Genetic diversity, population structure and conservation implication of the endemic Sumatran lowland dipterocarp tree species (Shorea javanica)

Genetic diversity and relationships of 40 accessions of Ipomoea, representing ten species of series Batatas, were examined using ISSR markers and restriction-site variation in four non-coding regions of chloroplast DNA. A total of 2071 ISSR fragments were generated with 15 primers in these accessions and, on average, 52 bands per accession were amplified. Most of the primers contained dinucleotide repeats. The ISSR fragments were highly polymorphic (62.2%) among the 40 accessions studied. Restriction analysis of chloroplast (cp) DNA revealed 47 informative restriction-site and length mutations. Phylogenetic analyses of ISSR and cpDNA datasets generally revealed similar relationships at the interspecific level, but the high polymorphism of ISSRs resulted in a better separation of intraspecific accessions. However, the combined ISSR and cpDNA dataset appeared to be appropriate in resolving both intra- and interspecific relationships. Of the species examined, I. trifida was found to be the most closely related to cultivated sweetpotato, the hexaploid I.batatas, while I. ramosissima and I. umbraticola were the most distantly related to I. batatas within the series. Ipomoea triloba, hitherto considered to be one of the ancestors of sweetpotato, was only distantly related to sweetpotato based on ISSR similarity index.

Alloplasmic lines combining alien nuclear and cytoplasmic genomes are convenient models for studying the mechanisms of nuclear-cytoplasmic compatibility/incompatibility. In the.present study, we have investigated the correlation between the characters and state of mitochondrial (mt) and chloroplast (cp) DNA regions in alloplasmic recombinant common wheat lines with barley cytoplasm characterized by partial or total fertility. Fertility restoration in the studied lines (Hordeum vulgare)-Triticum aestivum is determined by different ratios of the genetic material of common wheat variety Pyrotrix 28, which is a fertility restorer in the cytoplasm of barley, and varietySaratovskaya 29, which is a fixer of sterility. In partially fertile lines with nuclear genomes dominated by the genetic material of Saratovskaya 29, plant growth and development are suppressed. In these lines we have identified the barley homoplasmy of cpDNA regions infA and rpoB and the heteroplasmy of the 18S/5S mt repeat and the cpDNA ycf5 region. Nuclear-cytoplasmic compatibility in lines with reduced fertility (the genetic material of Pyrotrix 28 predominates in their nuclear genomes) is associated with restoration of normal plant growth and development and the changes in thestate of the studied cpDNA and mtDNA regions towards the wheat type. Thus, in fertile lines, the cpDNA regions (infA, rpoB) and the 18S/5S mt repeat were identified in the homoplasmic wheat state; though the cpDNAycf5 region was in the heteroplasmic state, it was dominated by the wheat type of the copies. The nuclearicytoplasmic compatibility is not broken as a result of introgression of the alien genetic material into the nuclear genome of one of the fertile lines; the plants of introgressive lines are fertile and normally developed, and the states of the cpDNA and mtDNA regions correspond to their states in fertile recombinant lines.

A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species Oryza sativa, Zea mays, Triticum aestivum and Arabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes in O. sativa, Z. mays, and T. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.

This research was undertaken with the aim to identify the robustness of available genetic markers (chloroplast DNA sequences and nuclear microsatellites) to differentiate G. parviflora subsp. parviflora (Gpp) from five closely related taxa within the Linearifolia Group of grevilleas; particularly G. humilis subsp. humilis (Ghh) in the Lake Macquarie area. One chloroplast region had a consistent character that separated the northern populations of Gpp (northern: Hunter area) from populations in the south of its range (southern: Cumberland Plains area) and all other taxa. This character was an 11 base pair sequence inversion. An assessment of over 50 microsatellite loci led to the identification of nine primer pairs that consistently amplified variable product in the target taxon. Genetic profiling using the microsatellites from a minimum of 10 individuals per taxon demonstrated a number of important issues: (1) some individuals amplify three alleles at one or more loci, suggesting possible aneuploidy or triploidy; (2) some individuals from the same population have identical, or near identical, genotypes which may be indicative of vegetative propagation; (3) genetic profiles among all samples were complex and the microsatellite loci provided moderate support for some of the taxa while other samples suggest a likely history of admixture, hybridisation, or the mis-identification of plant material. These possibilities need to be assessed along with morphological studies being undertaken by Mr Bob Makinson as a complementary component to this research. Particular consideration should be given to the southern populations of the focal taxon which, based on cpDNA and microsatellites, were genetically more similar to the geographically closer G. parviflora subsp. supplicans. Overall, the genetics tools (cpDNA and microsatellites) show great promise for delineating northern populations of G. parviflora subsp. parviflora and for deeper investigations into population genetic structure including the number of unique genotypes within and among populations, the physical spread of clonal genotypes within populations, the genetic differentiation and the genetic health (as assessed by heterozygosity and inbreeding) of populations of this threatened taxon.

Cyto-nuclear discordance in the genetic relationships among Tunisian fig cultivars ( Ficus carica L.): Evidence from non coding trnL– trnF and ITS regions of chloroplast and ribosomal DNAs

Malus hupehensis belongs to the Malus genus (Rosaceae) and is an indigenous wild crabapple of China. This species has received more and more attention, due to its important medicinal, and excellent ornamental and economical, values. In this study, the whole chloroplast (cp) genome of Malus hupehensis, using a Hiseq X Ten sequencing platform, is reported. The M. hupehensis cp genome is 160,065 bp in size, containing a large single copy region (LSC) of 88,166 bp and a small single copy region (SSC) of 19,193 bp, separated by a pair of inverted repeats (IRs) of 26,353 bp. It contains 112 genes, including 78 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). The overall nucleotide composition is 36.6% CG. A total of 96 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition, a total of 49 long repeats were identified, including 24 forward repeats, 21 palindromic repeats, and four reverse repeats. Comparisons of the IR boundaries of nine Malus complete chloroplast genomes presented slight variations at IR/SC boundaries regions. A phylogenetic analysis, based on 26 chloroplast genomes using the maximum likelihood (ML) method, indicates that M. hupehensis clustered closer ties with M. baccata, M. micromalus, and M. prunifolia than with M. tschonoskii. The availability of the complete chloroplast genome using genomics methods is reported here and provides reliable genetic information for future exploration on the taxonomy and phylogenetic evolution of the Malus and related species.

Efforts to obtain alternative and renewable energy continue to be carried out sustainably. Various natural materials continue to be studied for their feasibility in using alternative and renewable fuels. One of the natural materials that have the potential as a source of renewable energy is dammar resin (Shorea Javanica k. et v.). Therefore, it is necessary to analyze dammar resin's physical and chemical properties to determine its potential as an alternative fuel. This study evaluates dammar resin's physical and chemical properties as a renewable energy source. In this research, the physical and chemical properties of dammar resin were investigated related to its function as an alternative fuel compared to other alternative fuels. This study also aims to determine the advantages and disadvantages of dammar resin's physical and chemical properties as an alternative fuel. The American Society for Testing and Materials standard (ASTM), International Organization for Standardization (ISO), and the American Oil Chemists Society standard (AOCS) methods have been adopted to analyze the physical and chemical properties of dammar resins. This study's physical and chemical properties were cloud point, pour point, flash point, density, energy content, ash content, sulfur content, iodine value, saponification value, and cetane number. The result indicates that based on the physical and chemical property analysis, dammar resin has potency as a renewable energy source and can be developed as an alternative fuel. Dammar resin has a low flash point, sulfur content, and iodine value but a high saponification value and cetane number; these values have met European requirements. Moreover, the energy content of dammar resin is lower, and the ash content is higher than other biodiesel materials. However, dammar resin still requires advanced processes to be converted as alternative energy because it still has a high density, cloud, and pour point.

The states of 18S/5S mitochondrial (mt) repeat and some chloroplast (cp) DNA regions have been investigated in alloplasmic lines of common wheat carrying cytoplasm of the barley species Hordeum marinum subsp. gussoneanum Hudson and H. vulgare L. and in the progenies of the reciprocal hybrids between Triticum aestivum L. and Secale cereale L. The heteroplasmic state of the 18/5S mt repeat, which was a result of a biparental mtDNA transmission, has been observed in rye × wheat hybrids and in their progeny carrying rye cytoplasm. For the first time, the heteroplasmic state of cpDNA associated with the heteroplasmy of 18S/5S mt repeat has been detected in cereals with the use of alloplasmic wheat lines. The transition of mt- and cpDNA heteroplasmy and barley cpDNA homoplasmy to wheat homoplasmy is associated with complete restoration of fertility and elimination of the barley chromosome from the newly developing nuclear wheat genome of alloplasmic lines.

Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP), Chinese white pear (CWP), Chinese sand pear (CSP), and Ussurian pear (UP), but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR) markers and two non-coding chloroplast DNA (cpDNA) regions (trnL-trnF and accD-psaI). High levels of genetic diversity were detected for both nSSRs (HE = 0.744) and cpDNAs (Hd = 0.792). The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a) JPs; (b) cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c) cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be originated from the interspecific hybridization of wild Pyrus ussuriensis with cultivated Pyrus pyrifolia. The combination of uniparental DNA sequences and nuclear markers give us a better understanding of origins and genetic relationships for Asian pear groups and will be beneficial for the future improvement of Asian pear cultivars.

The complete chloroplast genome of Gentiana straminea (Gentianaceae), an endemic species to the Sino-Himalayan subregion

Shorea javanica (Dipterocarpaceae) is an economically important dammar-producing tree, endemic to the tropical lowland forests of Sumatra and Java, Indonesia. However, its total population size is limited and this species is endangered. Shorea selanica is one of the very limited numbers of species in genus Shorea (Dipterocarpaceae) that grows in Wallacean. This species can be found only in the central part of the Moluccas, eastern Indonesia. Six populations (77 individuals in total) were sampled for S. javanica while three populations (27 individuals in total) were sampled for S. selanica. To determine genetic variation and population structure, three non-coding chloroplast DNA regions of trnL-trnF, psbC-trnS, trnS-trnfM and two non-coding chloroplast DNA regions of trnT-trnL, trnL-trnF were sequenced from S. javanica and S. selanica, respectively. There was no variation in the chloroplast DNA regions from S. javanica, except for one unique indel polymorphism. Nucleotide diversity within S. selanica populations ranged from 0 (Seram) to 0.00044 (Buru), with a pooled value of 0.00041. S. javanica was determined as having no population structure while high levels of genetic differentiation was found among populations of S. selanica (F(ST) = 0.702). Different pattern of population structure among the two species in this study suggested the need for distinct management and conservation strategies for each species. For S. javanica, connectivity within and among populations, including augmentation of population size across the species range, should be promoted. For S. selanica, an in situ conservation plan that defines core areas completely free from perturbation within each population is necessary.

Young poplars of the Aigeiros-Tacamahca-complex in spontaneous rejuvenation in Germany that grew along shores, mainly in gravel mines, were sampled and cultivated ex situ. The leaf phenotype was assessed. The cpDNA marker locus trnDT was investigated which is suitable for the genetic assignment of the chloroplast DNA to a poplar species. The results of Heinze (1998), who investigated the locus trnDT in poplars, were chosen as a reference to account for potential methodological differences between the present fragment length analysis results and that obtained with classic gel electrophoresis. The assignment of each individual to a leaf phenotype category allowed a basic differentiation of P.-nigra– or P.-deltoides- like and other leaf shapes. At the cpDNA marker locus trnDT, fragment lengths referring to the two variants described by Heinze (1998) or referring to at least one more variant were found. The third genotype is of intermediate length between the two that were described by Heinze (1998) and, very likely, the related fragments (approx. 1,065 base pairs = bp long) are specific for balsam poplar species. Quantitatively, the P.-nigra-related genotype was the most important in the present collection. It is shown that phenotypically Aigeiros-like rejuvenation does predominantly, but not in all individuals, carried the related trnDT marker fragments specific for P. nigra. The seed cloud of theAigeiros-Tacamahaca-complex resulting in the present rejuvenation sample trees was predominantly based on diaspores of P. nigra or of intra-specifi Aigeiros-hybrids. However, the section Tacamahaca has contributed to the seed cloud. The results suggest that there must be significant gene flow from alien or hybrid poplars in Germany. Further genetic investigations with microsatellite markers are carried out in the present poplar collective for more detailed quantification of the taxonomic composition.

Population genetic study and barcoding in Iran saffron (Crocus sativus L.)

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.