Phylogenetic Relationships of the Sweetpotato [Ipomoea batatas (L.) Lam.] (original) (raw)
Related papers
Genetic Resources and Crop Evolution, 2002
Comparative analyses of genetic diversity and phylogenetic relationshipsof sweetpotato (Ipomoea batatas (L.) Lam.) and its wildrelatives in Ipomoea series Batataswere conducted using amplified fragment length polymorphism (AFLP) and sequencedata from the internal transcribed spacer (ITS) region of the ribosomal DNA. LowITS divergence among thirteen species of ser. Batatasresulted in poorly resolved relationships. More variable AFLP characters werefound to be more efficient in characterizing genetic diversity and phylogeneticrelationships at both intra- and interspecific levels within ser.Batatas. Highly informative AFLP fingerprints of 36accessions representing 10 species of ser. Batatas weregenerated using only six primer combinations. Of the species examined,I. trifida was found to be the mostclosely related to I. batatas, whileI. ramosissima andI. umbraticola were the most distantlyrelated to I. batatas. The highlypolymorphic AFLP markers are a valuable tool in assessing genetic diversity andphylogenetic relationships of sweetpotato and its wild relatives.
PLOS ONE
To better define the sweetpotato polyploidy, we sought to reconstruct phylogenies of its subgenomes based on hybridization networks that could trace reticulate lineages of differentiated homoeolog triplets of multiple single-copy genes. In search of such homoeolog triplets, we distinguished cDNA variants of 811 single-copy Conserved Ortholog Set II (COSII) genes from two sweetpotato clones into variation partitions specified by corresponding homologs from two I. trifida lines, I. tenuissima and I. littoralis using a phylogenetic partition method, and amplicon variants of the COSII-marker regions from 729 of these genes from two sweetpotato clones into putative homoeoallele groups using haplotype tree and the partition methods referenced by corresponding homologs from I. tenuissima. These analyses revealed partly or completely differentiated expressed-homoeologs and homoeologs from a majority of these genes with three important features. 1. Two variation types: the predominant interspecific variations (homoeoalleles), which are non-randomly clustered, differentially interspecifically conserved or sweetpotato-specific, and the minor intraspecific ones (alleles), which are randomly distributed mostly at non-interspecifically variable sites, and usually sweetpotato-specific. 2. A clear differentiation of cDNA variants of many COSII genes into the variation partition specified by I. tenuissima or I. littoralis from that by I. trifida. 3. Three species-homolog-specified and one sweetpotato-specific variation partitions among 293 different COSII cDNAs, and two or three out of the four partitions among cDNA variants of 306 COSII genes. We then constructed hybridization networks from two concatenations of 16 and 4 alignments of 8 homologous COSII cDNA regions each, which included three taxa of expressed homoeologs in a triple-partition combination from the 16 or 4 sweetpotato COSII genes and 5 taxa each of respective cDNA homologs from the three sweetpotato relatives and I. nil, and inferred a species tree embodying both networks. The species tree predicted close-relative origins of three partly differentiated sweetpotato subgenomes.
Scientific Reports
The discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato occurred before or after its speciation. Therefore, this study aims to evaluate the presence of IbT-DNAs in the genomes of sweetpotato's wild relatives belonging to the taxonomic group series Batatas. Both IbT-DNA1 and IbT-DNA2 were found in tetraploid I. batatas (L.) Lam. and had highly similar sequences and at the same locus to those found in the cultivated sweetpotato. Moreover, IbT-DNA1 was also found in I. cordatotriloba and I. tenuissima while IbT-DNA2 was detected in I. trifida. This demonstrates that genome integrated IbT-DNAs are not restricted to the cultivated sweetpotato but are also present in tetraploid I. batatas and other related species. The sweetpotato [6X Ipomoea batatas (L.) Lam] is a member of the genus Ipomoea, the largest genus in the morning glory (Convolvulaceae) family. This family contains approximately 50 genera and more than 1,000 species. Over half of these species are concentrated in the Americas, where they are distributed as cultigens, medicinal plants and weeds 1. Among the morning glories, I. batatas is the only species with an economic importance as a major food crop 2 , although I. aquatica is also cultivated and consumed as a leafy vegetable, mainly in SouthEast Asia. Series Batatas is a subdivision within the genus Ipomoea. This is a relatively young clade that diversified circa 12 million years ago 3. This group includes the cultivated hexaploid sweetpotato [I. batatas (L.) Lam], the tetraploid (4x) sweetpotato I. batatas (L.) Lam 4 , and 13 other species considered to be the wild relatives of the cultivated sweetpotato. These wild relatives are I. cordatotriloba, I. cynanchifolia, I. grandiflora, I. lacunosa, I. leucantha, I. littoralis, I. ramosissima, I. splendor sylvae (previously named umbraticola), I. tabascana, I. tenuissima, I. tiliacea, I. trifida and I. triloba 5,6. Members of the series Batatas are endemic to the Americas, except I. littoralis that is native to Madagascar, South and Southeast Asia, Australia, and the Pacific region 5. The basic chromosome number of the series Batatas species is 2n = 2 × = 30. While most species are diploid (2x), several are tetraploid (4x) or hexaploid (6x) 7. To avoid confusion, hereafter in the current text, the (6x) sweetpotato (I. batatas) will be referred to as Ib6x, the tetraploid form of I. batatas as Ib4x, and the combination of both as "the sweetpotato group". The sweetpotato is a crop native to the Americas and it was an important food crop for the Inca and Mayan cultures. Its origin and center(s) of genetic diversity have been proposed as somewhere between the Yucatan Peninsula of Mexico and the mouth of the Orinoco River in Venezuela 8,9 , Peru and Ecuador 9. Papua New Guinea, Indonesia and the Philippines are suggested as secondary centers of diversity 10. Today, sweetpotato is a major staple food in numerous tropical countries 11. However, its botanical origin and details about its domestication remain under debate.
Wx intron variations support an allohexaploid origin of the sweetpotato [Ipomoea batatas (L.) Lam]
2011
To clarify the polyploid origin of the sweetpotato, we analyzed retentions of three distinctive types of Waxy intron 2 (Wx-In2) variants among 27 sweetpotato lines and 24 selected relatives and their phylogenetic relationships with Wx-In2 from 11 closest relatives. The three types of Wx-In2 effectively distinguish three diploid constituent genomes of very close homeology in the sweetpotato: Type I is characteristic of some loci in Genome I and III, and Types II and III are specific to loci in Genome II and III. The Type I Wx-In2 variation was found to be retained in 19 sweetpotato lines, Ipomoea littoralis Blume (49), I. tabascana (49), and I. tenuissima (29); Type II to be retained in all 27 sweetpotato lines, I. littoralis Blume, and two I. trifida accessions; Type III to be retained in 13 sweetpotato lines, I. tenuissima, and four distantly related species. Because of the nature of independent random divergence of orthologous intronic sequences, these highly selective retentions of genome-specific or characteristic sweetpotato Wx-In2 variations among four diploid or tetraploid sweetpotato relatives are consistent only with separate lineages of diploid genomes of the sweetpotato. Such an allohexaploid origin of the sweetpotato probably occurred via hybridization between I. tenuissima and I. littoralis Blume, derived earlier from I. trifida and an unidentified species sibling to I. tenuissima. However, neither the involvement of I. tabascana nor a multiple origin of the sweetpotato can be ruled out. The inference is supported by maximal likelihood relationships between the three types of Wx-In2 from the sweetpotato and Wx-In2 from its 11 closest relatives.
Plant Science, 2006
The distribution and organization of 5S and 18S-5.8S-26S (18S) rDNA were studied in 10 varieties of hexaploid Ipomoea batatas, five accessions of tetraploid Ipomeoa trifida, and six related species (five diploids, I. trifida, I. triloba, I. tiliacea, I. leucantha and I. setosa and one tetraploid, I. tabascana), by using fluorescence in situ hybridization (FISH). The FISH data obtained indicated that polyploidization was followed by decrease in the number of 18S rDNA loci in higher ploidy level and provided evidence for major genomic rearrangements and/or diploidization in polyploid I. batatas. Among the five diploid species examined, I. trifida appeared to be the most closely related to I. batatas. By contrast, I. leucantha was closed to I. tiliacea, but both species were distant from sweet potato. I. triloba and I. setosa were distantly related to the rest of Ipomoea batatas complex. The close relationship between I. trifida and I. batatas was also demonstrated by the presence of one 18S and CMA marker in these two chromosome complements only. Based on chromosome morphology, tetraploid I. trifida appeared to be more closely related to sweet potato than I. tabascana. Taking all data obtained in this study, I. trifida might be the progenitor of I. batatas, and I. tabascana, interspecific hybrid between these two species.
Simple Sequence Repeats (SSRs) in Sweetpotato [Ipomoea batatas (L.) Lam.]
HortScience
Simple sequence repeats (SSRs) were isolated from a size-fractionated genomic DNA library of sweetpotato [Ipomoea batatas (L.) Lam.]. Screening of the library with five oligonucleotide probes, including; (GT)11, (AT)11, (CT)11, (GC)11, and (TAA)8, detected the occurrence of 142 positive colonies among ≈12,000 recombinants. Automated DNA sequencing revealed the presence of simple, compound, perfect, and imperfect SSRs. Five homologous PCR primer pairs were synthesized commercially and used to screen 30 sweetpotato clones for the occurrence of SSR polymorphisms. All primer pairs produced an amplification product of the expected size and detected polymorphisms among the genotypes examined. The potential for the use of SSRs as genetic markers for sweetpotato germplasm characterization is discussed.
Discovery and characterization of sweetpotato’s closest tetraploid relative
New Phytologist, 2022
Summary The origin of sweetpotato, a hexaploid species, is poorly understood, partly because the identity of its tetraploid progenitor remains unknown. In this study, we identify, describe and characterize a new species of Ipomoea that is sweetpotato’s closest tetraploid relative known to date and probably a direct descendant of its tetraploid progenitor. We integrate morphological, phylogenetic, and genomic analyses of herbarium and germplasm accessions of the hexaploid sweetpotato, its closest known diploid relative Ipomoea trifida, and various tetraploid plants closely related to them from across the American continent. We identify wild autotetraploid plants from Ecuador that are morphologically distinct from Ipomoea batatas and I. trifida, but monophyletic and sister to I. batatas in phylogenetic analysis of nuclear data. We describe this new species as Ipomoea aequatoriensis T. Wells & P. Muñoz sp. nov., distinguish it from hybrid tetraploid material collected in Mexico; and sh...