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Wild tomatoes (Solanum section Lycopersicon) are native to western South America. The delimitation and relationships of tomato species have differed widely depending upon whether morphological or biological species concepts are considered more important. Molecular data from mitochondrial, nuclear, and chloroplast DNA restriction fragment length polymorphisms (RFLPs), nuclear microsatellites, isozymes, and gene sequences of internal transcribed spacers of nuclear ribosomal DNA (ITS; multiple-copy), the single-copy nuclear encoded Granule-bound Starch Synthase gene (GBSSI or waxy), and morphology, have been used to examine hypotheses of species relationships. This study is a companion to the previous GBSSI gene sequence study and to the morphological study of relationships of all ten wild tomato species (including the recently described S. galapagense), with a concentration on the most widespread and variable species S. peruvianum s.1. These new AFLP data are largely concordant with the GBSSI and morphological data and in general support the species outlined in the latest treatment by C.M. Rick, but demonstrate the distinct nature of northern and southern Peruvian populations of S. peruvianum, and suggest that their taxonomy needs revision. Solanum ochranthum is supported as sister to wild tomatoes, and S. habrochaites and S. pennellii reside in a basal polytomy in the tomato clade. [ABSTRACT FROM AUTHOR]

Abstract Background Recent 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. Results Our 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. Conclusions Our 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.

Abstract Background Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. Conclusions This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

Abstract Background The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of LEAFY and the alcohol dehydrogenase gene (Adh) were selected to investigate their molecular evolution and phylogenetic utility. Results DNA sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some Adh homologs are putatively nonfunctional. A partial region of Adh1 was sequenced for 18 Pyrus species and three subparalogs representing Adh1-1 were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of LEAFY, multiple inparalogs were discovered for both LFY1int2 and LFY2int2. LFY1int2 is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of Pyrus using LFY2int2-N. Conclusions Our study represents the first phylogenetic analyses based on LCNGs in Pyrus. Ancient and recent duplications lead to a complex structure of Adh outparalogs and inparalogs in Pyrus and Malus, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs, LFY2int2-N is the best nuclear marker for phylogenetic reconstruction of Pyrus due to suitable sequence divergence and the absence of lineage sorting.

Abstract Background Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species. Results Among potatoes, when total evidence is invoked, one single predominant history is highlighted with complete resolution within and among the three main clades. It also supports the hypothesis of the North and Central American B-genome origin of the tuber-bearing members of Solanum sect. Petota and shows a clear division between A genomes in clades 3 and 4, and B genomes in clade 1+2. On the other hand, when a prior agreement approach is invoked other potato evolutionary histories are revealed but with less support. These alternative histories could be explained by past hybridization, or fast rates of speciation. In the case of tomato, the analyses with all sequence data completely resolved 19 of 21 clades, for the first time revealed the monophyly of five clades, and gave further support for the recent segregation of new species from the former Solanum peruvianum. Concordance analyses revealed and summarized the extensive discordance among COSII markers. Some potential reasons for discordance could be methodological, to include systematic errors due to using a wrong model of sequence evolution, coupled with long branches, or mixtures of branch lengths within COSII, or undetected paralogy or alignment bias. Other reasons could be biological processes such as hybridization or lineage sorting. Conclusion This study confirms and quantifies the utility of using DNA sequences from different parts of the genome in phylogenetic studies to avoid possible bias in the sampling. It shows that 11–18 loci are enough to get the dominant history in this group of Solanum, but more loci would be needed to discern the distribution of gene genealogies in more depth, and thus detect which mechanism most likely shaped the discordance.

Background: The National Epirubicin Adjuvant Trial (NEAT) and BR9601 trials tested the benefit of epirubicin when added to cyclophosphamide, methotrexate and 5-fluorouracil (E-CMF) compared with standard CMF in adjuvant chemotherapy for women with early breast cancer. This report details longer follow-up with interesting additional time-dependent analyses., Methods: National Epirubicin Adjuvant Trial used epirubicin (E) 3-weekly for four cycles followed by classical (c) CMF for four cycles (E-CMF) compared with cCMF for six cycles. BR9601 used E 3-weekly for four cycles followed by CMF 3-weekly for four cycles, compared with CMF 3-weekly for eight cycles., Results: In all, 2391 eligible patients were randomised and with a median 7.4-year follow-up, E-CMF confirmed a significant benefit over CMF in both relapse-free survival (RFS) (78% vs 71% 5 years RFS, respectively, hazard ratio (HR)=0.75 (95% CI: 0.65-0.86), P<0.0001) and overall survival (OS) (84% vs 78% 5 years OS, respectively, HR=0.76 (95% CI: 0.65-0.89), P=0.0007). Interaction of treatment effect and prognostic factors was demonstrated for duplication of chromosome 17 centromeric enumeration (Ch17CEP) as previously reported. Poor prognostic factors at diagnosis (ER and PR negative and HER2 positive) showed time-dependent annual hazard rates for RFS and OS. In univariate analysis, these factors demonstrated more favourable HRs for RFS after 5 years. Treatment effects also suggested a differential benefit for E-CMF within the first 5 years for poor prognosis tumours., Conclusion: Longer follow-up has confirmed E-CMF as significantly superior to CMF for all patients. Ch17CEP duplication was the only biomarker that demonstrated significant treatment interaction. Standard poor prognostic factors at diagnosis were time-dependent, and after 5 years disease-free, poor prognosis patients demonstrated favourable HRs for survival.

Purpose: To examine the activity and safety of two sequentially scheduled chemotherapy regimens comprising four cycles of paclitaxel (pctx) 200 mg/m2/3 hours then four cycles ofcisplatin (cisDDP) 100 mg/m2, and vice versa, in patients with previously untreated advanced ovarian cancer., Patients and Methods: Between January 1994 and February 1996, we recruited 30 patients to the pctx-then-cisDDP regimen and 29 to cisDDP-then-pctx, in parallel phase II trials., Results: Both regimens were predictably active with responses seen in 22 of 30 patients (OR 74%; CR 27%, PR 47%) treated with pctx-then-cisDDP, as against 13 of 21 patients (OR 62%; CR 38%, PR 24%) treated with cisDDP-then-pctx. The OR rate to four cycles of pctx (induction) was 43%, with 27% disease progression; the OR to four cycles of cisDDP (induction) was 57%, with 5% progression. However, progression rates across both induction and consolidation phases were 16% (pctx-then-cisDDP) and 29% (cisDDP-then-pctx). Both regimens were unacceptably neurotoxic. II patients suffering grade 3 sensory neurotoxicity (5 on pctx-then-cisDDP, 6 on cisDDP-then-pctx) and 20 having grade 3 deafness (9 on pctx- then-cisDDP, 11 on cisDDP-then-pctx)., Conclusion: The activity of these sequential regimens justifies their further development using the less neurotoxic platinum analogue carboplatin, perhaps combining paclitaxel with other platinum non-cross resistant drugs.