solve the taxonomic relationships in plants.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #3 of "A systematic comparison of eight new plastome sequences from Ipomoea L (v0.1)"

Kj¹

2019

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Background. Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than fifty chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato's closely wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods. Eight chloroplast genomes were assembled using short DNA sequences generated by nextgeneration sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive (https://doi.org/10.5287/bodleian:yrYKneXED), we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results. The eight newly sequenced chloroplast genomes ranged from 161,225 bp to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798-30,910 bp each) separated by a large single copy (LSC) region (87,575-88,004 bp) and a small single copy (SSC) region (12,018-12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5 % in the IR region, 36.1 % in the LSC region, 32.2 % in the SSC regions, and 37.5 % in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and inverted repeat regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57-89 pairs of repetitive sequences and 39-64 SSRs were found.

show abstract

Congruence Between Morphological and Molecular Approach in Understanding Species Relationship in Ipomoea spp.: A Rare Event in Taxonomy

Cited by 8 publications

References 11 publications

A systematic comparison of eight new plastome sequences from Ipomoea L

A systematic comparison of eight new plastome sequences from Ipomoea L

The challenges of classifying big genera such asIpomoea

Peer Review #3 of "A systematic comparison of eight new plastome sequences from Ipomoea L (v0.1)"

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