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Introduction Wagholi, a historical village, that prospered in the Maratha period is situated 16 km east of Pune city. It is surrounded by a stone rampart with two entrances. The traces of which are still visible. This is the village of Pilajirao Jadhav, one of the eminent warriors who played an important role in the spread of the Maratha Empire. He constructed many buildings in and around this village. Since the beginning, Wagholi was facing severe scarcity of drinking water. Thus, Pilajirao Jadhav dug two large lakes in the village premises.1 Also, there is a beautiful barav (step-well) along with an inscription near the northern entrance. In the centre of the village, the remains of the palace are still visible. Besides, probably he built beautiful temples of Hanuman, Shiva and Ram apart from Wagheshwar in this village. Another striking feature of Wagholi is the very important and rare blue metallic stone (Cavansite) found in the quarries here. All over the world, this metal is found in large quantities only in Wagholi.2

Key message Lipoxygenases mediate important biological processes. Through comparative genomics, domain-scan analysis, sequence analysis, phylogenetic analysis, homology modelling and transcriptional analysis the lipoxygenase gene family of pepper (Capsicum annuum) has been identified. Abstract Lipoxygenases (LOXs) are non-heme, iron-containing dioxygenases playing a pivotal role in diverse biological processes in plants, including defence and development. Here, we exploited the recent sequencing of the pepper genome to investigate the LOX gene family in pepper. Two LOX classes are recognized, the 9- and 13-LOXs that oxygenate lipids at the 9th and 13th carbon atom, respectively. Using two main in-silico approaches, we identified a total of eight LOXs in pepper. Phylogenetic analysis classified four LOXs (CaLOX1, CaLOX3, CaLOX4 and CaLOX5) as 9-LOXs and four (CaLOX2, CaLOX6, CaLOX7 and CaLOX8) as 13-LOXs. Furthermore, sequence similarity/identity and subcellular localization analysis strengthen the classification predicted by phylogenetic analysis. Pivotal amino acids together with all domains and motifs are highly conserved in all pepper LOXs. Expression of 13-LOXs appeared to be more dynamic compared to 9-LOXs both in response to exogenous JA application and to thrips feeding. Bioinformatic and expression analyses predict the putative functions of two 13-LOXs, CaLOX6 and CaLOX7, in the biosynthesis of Green Leaf Volatiles, involved in indirect defence. The data are discussed in the context of LOX families in solanaceous plants and plants of other families. Electronic supplementary material The online version of this article (10.1007/s11103-018-0785-y) contains supplementary material, which is available to authorized users.

In nature, plants continuously face the attack from insect herbivores. To defend themselves, plants have evolved a plethora of direct and indirect defence mechanisms that are present either constitutively or induced upon insect herbivory. In response to insect herbivory, plants activate phytohormonal signal-transduction pathways, transcriptional responses and biological processes. These changes in transcriptional and biological processes level influence the plant’s phenotype and consequently plant ecology during the current season or over seasons. To gain more insight into the dynamics of plant phenotype, elucidating transcriptomic responses to insect herbivory is critical. Various studies have investigated whole-genome transcriptional responses of plants against different insect herbivores, but only few have reported on responses to cell-content feeding thrips. Thrips (Thysanoptera) are minute cell-content feeding insects and are serious pests on many commercial and ornamental plants. Thrips species such as western flower thrips (WFT) and onion thrips are among the most devastating pests on e.g. sweet pepper and white cabbage plants, respectively. Therefore, using a high-density time-series approach, the focus of this thesis was to investigate whole-genome transcriptional responses of sweet pepper and white cabbage plants upon WFT and onion thrips feeding, respectively, and the underlying genetic mechanisms. In addition, I focussed on one particular gene family, the lipoxygenases and a gene in this family that is involved in thrips-induced crop resistance. Chapter 2 was focused on the identification of the lipoxygenase gene family in pepper (Capsicum annuum). Lipoxygenases (LOXs) are non-heme, iron-containing dioxygenases involved in several developmental and defence-related plant processes, such as seed germination, fruit ripening, tuber development and JA-regulated plant defences. Through multiple in-silico analysis, a total of eight LOX genes were identified in pepper classifying four LOXs (CaLOX1, CaLOX3, CaLOX4 and CaLOX5) as 9-LOXs and four (CaLOX2, CaLOX6, CaLOX7 and CaLOX8) as 13-LOXs. Chapter 3 further narrowed down the LOX gene-family to one lipoxygenase (CaLOX2) gene through in-silico analysis and functionally characterized its involvement in jasmonate-dependent induced defence against WFT. Overall, this chapter shows involvement of CaLOX2 in JA-mediated plant resistance to thrips feeding. Chapter 4 elucidates the dynamics of transcriptional reprogramming of sweet pepper in response to WFT feeding. Approximately 8.6% (2060 up and 1002 downregulated) of the pepper genes were differentially expressed that categorized into 23 clusters (16 upregulated and 7 downregulated), each possessing a unique temporal expression pattern. Upregulated gene clusters were overrepresented with defence-related biological processes, whereas downregulated gene clusters were overrepresented with developmental processes. The transcription factor families ERF, MYB, NAC, bHLH and WRKY emerged as pivotal regulators in response to WFT feeding. The data show a chronological order in the activation of hormonal (JA, ET) and secondary metabolite (phenylpropanoids, flavonoids and terpenoids) pathways. Eventually, the comparative analysis of the WFT-induced transcriptional responses of Arabidopsis and sweet pepper plants to WFT feeding shows a conservation in the induction of the JA-pathway in both plants, whereas the majority of transcriptional responses are plant-specific. Chapter 5 focused on 1) elucidating whole-genome transcriptional reprogramming of white cabbage plants in response to onion thrips feeding and 2) comparative transcriptomics to disentangle similarities and differences in transcriptional responses between WFT-induced Arabidopsis and sweet pepper as well as onion-thrips-induced white cabbage. Approximately 9.7 % of the white cabbage genes showed differential expression with 48 (32 upregulated and 16 downregulated) gene clusters with upregulated clusters associated with defence and downregulated clusters with development-related biological processes. Phytohormone-related processes (JA, ET and SA) and secondary metabolite (phenylpropanoids, flavonoids, green-leaf volatiles and indolic glucosinolates) biosynthesis genes were induced, whereas aliphatic glucosinolate biosynthetic genes were suppressed. Comparative analysis of the transcriptional responses of Arabidopsis and sweet pepper to WFT and of white cabbage to onion thrips showed 1) conservation of the JA biosynthesis and signalling pathways, 2) conservation of involvement of TF families, such as MYB, bHLH and WRKY in regulating responses, 3) that the majority of the transcriptional responses to thrips are system-specific, 4) that genes involved in indole glucosinolate biosynthesis are upregulated, whereas genes involved in aliphatic glucosinolate biosynthesis are downregulated in both brassicaceous plants Arabidopsis and white cabbage and 5) that the white-cabbage transcriptomic response to onion thrips is relatively rapid and complex compared to the WFT-induced Arabidopsis and sweet pepper transcriptomic responses. The data presented in this thesis contributes to understand the intensity and complexity of dynamic plant transcriptional responses to thrips feeding, and this is discussed in Chapter 6.

Insect herbivory can seriously hinder plant performance and reduce crop yield. Thrips are minute cell‐content‐feeding insects that are important vectors of viral plant pathogens, and are serious crop pests. We investigated the role of a sweet pepper (Capsicum annuum) lipoxygenase gene, CaLOX2, in the defense of pepper plants against Western flower thrips (Frankliniella occidentalis). This was done through a combination of in‐silico, transcriptional, behavioral and chemical analyses. Our data show that CaLOX2 is involved in jasmonic acid (JA) biosynthesis and mediates plant resistance. Expression of the JA‐related marker genes, CaLOX2 and CaPIN II, was induced by thrips feeding. Silencing of CaLOX2 in pepper plants through virus‐induced gene silencing (VIGS) resulted in low levels of CaLOX2 transcripts, as well as significant reduction in the accumulation of JA, and its derivatives, upon thrips feeding compared to control plants. CaLOX2‐silenced pepper plants exhibited enhanced susceptibility to thrips. This indicates that CaLOX2 mediates JA‐dependent signaling, resulting in defense against thrips. Furthermore, exogenous application of JA to pepper plants increased plant resistance to thrips, constrained thrips population development and made plants less attractive to thrips. Thus, a multidisciplinary approach shows that an intact lipoxygenase pathway mediates various components of sweet pepper defense against F. occidentalis., Through a combination of in‐silico, transcriptional, behavioural and chemical analyses, here we demonstrate that the lipoxygenase gene, CaLOX2, mediates jasmonate‐dependent induced defence of sweet pepper plants against Western flower thrips.

Made available in DSpace on 2018-11-26T16:04:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-04-01. Added 1 bitstream(s) on 2021-07-15T15:20:22Z : No. of bitstreams: 1 S2317-48892018000200177.pdf: 10956683 bytes, checksum: 288814a4f6468b50e5c268cb527734e2 (MD5) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The Parana Continental Flood Basalt (PCFB) province is one of the largest igneous provinces on Earth, but little is known about the architecture and geochemical characteristics of the lava flows. In this context, a set of borehole samples arranged in an NEE-SWW profile - more than 600 km long - located in the northern PCFB was used to define its chemostratigraphy. In this region, the outcrops are rare, and the volcanic piles are covered by hundreds of meters of sedimentary rocks from the Bauru Sub-Basin. This study aimed to explore the chemostratigraphic column from northern PCFB to improve the understanding of its internal architecture and to characterize the flood basalt sequences by using the petrography and elemental geochemistry of surface and borehole samples. The results showed the presence of the main four magma types, which were essentially distinguished by their P2O5, TiO2 and Sr concentrations, as well as Zr/Y ratios, with excellent chemostratigraphy relations. Univ Fed Sao Paulo, Inst Ciencias Ambientais, Dept Ciencias Ambientais, Sao Paulo, SP, Brazil Univ Fed Bahia, Dept Fis Terra & Meio Ambiente, Inst Fis, Salvador, BA, Brazil Univ Sao Paulo, Inst Astron Geofis & Ciencias Atmosfer, Sao Paulo, SP, Brazil Univ Estadual Paulista Julia Mesquita Filho, Inst Geociencias & Ciencias Exatas, Rio Claro, SP, Brazil Univ Sao Paulo, Inst Geociencias, Sao Paulo, SP, Brazil Univ Estadual Paulista Julia Mesquita Filho, Inst Geociencias & Ciencias Exatas, Rio Claro, SP, Brazil CNPq: 482911/2011-5 FAPESP: 2012/06082-6

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Conjugated linoleic acids (CLAs) have been found to have beneficial effects on human health when used as dietary supplements. However, their availability is limited because pure, chemistry-based production is expensive, and biology-based fermentation methods can only create small quantities. In an effort to enhance microbial production of CLAs, four genetically modified strains of the oleaginous yeast Yarrowia lipolytica were generated. These mutants presented various genetic modifications, including the elimination of beta-oxidation (pox1-6a dagger), the inability to store lipids as triglycerides (dga1a dagger dga2a dagger are1a dagger lro1a dagger), and the overexpression of the Y. lipolytica a dagger 12-desaturase gene (YlFAD2) under the control of the constitutive pTEF promoter. All strains received two copies of the pTEF-oPAI or pPOX-oPAI expression cassettes; PAI encodes linoleic acid isomerase in Propionibacterium acnes. The strains were cultured in neosynthesis or bioconversion medium in flasks or a bioreactor. The strain combining the three modifications mentioned above showed the best results: when it was grown in neosynthesis medium in a flask, CLAs represented 6.5% of total fatty acids and in bioconversion medium in a bioreactor, and CLA content reached 302 mg/L. In a previous study, a CLA degradation rate of 117 mg/L/h was observed in bioconversion medium. Here, by eliminating beta-oxidation, we achieved a much lower rate of 1.8 mg/L/h.

HSP47/SERPINH1 is key-regulator for collagen biosynthesis and its structural assembly. To date, there is no comprehensive study on the phylogenetic history of HSP47. Herein we illustrate the evolutionary history of HSP47/SERPINH1 along with sequence, structural and syntenic traits for HSP47/SERPINH1. We have identified ancestral HSP47/SERPINH1 locus in Japanese lamprey (Lethenteron japonicum). This gene remains on the same or similar locus for ~500 million years (MY), but chromosomal duplication was observed in ray-finned fishes, leading into three sets of three sets (I-III) of HSP47/SERPINH1. Two novel introns were inserted at the positions 36b and 102b in the first exon of only HSP47_1 gene from the selected ray-finned fishes. On the evolutionary time scale, the events of HSP47 duplications took placed between 416–360 MY ago (MYA) while intron insertion dates back to 231–190 MYA after early divergence of ray-finned fishes.

International audience; Having a glimpse of the relationships between the zinc and cadmium hyper accumulator Arabidopsis halleri and its rhizospheric bacteria may represent an interesting step towards the implementation of a rhizoremediation strategy based on this plant. Until now, these relationships remained unraveled. This work aimed to give some insights into the composition of the bacterial communities surrounding A. halleri when it grows on a soil harboring elevated amounts of zinc and cadmium, as well as into the influence that plant roots may exert on them. Industrial highly polluted soils containing different amounts of zinc and cadmium and surrounding A. halleri plants were sampled and their bacterial contents were harvested at various distances from A. halleri root system. Genetic diversity was assessed through DNA extraction, PCR amplification, 16S rDNA libraries construction, RFLP analysis and partial sequencing. Nine mini-libraries of hundred clones each were established and analyzed. Up to 481 independent clones were sequenced and identified at genus level. Twelve genera among 48 were found particularly well represented in the different sub-fractions analyzed. At class level, ten different classes were identified. Alpha-proteobacteria, Gamma-proteobacteria, Flavobacteria and Sphingobacteria were the main contributors to flora diversity. In the less polluted soil, roots proximity seems to affect negatively Alpha-proteobacteria and Flavobacteria and positively Gamma-proteobacteria. A rhizospheric selection limited to some specific genera was also observed when pollution raised.