Polyploidy

The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.

The first microsatellite primers were developed for Solanum centrale, a native Australian species used in the bush foods industry. Existing markers developed for other Solanum species were also amplified. Using an enrichment cloning protocol, seven novel markers were developed, and 48 existing markers from other Solanum species were tested, resulting in the characterization of a set of six highly polymorphic co-dominant loci for use in S. centrale. Microsatellite screening revealed polyploidy. Among the six highly polymorphic loci, allelic diversity ranged from 7 to 14. These markers will be useful for investigating genetic diversity and as a simple way of estimating ploidy of wild populations.

The gluten proteins from wheat, barley and rye are responsible both for celiac disease (CD) and for non-celiac gluten sensitivity, two pathologies affecting up to 6-8% of the human population worldwide. The wheat α-gliadin proteins contain three major CD immunogenic peptides: the p31-43, which induces the innate immune response; the 33-mer, formed by six overlapping copies of three highly stimulatory epitopes; and an additional DQ2.5-glia-α3 epitope which partially overlaps with the 33-mer. NGS and Sanger sequencing of α-gliadin genes from diploid and polyploid wheat provided six types of α-gliadins (named 1 to 6) with strong differences in their frequencies in diploid and polyploid wheat, and in the presence and abundance of these CD immunogenic peptides. Immunogenic variants of the p31-43 peptide were found in most of the α-gliadins. Variants of the DQ2.5-glia-α3 epitope were associated with specific types of α-gliadins. Remarkably, only Type 1 α-gliadins contained 33-mer epitopes...

Yeasts of the Saccharomyces sensu stricto species complex are able to convert sugar into ethanol and CO2 via fermentation. They have been used for thousands years by mankind for fermenting food and beverages. In the Neolithic times, fermentations were probably initiated by naturally occurring yeasts, and it is unknown when humans started to consciously add selected yeast to make beer,

Preferential chromosome association at metaphase I has been analyzed and compared in autotetraploid cells obtained by colchicine treatment of hybrid diploid rye plants with different degrees of chromosomal divergence between homologs. The tendency to identical over homologous, but not identical, pairing preferences detected when homologous partners are contributed by less related parental lines indicates that chromosome differentiation may play an important role on preferential pairing behavior of polyploids. However, associations between more similar (identical) partners are not always favored, thus suggesting that additional factors must be considered. Other hypotheses for explaining pairing preferences in competitive situations are discussed. No clear relationship has been found between multivalent frequencies at metaphase I and chromosome differentiation between homologs or preferential pairing behavior. Therefore evolutionary divergences among related genomes should be carefull...

Bukan abstrak, ini bagian dari BAB 1

Tumbuhan paku merupakan tumbuhan yang sangat mudah dijumpai disekitar kita. Sifatnya yang kosmopolit membuat tumbuhan ini dapat dijumpai diberbagai daerah meliputi ketinggian rendah (0-500 mdpl), ketinggian sedang (500-1000 mdpl), hingga tinggi ( > 1000 mdpl). Pteridophyta atau lazim juga disebut tumbuhan paku merupakan divisi tumbuhan yang memiliki kormus. Karena memiliki pembuluh (kormus) maka disebut pula cormophyta. Menurut Loveless (1989), tumbuhan paku tersebar diseluruh dunia, tetapi paling banyak tumbuh di daerah tropik yang lembab. Kurang lebih sebanyak 10000 jenis yang hidup diseluruh dunia. Pteridophyta dibagi menjadi menjadi beberapa kelas, psilopsida, lycopsida, sphenopsida, pteropsida (Moertolo, 2004).
Daerah penyebaran tumbuhan paku dipengaruhi oleh faktor lingkungan termasuk ketinggian tempat. Dalam usaha untuk membandingkan tingkat ploidi dan kaitannya dengan ketinggian, maka harus ditentukan spesies tumbuhan paku yang sering dijumpai didaerah tinggi, sedang, dan rendah. Kelompok Pteropsida  yang sering dijumpai adalah Pteris vittata, Pteris biaurita, dan Pteris ensiformis, jenis ini banyak tumbuh baik di pegunungan maupun di dataran rendah. Faktor lingkungan utama yang berpengaruh adalah suhu dan kelembapan, yang mempengaruhi tumbuhan paku pada perkembangan siklus hidup sejak germinasi spora sampai maturasi sporofit (Masahiro dan Iwatsuki,  dalam Setyawati, 2000).
Sering ditemukan adanya peristiwa poliploidi secara alami pada tumbuhan tingkat tinggi. Menurut Rodriguez (dalam Khotimah, 2002) poliploidi merupakan fenomena dimana individu memiliki lebih dari 2 genom. Peristiwa poliploidi merupakan akibat dari berbagai proses baik meiotik maupun somatik. Hal senada juga dinyatakan oleh Stace (Zubaidah, dalam Khotimah, 2002). Berdasarkan kajian literatur yang kami dapat, tumbuhan paku merupakan tumbuhan yang juga mengalami poliploidi secara alami di alam.
Kami menentukan suatu kota dimana ketinggiannya mencakup ketinggian 0 - > 1500 mdpl. Salah satu kota yang memenuhi kriteria tersebut adalah kota lumajang. Ketinggian daerah Lumajang sangat bervariasi, mulai dari 0-3676 mdpl. Jenis tanah di Lumajang, berdasarkan Peta Tanah Tinjau yang dikeluarkan Lembaga Penelitian Bogor 1966, terdiri dari alivial, regosol, andosol, mediteran, dan latosol. Secara umum keadaan pengairan di kota Lumajang cukup baik mengingat keadaan topografi yang bervariasi mulai datar sampai curam, hal tersebut menguntungkan dalam segi pengelolaan air (Anonim a, 2011).
Iklim dan curah hujan di Lumajang didasarkan sistem Schmidt dan Ferguson dimana terdapat 3 macam iklim, tipe iklim kering, agak basah, dan basah (Anonim a, 2011).
Berdasarkan paparan diatas kami melaksanakan penelitian dengan judul “Pengaruh Jenis Pteris dan Ketinggian Tempat terhadap Tingkat Ploidi Tumbuhan Paku di Daerah Lumajang”.

Polyploidy, which arises through complex genetic and ecological processes, is an important mode of plant speciation. This review provides an overview of recent advances in understanding why plant polyploid species are so ubiquitous and diverse. We consider how the modern framework for understanding genetic mechanisms of speciation could be used to study allopolyploid speciation that occurs through hybrid genome doubling, that is, whole genome doubling of interspecific F1 hybrids by the union of male and female unreduced gametes. We outline genetic and ecological mechanisms that may have positive or negative impacts on the process of allopolyploid speciation through hybrid genome doubling. We also discuss the current status of studies on the underlying genetic mechanisms focusing on the wheat (Triticum and Aegilops) hybrid-specific reproductive phenomena that are well known but deserve renewed attention from an evolutionary viewpoint.

Cyprininae is the largest subfamily (>1300 species) of the family Cyprinidae and contains more polyploid species (􏰀400) than any other group of fishes. We examined the phylogenetic relationships of the Cyprininae based on extensive taxon, geographical, and genomic sampling of the taxa, using both mitochondrial and nuclear genes to address the phylogenetic challenges posed by polyploidy. Four datasets were analyzed in this study: two mitochondrial gene datasets (465 and 791 taxa, 5604 bp), a mitogenome dataset (85 taxa, 14,771 bp), and a cloned nuclear RAG1 dataset (97 taxa, 1497 bp). Based on resulting trees, the subfamily Cyprininae was subdivided into 11 tribes: Probarbini (new; Probarbus + Catlocarpio), Labeonini Bleeker, 1859 (Labeo & allies), Torini Karaman, 1971 (Tor, Labeobarbus & allies), Smiliogastrini Bleeker, 1863 (Puntius, Enteromius & allies), Poropuntiini (Poropuntius & allies), Cyprinini Rafinesque, 1815 (Cyprinus & allies), Acrossocheilini (new; Acrossocheilus & allies), Spinibarbini (new; Spinibarbus), Schizothoracini McClelland, 1842 (Schizothorax & allies), Schizopygopsini Mirza, 1991 (Schizopygopsis & allies), and Barbini Bleeker, 1859 (Barbus & allies). Phylogenetic relationships within each tribe were dis- cussed. Two or three distinct RAG1 lineages were identified for each of the following tribes Torini, Cyprinini, Spinibarbini, and Barbini, indicating their hybrid origin. The hexaploid African Labeobarbus & allies and Western Asian Capoeta are likely derived from two independent hybridization events between their respective maternal tetraploid ancestors and Cyprinion.

We look at the utility of flow cytometry in large- and small-scale population surveys of amphibians, work done to that point, and the implications for conservation projects ranging from the discovery of cryptic species to hybrid zones and toxicological impacts.

A 24-month-old female with severe physical and mental retardation is described. Peripheral lymphocytes demonstrated tetraploid/diploid mosaicism. That this does not represent an artifact in vitro was supported by the finding of buccal mucosal cells with two Barr bodies and tetraploid/diploid mosaicism in fibroblasts and bone marrow cells.

Using data gathered over a 4-year period from a large population of the A. laterale-jeffersonianum complex from Haliburton, Ontario, I examined four areas of reproductive ecology that may contribute to ecological partitioning: (1) fluctuating sex, hybrid, and ploidy ratios; (2) differential migratory response by triploid and tetraploid genomotypes; (3) ontogenetic differences among triploid and tetraploid genomotypes; and (4) genotypic differences within unisexual genomotypes. For each case I was able to reject a null hypothesis ascribing ecological equivalency to those biotypes involved. The most germane ecological differences among unisexuals were imbedded in the broad syndrome of delays in larval development, metamorphosis, and sexual maturity displayed by tetraploids. These findings parallel those reported in a large body of literature generated from laboratory studies of polyploid salamanders. Using these corresponding data, I conducted a broad review of potential developmental, physiological, and biotypic causes and consequences of the observed delays. The results indicated that several effects of polyploidy and hybridity directly influence community ecology and contribute to stable coexistence of bisexuals and unisexuals. Based on these findings, a strategic model summarizing interaction in these communities was constructed, from which testable hypotheses may be derived for future research. The findings of this study confirmed the ontological status of the biotypic distinctions (genomotype versus genotype) advanced here.

As a field naturalist, my doctoral research in plant ecology has focused on the biodiversity of open Mediterranean environments, conducted in parallel with a professional activity in a design office. This knowledge of botany, extended to the entire western Mediterranean, has subsequently allowed me to write chapters of books (monographs, identification keys, synonymic indexes, catalogs) on the flora of France and North Africa, then of the Middle East.
In collaboration with various European teams and Maghreb researchers, I started work on new lines of research (integrative systematics, biogeography and phylogeny). I diversified biological models (molluscs) and assimilated new methods (biochemistry, molecular genetics). Various endemic species have served as integrative models that we are studying at all levels, from in situ inventory and conservation, to the phylogenetic and paleo-ecological origins of endemism, works done in the context of several Ph.D. I participated and/or co-directed.
Within the research unit AMAP, I collaborated with Tela Botanica on the Pl@ntNet project (https://plantnet.org/) which continues through the Floris'Tic project (http://floristic.org/), with activities dedicated to the flora of North Africa and the Middle East. I refocused my research on descriptive botany and biodiversity cataloguing, through collaborative networking and the use of computerised information storage and taxonomic identification tools on the Mediterranean flora. I now focus on describing the unknown biodiversity in the Mediterranean hotspot, combining classical (morphological) and modern (molecular) approaches.
My research project is to continue the momentum that I initiated over the last dozen years. This project deals with biogeography, taxonomy and conservation in the service of knowledge, protection and promotion of biodiversity in the Mediterranean, particularly in the countries of the southern and eastern shores. It aims in the medium and long term to participate in the filling of the taxonomic deficit in areas of biodiversity hotspots but coldspots of knowledge, such as the Maghreb and the Mediterranean Middle East. The objective is the reappropriation, by the Maghrebian and Middle Eastern scientific corps, of a long and rich history of the biodiversity knowledge, partially interrupted for half a century, and whose historical collections of Montpellier (MPU), Paris (P), Geneva (G) or Barcelona (B) herbaria are its precious memory. The project draws its regional coherence through a natural biogeographic convergence and integrates all the disciplines from the biodiversity inventory to the decision support tools.
The project is structured around three objectives: 1) Improvement and capitalization of fundamental knowledge on Mediterranean botany in the Maghreb and the Middle East; 2) Training and assistance, in southern countries, of field teams, mixing professionals and amateurs; 3) Production of practical identification tools, classical or modern, adapted to the needs of botanists and ecologists.

The crop species within the genus Brassica have highly replicated genomes. Three base 'diploid' species, Brassica oleracea , B. nigra and B. rapa , are likely ancient polyploids, and three derived allopolyploid species, B. carinata , B. juncea and B. napus , are created from the interspecific hybridization of these base genomes. The base Brassica genome is thought to have hexaploid ancestry, and both recent and ancient polyploidization events have been proposed to generate a large number of genome rearrangements and novel genetic variation for important traits. Here, we revisit and refine these hypotheses. We have examined the B. oleracea linkage map using the Arabidopsis thaliana genome sequence as a template and suggest that there is strong evidence for genome replication and rearrangement within the base Brassicas, but less evidence for genome triplication. We show that novel phenotypic variation within the base Brassicas can be achieved by replication of a single gene, BrFLC , that acts additively to influence flowering time. Within the derived allopolyploids, intergenomic heterozygosity is associated with higher seed yields. Some studies have reported that de novo genomic variation occurs within derived polyploid genomes, whereas other studies have not detected these changes. We discuss reasons for these different findings. Large trans-locations and tetrasomic inheritance can explain some but not all genomic changes within the polyploids. Transpositions and other small-scale sequence changes probably also have contributed to genomic novelty. Our results have shown that the Brassica genomes are remarkably plastic, and that polyploidy generates novel genetic variation through gene duplication, intergenomic heterozygosity and perhaps epigenetic change.

Polyploid genomes evolve and follow a series of dynamic transfigurations along with adaptation and speciation. The initial formation of a new polyploid individual within a diploid population usually involves a triploid bridge, a two-step mechanism of cell fusions between ubiquitous (reduced) and rare (unreduced) gametes. The primary fusion event creates an intermediate triploid individual with unbalanced genome sets, a situation of genomic-shock characterized by gene expression dysregulation, high dosage sensitivity, disturbed cell divisions, and physiological and reproductive attributes drastically altered. This near-sterile neotriploid must produce (even) eupolyploids through secondary fusion events to restore genome steadiness, meiotic balance, and fertility required for the demographic establishment of a nascent lineage. Natural conditions locate several difficulties to polyploid establishment, including the production of highly unbalanced and rarely unreduced (euploid) gametes, frequency-dependent disadvantages (minority cytotype exclusion), severe fitness loss, and ecological competition with diploid parents. Persistence and adaptation of neopolyploids depend upon genetic and phenotypic novelty coupled to joint selective forces that preserve shock-induced genomic changes (subgenome homeolog partitioning) and drive meiotic (reproductive) stabilization and ecological diversification. Thus, polyploid establishment through the triploid bridge is a feasible but not ubiquitous process that requires a number of low-probability events and singular circumstances. Yet, frequencies of polyploids suggest that polyploid establishment is a pervasive process. To explain this disparity, and supported in experimental evidence, I propose that situations like hybridization and ploidy-state transitions associated to genomic shock and substantial developmental alterations can transiently activate apomixis as a mechanism to halt genomic instability and cancel factors restraining neopolyploid's sexual fertility, particularly in triploids. Apomixis –as a temporal alternative to sex– skip meiosis and syngamy, and thus can freeze genomic attributes, avoid unbalanced chromosomal segregation and increase the formation of unreduced euploid gametes, elude frequency-dependent reproductive disadvantages by parthenogenetic development of the embryo and permissive development of endosperm during seed formation, and increase the effective population size of the neopolyploid lineage favoring the formation rate of eupolyploids compared to aneuploids. The subsequent action of genome resilience mechanisms that alleviate transcriptomic shock and selection upon gene interactions might restore a stable
meiosis and sexual fertility within few generations, as observed in synthetic polyploids. Alternatively, provided that resilience mechanisms fail, the neopolyploid might retain apomixis and hold genomically and transcriptionally altered states for many generations.

Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) analyses were used to evaluate genetic variability and relationships of Greek Aegilops species. Thirty-eight accessions of seven Greek Aegilops species [Ae. triuncialis (genome UC), Ae. neglecta (UM), Ae. biuncialis (UM), Ae. caudata (C), Ae. comosa (M), Ae. geniculata (MU) and Ae. umbellulata (U)] as well as Triticum accessions were studied. Nineteen RAPD and ten ISSR primers yielded 344 and 170 polymorphic bands, respectively, that were used for the construction of dendrograms. Regardless of the similarity coefficient and marker type used, UPGMA placed 38 Aegilops accessions into one branch while the other branch consisted of wheat species. Within the Aegilops cluster, subgroups were identified that included species that shared the same genome or belonged to the same botanical section. Within the Triticum cluster, two robust subgroups were formed, one including diploid wheat and another including polyploid wheat. In conclusion, results showed that there is genetic diversity in the Greek Aegilops species studied, and clustering based on genetic similarities was in agreement with botanical classifications.

•The micro-evolutionary mechanisms that drive large-scale radiations are not completely understood, partly because of a shortage of population-level studies aimed at identifying putative causes of rapid evolutionary change. The Dianthus broteri complex, representing the largest polyploid series known to date for any species in the genus (2×, 4×, 6× and 12× cytotypes), belongs to a lineage that was recently found to have diversified at unusually rapid rates.•We used a combination of genome sequencing (internal transcribed spacer (ITS), plus chloroplast DNA (cpDNA) regions trnH-psbA, psbA-trnK and trnK-matK) and amplified fragment length polymorphism (AFLP) fingerprinting in 25 populations to infer the evolutionary history of extant polyploid races.•The haplotype, ribotype and AFLP reconstructions showed a star-shaped arrangement suggesting a pattern of radiative evolution. The major, widespread haplotype occurred at all ploidy levels, whereas 20 minor haplotypes were restricted to single populations and cytotypes. In addition, AFLP analyses retrieved well-supported cytogeographic groups: six clades were clearly differentiated in terms of ploidy level and geography. Molecular data indicate that gene flow among different cytotypes is rare or nonexistent.•Our study supports a scenario of rapid diversification in carnations in which autopolyploidy and allopolyploidy, in interaction with geography and/or isolation, have played prominent roles.The micro-evolutionary mechanisms that drive large-scale radiations are not completely understood, partly because of a shortage of population-level studies aimed at identifying putative causes of rapid evolutionary change. The Dianthus broteri complex, representing the largest polyploid series known to date for any species in the genus (2×, 4×, 6× and 12× cytotypes), belongs to a lineage that was recently found to have diversified at unusually rapid rates.We used a combination of genome sequencing (internal transcribed spacer (ITS), plus chloroplast DNA (cpDNA) regions trnH-psbA, psbA-trnK and trnK-matK) and amplified fragment length polymorphism (AFLP) fingerprinting in 25 populations to infer the evolutionary history of extant polyploid races.The haplotype, ribotype and AFLP reconstructions showed a star-shaped arrangement suggesting a pattern of radiative evolution. The major, widespread haplotype occurred at all ploidy levels, whereas 20 minor haplotypes were restricted to single populations and cytotypes. In addition, AFLP analyses retrieved well-supported cytogeographic groups: six clades were clearly differentiated in terms of ploidy level and geography. Molecular data indicate that gene flow among different cytotypes is rare or nonexistent.Our study supports a scenario of rapid diversification in carnations in which autopolyploidy and allopolyploidy, in interaction with geography and/or isolation, have played prominent roles.