The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence

The complete nucleotide sequence of the chloroplast genome of potato Solanum tuberosum L. cv. Desiree was determined. The circular double-stranded DNA, which consists of 155,312 bp, contains a pair of inverted repeat regions (IRa, IRb) of 25,595 bp each. The inverted repeat regions are separated by small and large single copy regions of 18,373 and 85,749 bp, respectively. The genome contains 79 proteins, 30 tRNAs, 4 rRNAs, and unidentified genes. A comparison of chloroplast genomes of seven Solanaceae species revealed that the gene content and their relative positions of S. tuberosum are similar to the other six Solanaceae species. However, undefined open reading frames (ORFs) in LSC region were highly diverged in Solanaceae species except N. sylvestris. Detailed comparison was identified by numerous indels in the intergenic regions that were mostly located in the LSC region. Among them, a single large 241-bp deletion, was not associated with direct repeats and found in only S. tuberosum, clearly discriminates a cultivated potato from wild potato species Solanum bulbocastanum. The extent of sequence divergence may provide the basis for evaluating genetic diversity within the Solanaceae species, and will be useful to examine the evolutionary processes in potato landraces.     

Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae

To study the phylogenetics of sugarcane (Saccharum officinarum L.) and its relatives we sequenced four loci on cytoplasmic genomes (two chloroplast and two mitochondrial) and analyzed mitochondrial RFLPs generated using probes for COXI, COXII, COXIII, Cob, 18S+5S, 26S, ATPase 6, ATPase 9, and ATPase (D'Hont et al. 1993). Approximately 650 bp of DNA in the intergenic spacer region between rbcL and atpB and approximately 150 bp from the chloroplast 16S rDNA through the intergenic spacer region tRNA^val gene were sequenced. In the mitochondrial genome, part of the 18S rRNA gene and approximately 150 bp from the 18S gene 3 end, through an intergenic spacer region, to the 5S rRNA gene were sequenced. No polymorphisms were observed between maize, sorghum, and Saccharum complex members for the mitochondrial 18S internal region or for the intergenic tRNA^val chloroplast locus. Two polymorphisms (insertion-deletion events, indels) were observed within the 18S-5S mitochondrial locus, which separated the accessions into three groups: one containing all of the Erianthus, Eccoilopus, Imperata, Sorghum, and 1 Miscanthus species; a second containing Saccharum species, Narenga porphyrocoma, Sclerostachya fusca, and 1 presumably hybrid Miscanthus sp. from New Guinea; and a third containing maize. Eighteen accessions were sequenced for the intergenic region between rbcL and atpB, which was the most polymorphic of the regions studied and contained 52 site mutations and 52 indels, across all taxa. Within the Saccharum complex, at most 7 site mutations and 16 indels were informative. The maternal lineage of Erianthus/Eccoilopus was nearly as divergent from the remaining Saccharum complex members as it was from sorghum, in agreement with a previous study. Sequences from the rbcL-atpB spacer were aligned with GENBANK sequences for wheat, rice, barley, and maize, which were used as outgroups in phylogenetic analyses. To determine whether limited intra-complex variability was caused by under sampling of taxa, we used seven restriction enzymes to digest the PCR-amplified rbcL-atpB spacer of an additional 36 accessions within the Saccharum complex. This analysis revealed ten restriction sites (none informative) and eight length variants (four informative). The small amount of variation present in the organellar DNAs of this polyploid complex suggests that either the complex is very young or that rates of evolution between the Saccharum complex and outgroup taxa are different. Other phylogenetic information will be required to resolve systematic relationships within the complex. Finally, no variation was observed in commercial sugarcane varieties, implying a world-wide cytoplasmic monoculture for this crop.     

Nuclear-organelle interaction in Solanum: interspecific cybridizations and their correlation with a plastome dendrogram.

Summary Alloplasmic compatibility, namely the functional interaction between the nuclear genome of a given species with plastomes and chondriomes of alien species, is of considerable relevance in plant biology. The genus Solanum encompasses a wide spectrum of species and is therefore suitable for a study of this compatibility. We thus chose the nuclear genome of Solanum tuberosum (potato) and organelles (chloroplast and mitochondria) from 14 other Solanum species to initiate an investigation of intrageneric nucleus/organelle interactions. An assessment of the diversity of the chloroplast DNAs from these 15 species resulted in the construction of a plastome dendrogram (phylogenetic tree). In parallel we extended a previous study and performed ten additional fusion combinations by the donor-recipient protoplast fusion procedure, using potato protoplasts as recipients and protoplasts from any of ten other Solanum species as donors. We found that two fusion combinations did not yield cybrids and that the chloroplasts of S. polyadenium and the mitochondria (or mitochondrial components) from S. tarijense could not be transferred to cybrids bearing potato nuclei. In general, there is a correlation, albeit not perfect, between the cybridization data and the plastome dendrogram. These results furnish valuable information toward future transfer of plasmoneencoded breeding traits from wild Solanum species into potato. This information should also be useful for the planning of asymmetric protoplast fusion between potato and wild accessions for the improvement of pathogen and stress resistance of potato cultivars.     

Collapse of species boundaries in the wild potatoSolanum brevicaule complex (Solanaceae, S. sect.Petota): Molecular data

TheSolanum brevicaule complex is a group of morphologically very similar wild and cultivated potato taxa (Solanum sect.Petota). This study uses single to low-copy nuclear RFLPs and RAPDs to investigate their species boundaries and relationships. Cladistic analyses of both data sets are largely concordant with each other and with a recently published phenetic analyses of the same accessions using morphology. All three data sets separate members of the complex into populations from Peru and immediately adjacent northwestern Bolivia, including most cultivated species accessions, and populations from northwestern Bolivia to Argentina. The molecular results suggest that the complex is paraphyletic as currently circumscribed. Many species of theS. brevicaule complex should be relegated to synonymy.     

Sedum surculosum andS. jaccardianum (Crassulaceae) share a unique 70 bp deletion in the chloroplast DNA trnL (UAA)-trnF (GAA) intergenic spacer

TrnL (UAA)-trnF (GAA) chloroplast DNA spacer sequences of three species ofMonanthes, Sedum surculosum (=Monanthes atlanticum) andS. jaccardianum were compared.S. surculosum, the systematic position of which has been disputed ever since its discovery, shares a phylogenetically highly significant 70 bp deletion withS. jaccardianum. In addition to this large deletion the two Moroccan species ofS. ser.Monanthoidea differ in three more indels as well as in four nucleotide substitutions from the species ofMonanthes. These data render strong support for the monophyly ofS. ser.Monanthoidea andMonanthes. Spacer length in seven species and one subspecies ofMonanthes is relatively uniform.     

Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe)

We evaluated chloroplast DNA (cpDNA), isozymes, single to low-copy nuclear DNA (RFLPs), and random amplified polymorphic DNAs (RAPDs) in terms of concordance for genetic distance of 15 accessions each of Solanum etuberosum and S. palustre, and 4 accessions of S. fernandezianum. These self-compatible, diploid (2n=24), and morphologically very similar taxa constitute all species in Solanum sect. Etuberosum, a group of non-tuber-bearing species closely related to Solanum sect. Petota (the potato and its wild relatives). Genetic distance and multidimentional scaling results show general concordance of isozymes, RFLPs and RAPDs between all three taxa; cpDNA shows S. etuberosum and S. palustre to be more similar to each other than to S. fernandezianum. Interspecific sampling variance shows a gradation of resolution from allozyme (low) to RAPD to RFLP (high); while intraspecific comparisons graded from RFLPs (low) to RAPDs (high; lack of sufficient allozyme variability within species precluded comparisons for allozymes). Experimental error was low in RFLPs and RAPDs.Names are necessary to report factually and available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable     

Phylogenetic analysis of Asian<Emphasis Type="Italic"> Symplocos</Emphasis> (Symplocaceae) based on nuclear and chloroplast DNA sequences

Thirty species and one variety of Symplocos (Symplocaceae), including all taxa distributed in Japan, were phylogenetically analyzed with DNA sequence data. The evolution of morphological characters is discussed on the basis of the phylogenetic relationships obtained. All species were Asian, except one, S. austromexicana, from Mexico. The nuclear ribosomal internal transcribed spacer (ITS) region and two intergenic spacer regions, between trnL and trnF, and between trnH and psbA of chloroplast DNA were used. The topologies of trees obtained from ITS and the chloroplast intergenic spacers are largely congruent. S. sonoharae, the representative of the subgenus Symplocos in Asia, was sister to all other species. The position of the American species, S. austromexicana, which also belongs to the subgenus Symplocos, was not well resolved. The phylogenetic tree based on combined sequence data largely supports the monophyletic origin of the infrageneric sections proposed earlier. However, the phylogenetic relationship between them is not well resolved, probably due to rapid diversification. The section Palura, a deciduous group, is well defined in the DNA analysis, suggesting its independent status in the genus Symplocos. In spite of their morphological divergence, the three endemic species of the Bonin Islands are monophyletic. The occurrence of curved seeds seems to be homoplastic, scattered over the phylogenetic tree without showing a particular infrageneric relationship.     

TrnL–trnF Intergenic Spacer and trnL Intron Define Major Clades Within Luzula and Juncus (Juncaceae): Importance of Structural Mutations

Seven hundred fifty-two to one thousand ninety-seven base pairs of the trnL intron and trnL–trnF intergenic spacer of the chloroplast DNA of 55 Juncaceae taxa (Juncus, Luzula, Rostkovia, and Oxychloë) was sequenced. Seventeen structural mutations (13 indels marked A to M, 3 parts of the trnF pseudogene, and insertion o within a pseudogene) within the chloroplast trnL–trnF region were examined as possible indicators for phylogenetic relationships in Juncaceae. Juncus trifidus (section Steirochloa) was clearly separated from the other taxa by two large (>80 bp) indels. The Southern Hemisphere clade was strongly supported by a unique insertion (334 bp) in the trnL intron. The monophyly of Luzula was supported by three small (<10 bp) indels in the trnL-F spacer. They were found in all 22 examined members that represent the taxonomic and geographical diversity of the genus Luzula. A tandemly duplicated tRNA pseudogene was found in the Juncus subgenus Juncus species and is supported by four small unique indels too. The acceptor stem and D-domain-encoding regions are separated by a unique 8-bp insertion. The T-domain and acceptor stem-encoding regions were not found in the pseudogene repeats. Only the Juncus sections Ozophyllum and Iridifolii contain the 5 acceptor stem, D-domain, and anticodon domain of the tRNAF encoding DNA. The structural mutations in the trnL intron and the trnL–trnF intergenic spacer are useful for phylogenetic reconstruction in the Juncaceae.     

Variability of chloroplast DNA and nuclear ribosomal DNA in cassava (Manihot esculenta Crantz) and its wild relatives

Chloroplast DNA (cp) and nuclear ribosomal DNA (rDNA) variation was investigated in 45 accessions of cultivated and wild Manihot species. Ten independent mutations, 8 point mutations and 2 length mutations were identified, using eight restriction enzymes and 12 heterologous cpDNA probes from mungbean. Restriction fragment length polymorphism analysis defined nine distinct chloroplast types, three of which were found among the cultivated accessions and six among the wild species. Cladistic analysis of the cpDNA data using parsimony yielded a hypothetical phylogeny of lineages among the cpDNAs of cassava and its wild relatives that is congruent with morphological evolutionary differentiation in the genus. The results of our survey of cpDNA, together with rDNA restriction site change at the intergenic spacer region and rDNA repeat unit length variation (using rDNA cloned fragments from taro as probe), suggest that cassava might have arisen from the domestication of wild tuberous accessions of some Manihot species, followed by intensive selection. M. esculenta subspp flabellifolia is probably a wild progenitor. Introgressive hybridization with wild forms and pressures to adapt to the widely varying climates and topography in which cassava is found might have enhanced the crop's present day variability.     

Variation in Coding (NADH Dehydrogenase Subunits 2, 3, and 6) and Noncoding Intergenic Spacer Regions of the Mitochondrial Genome in Octocorallia (Cnidaria: Anthozoa)

Low rates of evolution in cnidarian mitochondrial genes such as COI and 16S rDNA have hindered molecular systematic studies in this important invertebrate group. We sequenced fragments of 3 mitochondrial protein-coding genes (NADH dehydrogenase subunits ND2, ND3 and ND6) as well as the COI-COII intergenic spacer, the longest noncoding region found in the octocoral mitochondrial genome, to determine if any of these regions contain levels of variation sufficient for reconstruction of phylogenetic relationships among genera of the anthozoan subclass Octocorallia. Within and between the soft coral families Alcyoniidae and Xeniidae, sequence divergence in the genes ND2 (539 bp), ND3 (102 bp), and ND6 (444 bp) ranged from 0.5% to 12%, with the greatest pairwise distances between the 2 families. The COI-COII intergenic spacer varied in length from 106 to 122 bp, and pairwise sequence divergence values ranged from 0% to 20.4%. Phylogenetic trees constructed using each region separately were poorly resolved. Better phylogenetic resolution was obtained in a combined analysis using all 3 protein-coding regions (1085 bp total). Although relationships among some pairs of species and genera were well supported in the combined analysis, the base of the alcyoniid family tree remained an unresolved polytomy. We conclude that variation in the NADH subunit coding regions is adequate to resolve phylogenetic relationships among families and some genera of Octocorallia, but insufficient for most species - or population-level studies. Although the COI-COII intergenic spacer exhibits greater variability than the protein-coding regions and may contain useful species-specific markers, its short length limits its phylogenetic utility.     

Phylogenetic reconstruction at the species and intraspecies levels in the genus Pisum (L.) (peas) using a histone H1 gene

A phylogenetic analysis of the genus Pisum (peas), embracing diverse wild and cultivated forms, which evoke problems with species delimitation, was carried out based on a gene coding for histone H1, a protein that has a long and variable functional C-terminal domain. Phylogenetic trees were reconstructed on the basis of the coding sequence of the gene His5 of H1 subtype 5 in 65 pea accessions. Early separation of a clear-cut wild species Pisum fulvum is well supported, while cultivated species Pisum abyssinicum appears as a small branch within Pisum sativum. Another robust branch within P. sativum includes some wild and almost all cultivated representatives of P. sativum. Other wild representatives form diverse but rather subtle branches. In a subset of accessions, PsbA-trnH chloroplast intergenic spacer was also analysed and found less informative than His5. A number of accessions of cultivated peas from remote regions have a His5 allele of identical sequence, encoding an electrophoretically slow protein product, which earlier attracted attention as likely positively selected in harsh climate conditions. In PsbA-trnH, a 8bp deletion was found, which marks cultivated representatives of P. sativum.     

Molecular variation in Galdieria sulphuraria (Galdieri) Merola and its bearing on taxonomy

Cyanidium caldarium, Cyanidioschyzon merolae and Galdieria sulphuraria are three unicellular algae characteristic, of acid thermal environments. Recently, on the basis of morphological characters, three new species of Galdieria (G. partita, G. daedala, G. maxima ) isolated from acid-thermal springs in Russia have been instituted. A selected region of rbcL and the sequence of the intergenic spacer between the rbcL and rbcS have been amplified and sequenced from different Galdieria species and strains, in order to define molecular relationship among these interesting algae. The obtained cladogram shows that Cyanidium caldarium and Cyanidioschyzon merolae form a sister group which, in turn, is in a sister group relationship with Galdieria. This last genus is divided in two clades, one of which includes G. sulphuraria accessions from Naples (Italy), California, and Yellowstone and the other one includes G. sulphuraria accessions from Java (Indonesia) and from the Russian species. These results support the status of the genus Galdieria and suggest that G. daedala, G. maxima and G. partita are three very similar strains of G. sulphuraria; the rbcL variation within Galdieria accessions has a pattern which is broadly connected to the geographial distribution. The data obtained from the intergenic rbcL-rbcS spacer partly confirm those from the rbcL analysis.     

Structure and polymorphism of a fragment of the Pain-1 vacuolar invertase locus in Solanum species

A fragment of the Pain-1 vacuolar invertase locus was sequenced and its structure and polymorphism were characterized in 17 species of the genus Solanum, including the subgenera Potatoe, Solanum, Leptostemonum, Minon, and Brevantherum. The fragment size varied from 603 to 977 bp as a result of multiple indels in the region of intron III. A total of 80 single nucleotide polymorphisms were found in the coding region, of which 34 caused amino acid substitution in the protein product. Several substitutions and indels were specific to individual taxons or taxon groups, including potato and tomato species. The genetic distances and phylogenetic trees obtained supported the commonly accepted taxonomic classification of the species, indicating that the Pain-1 fragment is suitable for taxonomic identification and phylogenetic studies in Solanaceae.     

Schottarum (Schismatoglottideae: Araceae) substantiated based on combined nuclear and plastid DNA sequences

Recent studies on Schismatoglottideae have resulted in the recognition of four new monophyletic genera, the resurrection of two additional genera following clarification of their monophyly, and the publication of many taxonomically novel species. However, generic boundaries among some parts of Schismatoglottideae remain unclear owing to several reasons: (1) more taxa are being revealed through our on-going fieldwork, now expanded to previously unsampled localities on Borneo; (2) established occurrence of a high level of homoplasies among the morphological characteristics hitherto used to delimitate genera; and (3) gene regions used in previous studies contradicted some of current taxonomic placements. Among the unsolved groups from previous studies a clade comprising Schismatoglottis sarikeensis and S. josefii needs further investigation. Therefore, phylogenetic analyses were carried out to investigate the position of these two species using the nuclear region, internal transcribed spacer and combined plastid regions: trnL intron and trnL-F intergenic spacer, coding matK+partial 3′ trnK, intergenic spacer trnH-psbA. A total of 23 accessions representing 16 taxa of Schismatoglottideae and Philonotieae were included in the study. Phylogenetic analyses of a total 4,658 bp combined dataset using parsimony, maximum likelihood, and Bayesian methods revealed that S. sarikeensis and S. josefii do not belong to Schismatoglottis, and therefore are transferred to Schottarum (≡Hottarum sarikeense ≡ Schismatoglottis sarikeense). Flowering mechanism, pollination strategy, and fruitset of S. sarikeense are also presented in the paper.     

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

The taxonomy of Bambusoideae is in a state of flux and phylogenetic studies are required to help resolve systematic issues. Over 60 taxa, representing all subtribes of Bambuseae and related non-bambusoid grasses were sampled. A combined analysis of five plastid DNA regions, trnL intron, trnL-F intergenic spacer, atpB-rbcL intergenic spacer, rps16 intron, and matK, was used to study the phylogenetic relationships among the bamboos in general and the woody bamboos in particular. Within the BEP clade (Bambusoideae s.s., Ehrhartoideae, Pooideae), Pooideae were resolved as sister to Bambusoideae s.s. Tribe Bambuseae, the woody bamboos, as currently recognized were not monophyletic because Olyreae, the herbaceous bamboos, were sister to tropical Bambuseae. Temperate Bambuseae were sister to the group consisting of tropical Bambuseae and Olyreae. Thus, the temperate Bambuseae would be better treated as their own tribe Arundinarieae than as a subgroup of Bambuseae. Within the tropical Bambuseae, neotropical Bambuseae were sister to the palaeotropical and Austral Bambuseae. In addition, Melocanninae were found to be sister to the remaining palaeotropical and Austral Bambuseae. We discuss phylogenetic and morphological patterns of diversification and interpret them in a biogeographic context.     

Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications

The evolution of 5S rRNA gene unit (5S gene unit) was studied among the ten species belonging to Vigna subgenus Ceratotropis by sequencing and analyzing the intra- and inter-specific sequence heterogeneity. The 5S unit from these species ranged from 214 to 342 bp in length as a result of several indels in the intergenic spacer (IGS) region. A large deletion (>100 bp) was found specifically in the IGS of V. radiata accessions. IGS showed high sequence variation with more than 50% polymorphic and 35.4% parsimony informative sites. However, the coding region (5S gene) was highly conserved, both in length and in sequence. Intra-genomic and intra-specific divergence was observed among some species, which indicated that the 5S unit is evolving at different rates among the Vigna species. Most Vigna species harbored one type of 5S unit indicating complete homogenization among them. Vigna glabrescens, a tetraploid species, also showed single type of 5S rDNA from only one of the diploid progenitor indicating loss or homogenization of the other type. However, V. nakashimae and V. riukiuensis harbored multiple, diverse, ‘intra-genomic 5S types’ indicating that 5S rDNA is not completely homogenized by concerted evolution and is still evolving. In general, the phylogeny based on IGS sequences was in agreement with many of the earlier reports except some surprising observations such as, V. glabrescens clustered with V. mungo in section Ceratotropis and unlike most of the species, wild and cultivated types of V. umbellata were present in different subclusters. Presence of divergent 5S sequences in V. nakashimae and V. riukiuensis caused errors in phylogeny reconstruction at species level and suggested a horizontal ‘gene transfer’ as a result of inter-species hybridization. The comparative analysis showed that 5S IGS sequences have better phylogenetic utility than chloroplast DNA sequences, such as atpB-rbcL and is comparable to ITS1 and ITS2 in this respect.     

Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes

Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals significant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf2 or ribosomal binding sites in ycf2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP, cemA, ccsA, and matK. Repeat analyses identified 33–45 direct and inverted repeats ≥30 bp with a sequence identity of at least 90%; all but five of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the first time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa. It is possible that there has been a loss of conserved editing sites in potato and tomato.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Resistance of three wild tuber-bearing potatoes to the Colorado potato beetle

The resistance of Solanum okadae Hawkes & Hjert. (PI 458367), Solanum oplocense Hawkes (PI 473368), and Solanum tarijense Hawkes (PI 414150) to the Colorado potato beetle, Leptinotarsa decemlineata (Say) (Chrysomelidae: Chrysomelini), was studied. In replicated field trials all three accessions showed a high level of resistance to the beetle. No significant genetic variability between genotypes of the same species was found. Results from host acceptance behavior experiments, suitability for larval development tests, foliage consumption tests, and adult survival and oviposition tests supported the hypothesis that the mode of resistance differs between the three wild Solanum species. Solanum okadae and S. oplocense affected host acceptance and consumption. Because the beetle reacted differently to these two species it was hypothesized that the antifeedant chemical(s) differed in nature or quantity. S. tarijense contrasted with the other two species by affecting mostly adult colonization and oviposition.     

Acrylamide gel electrophoresis of seed proteins from someSolanum (sectionSolanum) species

Polyacrylamide gel electrophoresis was used to investigate the seed proteins of 36 accessions belonging toSolanum sect.Solanum (Solanaceae). These accessions represented 20 species, of four differing ploidy levels, and included infraspecific morphological variants. The resultant band patterns tended to reflect the morphological differences and genetical isolation displayed by many of the species. The most variable band patterns were encountered in the taxa with the greatest infraspecific variation, while many of the more morpho-genetically distinct taxa seemed to have species-specific band patterns.Good matches were found between the band patterns of artificial hybrids, those of their known parents, and mixtures of the parental protein extracts. This illustrates the potential use of such a technique for pinpointing possible genome donors of natural hybrids, and especially of polyploids. These comparative band patterns confirmed experimental work on the origin of the hexaploidS. nigrum from the diploidS. americanum and the tetraploidS. villosum, and also supported the suggestion thatS. nigrum contains two genomes from the diploidS. sarrachoides, but not four genomes of the diploidS. americanum.     

Molecular evolution of 5S rDNA of Solanum species (sect. Petota): application for molecular phylogeny and breeding

Nucleotide sequences of 5S rRNA genes (5S rDNA) of 26 wild species of the genus Solanum (sect. Petota) originating from Middle or South America, four Solanum tuberosum breeding lines and one European species, Solanum dulcamara (sect. Dulcamara) were compared with each other and with the 5S rDNA of Lycopersicon esculentum. The length of the repeat ranges from 285 bp to 349 bp. The complete 5S repeat unit consists of the 120-bp long conserved coding region and of a intergenic spacer with a high variability in the central portion as result of deletions/duplications of short motifs demonstrating sequence similarity to box C in the 5S rRNA coding region. Numerous structural rearrangements found in the spacer region can be applied to design species-specific molecular markers for Solanum species involved in breeding programs. Characteristic insertions/deletions (indels) were used to reconstruct phylogenetic relationships among the species studied. S. dulcamara forms a separate clade; L. esculentum is more related to Solanum species of sect. Petota. Conservation of ancestral 5S spacer organization was demonstrated for the representatives of several series of sect. Petota, both Stellata and Rotata. Further rearrangements of the spacer organization occurred in at least four independent lineages: (1) L. esculentum, (2) ser. Polyadenia, (3) other Stellata species from Middle America (ser. Pinnatisecta and Bulbocastana), (4) superser. Rotata. In this last group, series Megistacroloba and Conocibaccata show a common origin, and separation from ser. Tuberosa. Solanum chacoense and Solanum maglia demonstrate a close relatedness to species of ser. Tuberosa and should be included into this group, whereas Solanum bukasovii should be excluded due to conservation of ancestral spacer organization. Three major subgroups may be distinguished for species from ser. Tuberosa, although a high sequence similarity was found here. Several wild species (diploids Solanum phureja and Solanum spegazzinii) probably participated in the natural origin of tetraploid S. tuberosum;others were later used for crossing in breeding programs (e.g. Solanum demissum). Clear separation of Middle-American Stellata species from South-American Stellata and from Middle-American Rotata polyploids is shown. Received: 11 January 2001 / Accepted: 18 April 2001