Fixation of genetic variation and optimization of gene expression: The speed of evolution in isolated lizard populations undergoing Reverse Island Syndrome

The ecological theory of island biogeography suggests that mainland populations should be more genetically divergent from those on large and distant islands rather than from those on small and close islets. Some island populations do not evolve in a linear way, but the process of divergence occurs more rapidly because they undergo a series of phenotypic changes, jointly known as the Island Syndrome. A special case is Reversed Island Syndrome (RIS), in which populations show drastic phenotypic changes both in body shape, skin colouration, age of sexual maturity, aggressiveness, and food intake rates. The populations showing the RIS were observed on islets nearby mainland and recently raised, and for this they are useful models to study the occurrence of rapid evolutionary change. We investigated the timing and mode of evolution of lizard populations adapted through selection on small islets. For our analyses, we used an ad hoc model system of three populations: wild-type lizards from the mainland and insular lizards from a big island (Capri, Italy), both Podarcis siculus siculus not affected by the syndrome, and a lizard population from islet (Scopolo) undergoing the RIS (called P. s. coerulea because of their melanism). The split time of the big (Capri) and small (Scopolo) islands was determined using geological events, like sea-level rises. To infer molecular evolution, we compared five complete mitochondrial genomes for each population to reconstruct the phylogeography and estimate the divergence time between island and mainland lizards. We found a lower mitochondrial mutation rate in Scopolo lizards despite the phenotypic changes achieved in approximately 8,000 years. Furthermore, transcriptome analyses showed significant differential gene expression between islet and mainland lizard populations, suggesting the key role of plasticity in these unpredictable environments

Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora

Background Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. Results All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05–2.6] Myr) or assuming rate homogeneity (0.4 [0.14–0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. Conclusions Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms.info:eu-repo/semantics/publishedVersio

Identification and characterization of novel genes contributing to wheat grain yield

Grain yield is one of the most important aspects of wheat breeding. Being a polygenic trait, wheat grain yield is regulated by multiple genes and influenced by environmental factors. It is a complex trait which is linked to several traits such as seed number, thousand kernels’ weight etc. The interaction of these yield components with environmental stimulus are poorly understood. In the current study, to improve our understanding, phenotypic plasticity of contributing traits to the grain yield was explored. The phenotypic plasticity is the variations in the expressed phenotype by an individual genotype under environmental influences. The experiment consisted of 225 Westonia-Kauz double haploid (DH) lines and evaluated in five environmental conditions. The result demonstrated that, across the DH lines, the spikelets/spike was the most plastic trait. The least plastic character was the grain protein content. Yield plasticity was found higher at favourable conditions. An increase in yield plasticity by 0.1 units was associated with an increase in maximum yield by 4.45 kg ha−1 (p≤0.001). The generated knowledge regarding trait plasticity will be useful in dissecting the genetics for yield improvement particularly at the situation of rapid climate change. Identifying quantitative trait loci (QTL) and incorporating them in the breeding program has been a widely used approach for genetic improvement of yield and its components. QTL mapping suggests a considerable size of chromosomal location harbouring genes contributing to the trait which also contains many non-target genes. Thus, a more precise identification of contributing gene would be much helpful for an efficient breeding approach. However, functional confirmation of each individual gene of a QTL region is quite laborious and expensive work. In-silico approach provides the opportunity to reduce the down-stream workload by reducing the number of candidate genes in a systematic approach. Apart from the trait plasticity research, the current study also used a pipeline combining bioinformatics and laboratory approaches to identify the contributing genes of a grain yield QTL from a double haploid (DH) population of Westonia × Kauz. Assembling the QTL region on the International Wheat Genome Sequence Consortium (IWGSC) whole-genome sequence using the flanking 90K SNP markers identified the genomic region of 20 Mbp. Gene annotation revealed 16 high confidence genes and 41 low confidence genes in that genomic region. Further functional gene annotation, ontology investigation, pathway exploration, and gene network study using publicly available expressional data enabled short-listing of four genes for down-stream functional confirmation. Complete sequencing of those four genes demonstrated that only two genes namely ferredoxin-like protein and tetratricopetide-repeat (TPR) protein gene are polymorphic between the parental cultivars. Two single nucleotide polymorphism (SNP) variations were observed in the exon for both genes, and one SNP resulted in changes in amino acid sequence. The qPCR-based gene expression showed that both genes were highly expressed in the high-yielding double haploid lines. In contrast, gene expression was significantly lower in low-yielding lines. Results indicate that these two genes are potentially the underlying genes for the grain yield QTL. To investigate the association of the selected genes with grain yield and yield components at a wider level, further genetic and phenotyping experiments were conducted on a set of 143 historical wheat cultivars of Australia. For both genes, the identified alleles in the parental cultivars have been named as Westonia and Kauz allele. Characterising the allelic composition of the genes demonstrated that, for ferredoxin gene, 34.9% cultivars possessed Westonia allele and 16.9% cultivars possessed Kauz allele. In case of TPR gene, 20.9% cultivars possessed Westonia allele and 23.8% cultivars possessed Kauz allele. For both genes, cultivars having Westonia allele showed significantly higher seed width, thousand kernels’ weight and grain yield at different environmental conditions which clearly indicated that these genes are playing important roles in determining grain yield. For further level of functional confirmation, CRISPR-Cas9 based genome editing experiment was carried out on the TPR gene in Arabidopsis using orthologous gene. Agrobacterium mediated floral dip transformation was performed using immature inflorescence containing Cas9 gene. Knock-out mutants were selected by sequencing the target gene. Phenotypic data were collected from T2 generation on leaf length, stem length, number of branches on the main stem, days to flowering, days to maturity, pods/plant, and pod length. A significant reduction was observed in pods/plant, leaf length, and days to flowering and maturity. Gene expression analyses was performed on the selected genes responsible for increased seed size, seed number, and vegetative growth, in transgenic lines of Arabidopsis. Significant reduction in gene expression was observed for ARGOS, GRF1 and GW2 genes suggesting the role of TPR gene in downregulating essential growth regulator genes and its involvement in grain yield indirectly. Overall, this study demonstrated successful use of multiple research approaches in identification of a novel candidate genes of a yield related QTL. This approach can be utilised in exploring the candidate genes of other QTLs. The identified novel genes demonstrated the potential of improving the wheat grain yield which might be included in the breeding program for further yield improvement

Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica)

Acknowledgements This study was funded by a BBSRC studentship (MA Wenzel) and NERC grants NE/H00775X/1 and NE/D000602/1 (SB Piertney). The authors are grateful to Mario Röder and Keliya Bai for fieldwork assistance; Alex Douglas for statistical advice; Tyler Stevenson, Heather Ritchie and three anonymous reviewers for helpful comments on manuscript drafts; and all estate owners, factors and keepers for access to field sites, most particularly MJ Taylor and Mike Nisbet (Airlie), Neil Brown (Allargue), RR Gledson and David Scrimgeour (Delnadamph), Andrew Salvesen and John Hay (Dinnet), Stuart Young and Derek Calder (Edinglassie), Kirsty Donald and David Busfield (Glen Dye), Neil Hogbin and Ab Taylor (Glen Muick), Alistair Mitchell (Glenlivet), Simon Blackett, Jim Davidson and Liam Donald (Invercauld) Richard Cooke and Fred Taylor (Invermark), Shaila Rao and Christopher Murphy (Mar Lodge), and Ralph Peters and Philip Astor (Tillypronie).Peer reviewedPublisher PD

Functional and Molecular Diversity of the Diatom Family Leptocylindraceae

The focus of this PhD project is the functional and molecular diversity of Leptocylindraceae diatom species, the study of which can lead to a better understanding of long standing questions regarding the ecology and evolution of phytoplankton. A wide range of tools, spanning from microscopical observations and physiological measurements to molecular techniques and high throughput sequencing, is utilized during this attempt. The genus Leptocylindrus has been chosen as the main target species due its worldwide and at the same time local importance in the Gulf of Naples and also because of the already extended study of the species in Stazione Zoologica Anton Dohrn (SZN) towards the direction mentioned above. Leptocylindraceae are centric diatoms that occupy a basal position in the diatom phylogeny and are abundant in marine plankton worldwide. In the Gulf of Naples (GoN), five out of the six species are found; L. minimus is known to be absent from the Mediterranean environment. The family shows a morphological conservation but the seasonal patterns between the species differ considerably. Indeed, physiological experiments of two Leptocylindrus species that show contrasting seasonality confirmed their opposed preferences regarding temperature as well as a high intraspecific phenological variability. In addition, the analysis of transcriptomes acquired for the three temperatures of one of them (L. aporus) indicated the possibly important role of transposable elements in response to stress and diatom adaptation. Furthermore, the transcriptomes of all Leptocylindrus species were explored in order to detect basic intra- and interspecific similarities and/or differences. HTS sequencing data from the MareChiara station in GoN and from the Tara expedition in the world’s seas were analyzed in order to assess the actual diversity of this important diatom family. A significant level of intraspecific variability was detected while the distribution of species and populations at spatial and temporal scale supported the functional differences among them that account for their distinct seasonality and their adaptation to different environmental conditions

A genomic view of food-related and probiotic Enterococcus strains

The study of enterococcal genomes has grown considerably in recent years. While special attentionis paid to comparative genomic analysis among clinical relevant isolates, in this study we performedan exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential tobe used as probiotics. Beyond common genetic features, we especially aimed to identify those thatare specific to enterococcal strains isolated from a certain food-related source as well as features presentin a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7different species, were examined and compared. Their phylogenetic relationship was reconstructedbased on orthologous proteins and whole genomes. Likewise, markers associated with a successfulcolonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clusteredregularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features.At the same time, a search for antibiotic resistance genes was carried out, since they are of bigconcern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteomeuniversally present among the genera and to determine that most of the accessory genes codefor hypothetical proteins, providing reasonable hints to support their functional characterization.Fil: Bonacina, Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Suárez, Nadia Elina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Hormigo, Daniel Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Fadda, Silvina G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Lechner, Marcus. University Marburg; AlemaniaFil: Saavedra, Maria Lucila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; Argentin

Alternative Splicing and Protein Structure Evolution

In den letzten Jahren gab es in verschiedensten Bereichen der Biologie einen dramatischen Anstieg verfügbarer, experimenteller Daten. Diese erlauben zum ersten Mal eine detailierte Analyse der Funktionsweisen von zellulären Komponenten wie Genen und Proteinen, die Analyse ihrer Verknüpfung in zellulären Netzwerken sowie der Geschichte ihrer Evolution. Insbesondere der Bioinformatik kommt hier eine wichtige Rolle in der Datenaufbereitung und ihrer biologischen Interpretation zu. In der vorliegenden Doktorarbeit werden zwei wichtige Bereiche der aktuellen bioinformatischen Forschung untersucht, nämlich die Analyse von Proteinstrukturevolution und Ähnlichkeiten zwischen Proteinstrukturen, sowie die Analyse von alternativem Splicing, einem integralen Prozess in eukaryotischen Zellen, der zur funktionellen Diversität beiträgt. Insbesondere führen wir mit dieser Arbeit die Idee einer kombinierten Analyse der beiden Mechanismen (Strukturevolution und Splicing) ein. Wir zeigen, dass sich durch eine kombinierte Betrachtung neue Einsichten gewinnen lassen, wie Strukturevolution und alternatives Splicing sowie eine Kopplung beider Mechanismen zu funktioneller und struktureller Komplexität in höheren Organismen beitragen. Die in der Arbeit vorgestellten Methoden, Hypothesen und Ergebnisse können dabei einen Beitrag zu unserem Verständnis der Funktionsweise von Strukturevolution und alternativem Splicing bei der Entstehung komplexer Organismen leisten wodurch beide, traditionell getrennte Bereiche der Bioinformatik in Zukunft voneinander profitieren können

Solution Structure and Phylogenetics of Prod1, a Member of the Three-Finger Protein Superfamily Implicated in Salamander Limb Regeneration

Prod1 is a cell-surface molecule of the three-finger protein (TFP) superfamily involved in the specification of newt limb PD identity. The TFP superfamily is a highly diverse group of metazoan proteins that includes snake venom toxins, mammalian transmembrane receptors and miscellaneous signaling molecules..The available data suggest that Prod1, and thereby its role in encoding PD identity, is restricted to salamanders. The lack of comparable limb-regenerative capability in other adult vertebrates could be correlated with the absence of the Prod1 gene