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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

Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.

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.

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.