A molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA rps16 intron sequences

Phylogenetic relationships among 13 genera of the subtribe Glycininae, two genera of the allied subtribe Diocleinae that were included within Glycininae by Polhill, and two genera of the subtribe Erythrininae as outgroups were inferred from chloroplast DNA rps16 intron sequence variation. Pairwise sequence divergence values ranged from identity between Teramnus mollis and T. micans and between T. flexilis and T. labialis to 7.89% between Pueraria wallichii and Pseudeminia comosa across all accessions. Phylogenies estimated using parsimony and neighbor-joining methods revealed that (1) Glycininae is monophyletic if Pachyrhizus and Calopogonium (both Diocleinae) are included within Glycininae; (2) the genus Teramnus is closely related to Glycine, and Amphicarpaea showed a sister relationship to the clade comprising Teramnus and Glycine; (3) the expanded Glycininae including two genera of Diocleinae is divided into three branches, temporarily named I (comprising the rest of the examined taxa), II (Pueraria wallichii), and III (Mastersia), but their relationships are equivocal; and (4) the genus Pueraria, regarded as a closely related genus to Glycine, is not monophyletic and should be divided into at least four genera (a hypothesis supported previously by Lackey).     

Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data

Phylogenetic relationships among the 22 genera of the palm subfamily Calamoideae were investigated using DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast rps16 intron. The rps16 intron displayed low levels of variation, corroborating previous reports that the chloroplast genome of palms is highly conserved. High levels of within-individual polymorphism were identified in the ITS region, indicating that concerted evolution is not effectively homogenizing the ITS repeats. In the majority of cases, multiple clones from individuals resolved as monophyletic. However, the high levels of homoplasy in the ITS dataset, along with generally poor jackknife support for many clades, led to concerns that topologies obtained from these data might be unreliable. Nevertheless, congruence between trees based on ITS data alone and those based on rps16 intron data was high. Simultaneous analyses of both datasets yielded well-resolved topologies with high levels of jackknife support. A number of exciting groups emerged from the analyses: the African rattan clade comprising the endemic African rattan genera Laccosperma, Eremospatha, and Oncocalamus; the Lepidocaryeae-Raphia clade comprising the fan-leaved New World tribe Lepidocaryeae and the African genus Raphia; and the Asian clade comprising all Asian genera except Eugeissona. The position of Eugeissona was variable, although it did not resolve inside any of the three major clades mentioned above.     

Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1.

The plant mitochondrial rps3 intron was analyzed for substitution and indel rate variation among 15 monocot and dicot angiosperms from 10 genera, including perennial and annual taxa. Overall, the intron sequence was very conserved among angiosperms. Based on length polymorphism, 10 different alleles were identified among the 10 genera. These allelic differences were mainly attributable to large indels. An insertion of 133 nucleotides, observed in the Alnus intron was partially or completely absent in the other lineages of the family Betulaceae. This insertion was located within domain IV of the secondary-structure model of this group IIA intron. A mobile element of 47 nucleotides that showed homology to sequences located in rice rps3 intron and in intergenic plant mitochondrial genomes was found within this insertion. Both substitution and indel rates were low among the Betulaceae sequences, but substitution rates were increasingly larger than indel rates in comparisons involving more distantly related taxa. From a secondary-structure model, regions involved in helical structures were shown to be well preserved from indels as compared to substitutions, but compensatory changes were not observed among the angiosperm sequences analyzed. Using approximate divergence times based on the fossil record, substitution and indel rate heterogeneity was observed between different pairs of annual and perennial taxa. In particular, the annual petunia and primrose evolved more than 15 and 10 times faster, for substitution and indel rates respectively, than the perennial birch and alder. This is the first demonstration of an evolutionary rate difference between perennial and annual forms in noncoding DNA, lending support to neutral causes such as the generation time, population size, and speciation rate effects to explain such rate heterogeneity. Surprisingly, the sequence from the rps3 intron had a high identity with the sequence of intron 1 from the angiosperm mitochondrial nad5 gene, suggesting a common origin of these two group IIA introns.     

Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms

According to PCR assays and sequencing, we now report the shared presence of two rps3 introns, namely the rps3i74 and the rps3i249, in the mitochondria of all the classes representing the surviving lineages of gymnosperms, and unveil several lineages experiencing intron loss.Interestingly, the rps3 intron gains and losses within the four groups of gymnosperms let us sort out the Pinaceae and the non-Pinaceae into intron (+)- and intron (?)-lineages, respectively. Worthy of mention is also the finding that only Gnetum within the Gnetales harbours both the rps3 introns.This intron distribution pattern is consistent with the hypothesis that the two rps3 introns were likely present in the common ancestor of the seed plants and, then, independently lost in the non-Pinaceae during gymnosperm evolution.The derived secondary structural model of the novel group IIA intron improves our understanding of the significance and origin of the extraordinary length polymorphisms observed among rps3i249 orthologs.Despite the remarkable structural plasticity to adopt and reject introns, the rps3 mRNAs undergo accurate processing by splicing and extensive editing in gymnosperm mitochondria.This study provides additional insights into the evolutionarily high dynamics of mitochondrial introns which may come and go in closely related plant species.The turnover of the mitochondrial rps3 group II introns seen among lineages of seed plants further suggests that these introns might be an additional signature to discriminate between particularly cryptical taxonomic groups for which there is a need of a further evaluation of their evolutionary affiliation.     

Mitochondrial DNA variation in cultivated and wild potato species (Solanum spp.).

The European cultivated potato, Solanum tuberosum subsp. tuberosum, has 6 related cultivated species and more than 200 wild relatives. In Solanum spp., studies of cytoplasmic organelles have been mainly confined to the plastid DNA composition of cultivated and wild species. In this study, 53 genotypes of 30 potato species belonging to the subsections Estolonifera and Potatoe, 2 tomato species, and a black nightshade genotype were examined using PCR markers to evaluate mitochondrial DNA diversity and assess whether mtDNA variability was correlated with series classification, geographical origin, ploidy, and endosperm balance number (EBN). The markers used revealed interspecific mtDNA variability in Solanum spp. and identified 13 different haplotypes. Intraspecific variability was also observed in a few species and genomic regions. Cluster analysis allowed arrangement of the 13 haplotypes into 7 subgroups, and statistical association tests showed significant relationships between mitochondrial patterns detected by molecular analysis and ploidy, EBN, and geographical origin. On the whole, the evolutionary patterns for the genomic regions analyzed reflected the species relationships established on the basis of morphological and molecular (nuclear and plastidial DNA) data. The mtDNA variability shown is also important for better characterization of genetic resources for potato breeding.     

S16, a novel S-RNase allele in the diploid species Solanum chacoense.

Wild potato species have a gametophytic self-incompatibility system controlled by a single multiallelic S locus. In the style, the S-RNase gene codes for an allele-specific ribonuclease that is involved in the rejection of pollen that carries the same S haplotype. This gene has 5 conserved regions (C1-C5) and highly variable regions outside of these areas that play a role in S-RNase allele specificity. In this work, PCR-mediated amplification of genomic DNA from 2 Solanum chacoense accessions was performed using primers designed on the basis of the C1 and C4 conserved regions. By sequencing the PCR products, a new S-RNase allele (S16) was identified in 1 plant of the QBCM argentinian accession. Comparison of the partial sequence (from C2 to C3) of S16 RNase with those of 11 S-RNase genes of other Solanaceae species showed the highest and the lowest similarity scores within the same plant species (respectively, 71% with the S11 and S13 RNase and 35% with the S2 RNase). Differences at the nucleotide level between S16 and S11 RNase alleles are discussed.     

Cytoplasmic male sterility-associated structural variation of the mitochondrial genome regions containing rps3 and orf215 in sugar beet Beta vulgaris L

Several 5'-degenerate primers were selected by computer analysis and used for mtDNA typing in sugar beet cultivars with cytoplasms of the S (typical for cytoplasmic male sterility) or N (normal) type. A number of N- or S-specific markers were found to correspond to transcribed mitochondrial genes. One was from the orf215 region of the N-type mtDNA. A physical map of the corresponding region was constructed for the S-type mtDNA, and a substantial difference observed for the two genome types. One N-specific marker proved to contain a rearranged rps3 region and a truncated atp9 copy. With the known nucleotide sequence of this marker, three-primer PCR was designed and showed that both variants of the rps3 region simultaneously take place in the mtDNA pool, the new one occurring in a substochiometric proportion.     

The basis of structural colour variation in two species of Papilio

An account is given of the ultrastructure and optical properties of the structural colour scales of Papilio karna and P.palinurus. The scales are Urania-type multilayers of 10 lamellae separated by air-spaces. A theoretical model is elaborated to account for the results and it is concluded that colour variation between species is achieved through control of film thickness. It is proposed that the surface structure functions as an anti-reflection coating. A generalised functional basis for the structural difference between Urania-type and Morpho-type scales is suggested.     

Phylogeny of Gardenieae (Rubiaceae) based on chloroplast DNA sequences from the rps16 intron and trnL(UAA)-F(GAA) intergenic spacer

Chloroplast DNA (cpDNA) sequences of the rps 16 intron and the trn L (UAA)-F(GAA) intergenic spacer were obtained from 59 species, to evaluate phylogenetic relationships among members of the Gardenieae, Rubiaceae. The results indicate that Gardenieae is polyphyletic and that genera included in the subtribe Diplosporinae should be transferred to the Coffeeae and Octotropideae. The Octotropideae tribe may also be polyphyletic. It is also demonstrated that the tribe Pavetteae is polyphyletic. In addition, the present data support a basal position for the disputed genus Bertiera within the Coffeeae clade. Of the informal groups proposed by Robbrecht & Puff within the Gardenieae, the Alibertia group is strongly supported, and is estimated to also include Ibetralia, Genipa aff. williamsii , and one undescribed taxon. However, Genipa americana was not part of this clade suggesting that Genipa is polyphyletic. The Tetrad group is not supported, and character optimisations suggest that pollen released in tetrads may have arisen three times. Most of these genera appear in the same clade as the three neotropical genera Sphinctanthus, Rosenbergiodendron , and Tocoyena , all of which bear pollen in monads. Atractogyne, Mitriostigma , and Oxyanthus form the second group with pollen in tetrads, whereas Gardenia is embedded in a third group. Massularia , with polyads, occurs either singly on a large polytomy or at the base of the Atractocarpus-Porterandia-Trukia clade.     

The variation and evolution of selected species of Solanum section Basarthrum (Solanaceae). II

Five taxa ofSolanum sect.Basarthrum were studied in an effort to clarify their taxonomic position and to determine the effective evolutionary mechanisms. Methods included an analysis of chromosome number and behavior, artificial hybridizations and a study of herbarium material. The data suggest thatS. canense andS. suaveolens are closely related and that 5.suaveolens may have been the progenitor ofS. canense. The only successful interspecific cross involving one of these two species was vigorous but highly sterile. Evidence from both morphology and crossing studies indicates a close relationship betweenS. basendopogon andS. caripense. Hybrids between these two species with relatively high fertility through the F₃ generation were secured. The status ofS. basendopogon f.obtusum remains a problem since there is but one collection of the typical form. The placement ofS. sanctae-marthae in sect.Basarthrum is considered problematic. Virtually none of 170 interspecific crosses with this species were successful. Seed size and the presence and size of a seed wing are proposed as useful morphological characters in sect.Basarthrum. There is apparently a correlation between short styles and self-compatibility. All species are diploid (n = 12) and no chromosomal or meiotic aberrations were noted in the species or hybrids. Most of the more than 1,000 interspecific crosses failed. Most of the hybrid fruits bore no seeds or seeds which did not germinate. The primary barriers separating species are considered to be strong prefertilization isolating mechanisms and ecogeographic factors.     

SNP identification and analysis in part of intron 2 of goat MSTN gene and variation within and among species

Part of intron 2 of the myostatin (MSTN) gene of 140 goats from 24 populations and 38 sheep from 8 breeds were sequenced, and similar sequences of different species from Gene bank were also obtained to study MSTN diversity within and among species. The results indicated that there were seven polymorphic sites in the sequenced region of goat, which have not been separated by recombination (or recurrent mutation), presented complete linkage disequilibrium, and could be sorted into three haplotypes. There was no polymorphic site in the sequenced region of sheep. The haplotype diversity, nucleotide diversity, and average number of single nucleotide polymorphism (SNP) differences of goats from the South group are higher than those of North group, and the corresponding value of the Foreign group is also higher than that of Chinese. The genetic differentiation (0.7558) between the Foreign and Chinese group is significant. There are two main haplotypes of the MSTN intron 2 in the goat, which may represent two ancestral types, in support of the theory that domestic goats in the world mainly originated from two ancestors based on morphology, history, archaeology, and molecular markers. The sequence differences of the MSTN intron 2 among species are greater than those within species.     

Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data

Phylogenetic relationships among 76 species of Oleaceae, representing all 25 recognized genera of the family, were assessed by a cladistic analysis of DNA sequences from two noncoding chloroplast loci, the rps16 intron and the trnL-F region. Consensus trees from separate and combined analyses are congruent and agree well with nonmolecular data (chromosome numbers, fruit and wood anatomy, leaf glycosides, and iridoids). The two debated genera Dimetra and Nyctanthes, previously suggested to belong to Verbenaceae (sensu lato) or Nyctanthaceae, are shown to belong to Oleaceae, sister to the hitherto genus incertae sedis Myxopyrum. This clade is also supported by anatomical and chemical data. The subfamily Jasminoideae is paraphyletic, and a new classification is presented. The subfamily level is abandoned, and the former Jasminoideae is split into four tribes: Myxopyreae (Myxopyrum, Nyctanthes, and Dimetra), Fontanesieae (Fontanesia), Forsythieae (Abeliophyllum and Forsythia), and Jasmineae (Jasminum and Menodora). The tribe Oleeae (previous subfamily Oleoideae) is clearly monophyletic, comprising the subtribes Ligustrinae (Syringa and Ligustrum), Schreberinae status novus (Schrebera and Comoranthus), Fraxininae status novus (Fraxinus), and Oleinae (12 drupaceous genera). An rps16 sequence obtained from Hesperelaea, known only from the type specimen collected in 1875, confirmed the placement of this extinct taxon in the subtribe Oleinae.     

Structural and distributional variation of mitochondrial rps2 genes in the tribe Triticeae (Poaceae)

The mitochondrial rps2 gene from barley, like that of rice, wheat, and maize, has an extended open reading frame (ORF) at the 3-region when compared to that from lower plants. However, the extended portions are variable among these cereals. Since barley and wheat belong to the same tribe (Triticeae), it would be interesting to know when and where the two types of rps2 were generated during evolution. To determine this, we utilized the mitochondrial (mt)DNA sequence to examine variations of the rps2 genes in the tribe Triticeae. By means of the variable 3-region, the distribution of barley (B)-type and wheat (W)-type rps2 sequences was studied in 19 genera of the tribe. The B-type sequence was identified in 10 of the 19 genera, whereas the W-type sequence was present in all 19 genera. Thus, ten of the examined genera have both types of rps2 sequences due to the presence of two copies of the gene. The W-type sequence was also present in the tribe Bromeae and the B-type sequence was also found in Aveneae and Poeae. Phylogenetic trees based on the B-type and W-type sequences were different from those based on other molecular data. This suggests that the mitochondrial genome in Triticeae has a unique evolutionary history.Electronic Supplementary Material Supplementary material is available for this article at     

Virus-induced gene silencing in Solanum species

Virus-induced gene silencing (VIGS) has been used routinely in Nicotiana benthamiana to assess functions of candidate genes and as a way to discover new genes required for diverse pathways, especially disease resistance signalling. VIGS has recently been shown to work in Arabidopsis thaliana and in tomato. Here, we report that VIGS using the tobacco rattle virus (TRV) viral vector can be used in several Solanum species, although the choice of vector and experimental conditions vary depending on the species under study. We have successfully silenced the phytoene desaturase (PDS) gene in the diploid wild species Solanum bulbocastanum and S. okadae, in the cultivated tetraploid S. tuberosum and in the distant hexaploid relative S. nigrum (commonly known as deadly nightshade). To test whether the system could be utilised as a rapid way to assess gene function of candidate resistance (R) genes in potato and its wild relatives, we silenced R1 and Rx in S. tuberosum and RB in S. bulbocastanum. Silencing of R1, Rx and RB successfully attenuated R-gene-mediated disease resistance and resulted in susceptible phenotypes in detached leaf assays. Thus, the VIGS system is an effective method of rapidly assessing gene function in potato.     

Polymorphism in the second intron of dopamine receptor D4 gene in humans and apes

The dopamine receptor D4 (DRD4) has received increasing research attention in behavioral science, psychiatry, and psychopharmacology. However, the number of available genetic markers for primates is still insufficient. We identified a novel variation/polymorphism in the second intron of DRD4 in humans based on the survey of 210 Japanese: a 6bp insertion (allele frequency: 0.002) and 8bp deletion (0.024); however, 94 Hungarian Caucasians were found to be monomorphic. Polymorphisms of the homologous region were also found in a survey of 93 specimens from four species of great apes and 51 specimens from seven species of gibbons. The polymorphisms consist of both single nucleotide substitutions and variations in the number of tandem duplications of short GC-rich sequences. Because of usefulness of primates in behavioral science, this polymorphism may be a useful marker for association studies with behavioral traits in both humans and apes.     

中国茄属一新归化种——羽裂叶龙葵

报道了中国茄科茄属的一新记录种——羽裂叶龙葵（Solanum triflorum Nutt.）。该种具有独特的匍匐习性,叶片通常为羽状深裂且稍肉质,花冠呈星芒状,花药细长,在花序轴的顶端通常具一枚叶状小苞片,与国内记载的茄属其他物种区别明显。该种为泛热带分布,原产于美洲,归化于欧洲、南非和澳大利亚,近年来在中国内蒙古自治区亦有归化。