Phylogenetic Relationships of Solanum Series Conicibaccata and Related Species in Solanum Section Petota Inferred from Five Conserved Ortholog Sequences

Fajardo, Diego; Spooner, David M.

doi:10.1600/036364411x553252

Cited by 14 publications

(11 citation statements)

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“…A COS is defined as a gene conserved in sequence and copy number that shares a common ancestor by descent, while paralogs are duplicated sequences resulting in gene duplications or polyploidization events [ 42 - 45 ]. COS markers have been successfully developed and used for phylogenetic inference among species in the Solanaceae and Poaceae families [ 44 , 46 , 47 ].…”

Section: Resultsmentioning

confidence: 99%

The American cranberry: first insights into the whole genome of a species adapted to bog habitat

et al. 2014

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BackgroundThe American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.ResultsThe genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).ConclusionsShotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.

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Section: Resultsmentioning

confidence: 99%

The American cranberry: first insights into the whole genome of a species adapted to bog habitat

et al. 2014

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“…Five of these loci were examined in a few of the diploid species of section Petota by Rodriguez et al. (), Ames and Spooner (), Fajardo and Spooner (), and Cai et al. ().…”

Section: Methodsmentioning

confidence: 99%

Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte)

Spooner

Ruess

Arbizu

et al. 2018

American J of Botany

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Solanum section Petota, which includes the potato and its wild relatives, is a difficult taxonomic group complicated by interspecific hybridization, introgression, allopolyploidy, a mixture of sexual and asexual reproduction, and possible recent species divergence (Spooner and van den Berg, 1992a;Spooner, 2009). Every taxonomist who has worked on the section has provided different hypotheses of the number of species, their interrelationships, and the hybrid origins of various taxa. A recent taxonomic conspectus (Spooner et al., 2014) recognized 107 species in section Petota, less than half as many as a treatment by Hawkes (1990) that recognized 232 species.Plastid DNA restriction site studies (Spooner et al., 1991;Spooner and Sytsma, 1992;Rodríguez and Spooner, 1997;Spooner and Castillo, 1997) recognized four main clades in section Petota, referred to as clades 1-4. Subsequent studies using nuclear orthologs (Spooner et al., 2008b;Rodríguez and Spooner, 2009;Cai et al., 2012) recovered three main clades, with similar interspecific relationships except they combined clades 1 and 2 with the nuclear clades then referred to as 1+2, 3, and 4. In-depth studies of these individual clades have been conducted with morphological and molecular data in clade 1+2 (Rodríguez and Spooner, 1997; LaraCabrera and Spooner, 2004, 2005) and clade 3 (Ames et al., 2008;Ames and Spooner, 2010).Putatively related species complexes within the cultivated potato clade (clade 4) have been studied with DNA markers and morphological data, but never with a broad-scale phylogenetic study using multiple nuclear orthologs. According to the taxonomy of Spooner et al. (2014), the cultivated potato clade contains 34 predominately diploid species (some with rare triploid or tetraploid populations), two exclusively tetraploid species, and one species with diploid, tetraploid, and hexaploid populations. An additional 17 allopolyploid species share alleles with clades 1 or 3 and clade 4 (the cultivated potato clade) and are not studied here. The best-studied species complex in PREMISE OF THE STUDY:The species boundaries of wild and cultivated potatoes are controversial, with most of the taxonomic problems in the cultivated potato clade. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these problems. METHODS:We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set of 14,072 DNA characters, 2171 of which are parsimony-informative. We analyzed the data to produce phylogenies and perform concordance analysis and goodness-of-fit tests. KEY RESULTS:There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of Solanum verrucosum), clade 3, and a newly discovered basal clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. The results highlight a clade of species in South America not shown before, 'neocardenasii' , sister to clade 1+2, t...

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“…As this study and others [34-36] demonstrate, it is also complicated by phylogenetic results that are often incongruent among different phylogenetic markers (in this case nuclear ortholog markers).…”

Section: Discussionmentioning

confidence: 87%

“…jamesii ) for the B genome donor, in concordance with the phylogenetic results using nuclear ortholog DNA sequences [ 32 , 33 ]. Nuclear DNA sequencing studies [ 32 - 36 ] supported clade 1 + 2 to contain B genome species, clade 3 to contain P genome species, and clade 4 to contain A genome species.…”

Section: Introductionmentioning

confidence: 99%

Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)

et al. 2012

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BackgroundRecent genomic studies have drastically altered our knowledge of polyploid evolution. Wild potatoes (Solanum section Petota) are a highly diverse and economically important group of about 100 species widely distributed throughout the Americas. Thirty-six percent of the species in section Petota are polyploid or with diploid and polyploid cytotypes. However, the group is poorly understood at the genomic level and the series is ideal to study polyploid evolution. Two separate studies using the nuclear orthologs GBSSI and nitrate reductase confirmed prior hypotheses of polyploid origins in potato and have shown new origins not proposed before. These studies have been limited, however, by the use of few accessions per polyploid species and by low taxonomic resolution, providing clade-specific, but not species-specific origins within clades. The purpose of the present study is to use six nuclear orthologs, within 54 accessions of 11 polyploid species, 34 accessions of 29 diploid species of section Petota representing their putative progenitors, and two outgroups, to see if phenomena typical of other polyploid groups occur within wild potatoes, to include multiple origins, loss of alleles, or gain of new alleles.ResultsOur results increase resolution within clades, giving better ideas of diploid progenitors, and show unexpected complexity of allele sharing within clades. While some species have little diversity among accessions and concur with the GBSSI and nitrate reductase results, such as S. agrimonifolium, S. colombianum, S. hjertingii, and S. moscopanum, the results give much better resolution of species-specific progenitors. Seven other species, however, show variant patterns of allele distributions suggesting multiple origins and allele loss. Complex three-genome origins are supported for S. hougasii, and S. schenckii, and one of the ten accessions of S. stoloniferum. A very unexpected shared presence of alleles occurs within one clade of S. verrucosum from Central America, and S. berthaultii from South America in six polyploid species S. demissum, S. hjertingii, S. hougasii, S. iopetalum, S. schenckii, and S. stoloniferum.ConclusionsOur results document considerable genomic complexity of some wild potato polyploids. These can be explained by multiple hybrid origins and allele losses that provide a clear biological explanation for the taxonomic complexity in wild potato polyploids. These results are of theoretical and practical benefit to potato breeders, and add to a growing body of evidence showing considerable complexity in polyploid plants in general.

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Phylogenetic Relationships of Solanum Series Conicibaccata and Related Species in Solanum Section Petota Inferred from Five Conserved Ortholog Sequences

Cited by 14 publications

References 36 publications

The American cranberry: first insights into the whole genome of a species adapted to bog habitat

The American cranberry: first insights into the whole genome of a species adapted to bog habitat

Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte)

Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)

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