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Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

Dittami SM, Scornet D, Petit J-L, et al. Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biology. 2009;10(6):R66.Background: Brown algae (Phaeophyceae) are phylogenetically distant from red and green algae and an important component of the coastal ecosystem. They have developed unique mechanisms that allow them to inhabit the intertidal zone, an environment with high levels of abiotic stress. Ectocarpus siliculosus is being established as a genetic and genomic model for the brown algal lineage, but little is known about its response to abiotic stress. Results: Here we examine the transcriptomic changes that occur during the short term acclimation of E. siliculosus to three different abiotic stress conditions (hyposaline, hypersaline and oxidative stress). Our results show that almost 70% of the expressed genes are regulated in response to at least one of these stressors. Although there are several common elements with terrestrial plants, such as repression of growth-related genes, switching from primary production to protein and nutrient recycling processes, and induction of genes involved in vesicular trafficking, many of the stress-regulated genes are either not known to respond to stress in other organisms or are have been found exclusively in E. siliculosus. Conclusions: This first large-scale transcriptomic study of a brown alga demonstrates that, unlike terrestrial plants, E. siliculosus undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress. We identify several new genes and pathways with a putative function in the stress response and thus pave the way for more detailed investigations of the mechanisms underlying the stress tolerance of brown algae

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FIGURE 45 in Observations on the biology of Afrotropical Hesperiidae (Lepidoptera). Part 6. Hesperiinae incertae sedis: palm feeders

Author: Congdon Colin E.
Collins Steve C.
Cock Matthew J. W.
Publication venue
Publication date: 08/07/2014
Field of study

FIGURE 45. Pupae of Pteroteinon caenira, collected 17 Mar 1993 on ornamental palm (?Dypsis lutescens), Ibadan, Nigeria. 1, dorsal view; 25mm; 94/101B; 2, lateral view 25mm; 94/101B; 3, lateral view formed up dead female pupa (mark in space 1B is a pin hole; frontal projection broken off); 94/101B; 4, lateral view formed up dead male pupa (head is missing); 94/101D.Published as part of Cock, Matthew J. W., Congdon, Colin E. & Collins, Steve C., 2014, Observations on the biology of Afrotropical Hesperiidae (Lepidoptera). Part 6. Hesperiinae incertae sedis: palm feeders, pp. 1-61 in Zootaxa 3831 (1) on page 46, DOI: 10.11646/zootaxa.3831.1.1, http://zenodo.org/record/492082

ZENODO

Gamelia bennetti Cock and Rougerie 2021, sp. nov.

Author: Rougerie Rodolphe
Cock Matthew J. W.
Publication venue
Publication date: 15/03/2021
Field of study

Gamelia bennetti Cock and Rougerie sp. nov. urn:lsid:zoobank.org:act: B890CE4B-A62A-4730-8BEC-6A823791DA08 Barcode Index Number (BIN): BOLD:ADW6987; Figs. 1–3, 6. Type material. Holotype &male;: TRINIDAD: TRINIDAD, W.I., Brigand Hill lighthouse, at MV security lights by 22.00h, 17.i.2004, M.J.W. Cock [leg.]/ DNA sampleID MJWC-248, M.J.W. Cock 2018 / Holotype, Gamelia bennetti Cock & Rougerie (to be deposited in NHMUK, ex MJWC). Paratype, 13. TRINIDAD: TRINIDAD, W.I., Brigand Hill lighthouse, attracted to lights the previous night, 24.iii.2003, M.J.W. Cock [leg.]/ DNA sampleID MJWC-249, M.J.W. Cock 2018 / M.J.W. Cock genitalia 1015 / Paratype, Gamelia bennetti Cock & Rougerie. (to be deposited in NHMUK, ex MJWC). Both types will be deposited in NHMUK once it is open following the closure for the covid-19 pandemic. Diagnosis. There are several similar Gamelia species from the Amazon-Guiana-Venezuela area with which this species can be confused, including G. abas, G. rubriluna (Walker, 1862), G. lichyi Lemaire, 1973 and G. berliozi Lemaire, 1967. Given the variability noted between the holotype, paratype and female photo of G. bennetti sp. nov., it is not really possible to point to reliable diagnostic characters of wing markings. The male genitalia are very similar to species in the Gamelia abas group (Lemaire 2002), particularly G. rubriluna and G. lichyi, and to a lesser extent G. septentrionalis (Bouvier, 1936) and G. berliozi (Lemaire 2002, Brechlin & Meister 2012), so we consider G. bennetti sp. nov. to be an additional species of the Gamelia abas group. The genital structure (Fig. 3 A, D) is more elongate than that of G. rubriluna, but less so than in the other three species. The saccus (Fig. 3 D–F) is longer than that of G. rubriluna, but shorter than that of G. lichyi. The long slender lobes of the succus (‘lobes of the vinculum’ in Lemaire (2002)) curl back over the saccus before arching back to emerge under the uncus; it is difficult to compare this curvature with the other species of the group as Lemaire only provides ventral views, and images in Brechlin & Meister (2012) are from microscope slides, whereas lateral or partial lateral views (Fig. 3 F–I) are needed to observe this character. The saccus lobes of G. rubriluna and G. lichyi joined in their basal half (see figures in Lemaire (2002) and Brechlin & Meister (2012)), but are completely separate throughout in G. bennetti sp. nov. The aedeagus of G. bennetti sp. nov. has a ventral spike (Fig. 3 N) as do G. rubriluna and G. lichyi, but not G. septentrionalis and G. berliozi (Lemaire 2002). The aedeagus caecum in G. bennetti sp. nov. is a quadrate flange with the distal margin concave (Fig. 3 L–N), whereas this flange is basally rounded in G. lichyi, G. rubriluna and G. berliozi and the distal margin is concave in G. lichyi, but straight or rounded in G. rubriluna and G. berliozi (Lemaire 2002; Brechlin & Meister 2012). The sternite of abdominal segment 8 (A8) (Fig. 3 J) resembles that of G. rubriluna. The tergite of abdominal segment 7 (A7) (Fig. 3 K) resembles that of G. lichyi, and does not have the bottleneck shape of G. rubriluna. At this time, G. bennetti sp. nov. is the only species of the genus Gamelia known from Trinidad, and is only known from the eastern part of the island of Trinidad and perhaps eastern Tobago (see Distribution paragraph). Hence location will give a good pointer as to its identity, although there is no reason to think G. bennetti sp. nov. will not be found to occur more widely in Trinidad or on the mainland in north-eastern Venezuela and/or Guyana. It is therefore fortunate that both the male genitalia and the DNA barcodes can be reliably used to separate G. bennetti sp. nov. from other Gamelia species. Description. Male. Wingspan of 48–55 mm, and forewing length of 28–30 mm. Head. Dorsal and ventral colour match adjacent forewing ground colour (Fig. 1). Antennae brown (matching dorsal forewing ground colour of paratype), quadri-pectinate, dorsal rami reaching two-thirds the width of ventral rami (Fig. 1 D); just over onefifth of forewing length. Thorax. Dorsally matching forewing ground colour; ventrally reddish brown in holotype, orange-brown in paratype. Dorsal forewing dark blackish brown in holotype (Fig. 2 left) and live photograph (Fig. 6), or brown in paratype (Fig. 2 right), in all cases darker in basal third which is well covered with dense hair-like setae, especially towards dorsum. An irregular antemedian line and a small dark brown discal spot apparent in paratype, but not in dark brown holotype (although discal spot obvious on ventral forewing). A postmedian line runs from near tornus on anal margin to apex, although hardly visible towards apex; narrow and dark brown with a distal pale margin and then a very narrow dark brown border; much more obvious in brown paratype. Broad marginal band very slightly paler. Dorsal hindwing predominantly grey brown in holotype, but with yellow-brown tone in paratype. A curved, double, postmedian line of dark grey (holotype) or grey (paratype), running from anal margin before tornus to apex; inner line fairly even in width, but outer line broadens considerably in lower half of wing approaching anal margin. Distal to this double line, holotype is uniformly grey-brown, whereas paratype is yellow-grey-brown. Basal to double line, ground colour is paler, with anal area darker and overlaid with hair-like cells. Eyespot displaced inward from postdiscal lines; red with small white centre and broad black border; size variable (compare Figs. 2 and 6). Ventral forewing. Holotype dark grey-brown, suffused with russet in basal half, and paler towards anal margin. Antemedian line absent and postmedian line only visible as a slight shadow. Discal spot small, round, and black at the distal end of cell. Paratype similarly marked but ground colour yellow-brown. Ventral hindwing. Ground colour as ventral forewing; eyespot faintly visible through the wing. A straight postmedian line runs from two-thirds on anal margin to external margin just below apex, nearly touching eyespot edge. Abdomen. Dorsally, colour matches marginal band of dorsal hindwing; distally and dorso-laterally it matches basal ground colour of dorsal hindwing; ventrally reddish brown at base, fading to brown distally in holotype; orange-brown basally and yellow brown distally in paratype. Male terminalia (paratype; Fig. 3). Central part of posterior margin of A7 tergite flattened; constricted to each side of this before dilating (Fig. 3 K). A8 sternite smoothly bilobed on posterior margin (Fig. 3 J). Genitalia symmetrical, except as indicated for aedeagus; 3.2 mm from anterior margin of saccus to posterior margin of uncus. Uncus (Fig. 3 u) very short (0.35 mm), rounded posteriorly. A long (4.8 mm), thin, pointed process arising from the base of the saccus (Fig. 3 sp) curves anteriorly, then dorsally and finally posteriorly to finish projecting beyond uncus; processes from each side fused in the basal portion but separate for most of their length. Saccus (Fig. 3 s) projects posteriorly, but not anteriorly. Valva bilobed; lower lobe (Fig. 3 ll) elongate, arching dorsally; upper lobe (Fig. 3 ul) rounded and partly sclerotised (Fig. 3 upm) with a strong, curved, sclerotised projection (Fig. 3 ulp). Aedeagus 2.96 mm long; straight, pointed on dorsal distal margin; vesica simple; caecum of aedeagus a lateral flange each side of base, basal margin (Fig. 3 bm) straight, lateral margin dilating distally to a point and then concave on distal margin (Fig. 3 dm); right distal lateral corner with two small teeth (Fig. 3 cc) (Fig. 3 L–N). Provisional description of female. No female specimens were available to us. However, Fig. 4 (left) shows a dorsal view of a living specimen that was not collected, but that is assumed to be the female of G. bennetti sp. nov. as it differs from the male in similar ways to other species of the genus (Lemaire 2002), although it is not impossible that it represents a second otherwise unknown species from Trinidad. Dorsal head and thorax same colour as basal forewing. Dorsal forewing. Compared to holotype male, wing of female more falcate and paler. Antemedian line strongly marked with a pale inner border, most pronounced on costa. Postmedian line strongly marked, double, black and runs all the way to apex. Discal area pale pinkish brown; no discal spot, although there are 2–3 discal dots, and a diffuse pale patch on costa towards apex. Postmedian area grey brown, with distinct border on external margin, similar in colour to discal area. Dorsal hindwing. Similar to male holotype, but generally paler. Eye spot larger, and distally overlies innermost postmedian line; black border proportionally narrower, and white pupil has a black mark in it. Dorsal abdomen matches thorax at base, but remainder matches basal ground colour of dorsal hindwing. DNA barcodes. The barcodes of the two specimens are almost identical (p-distance of 0.16%); G. lichyi, from Venezuela, is the nearest neighbour to G. bennetti sp. nov., with a minimum p-distance of 3.37% (Fig. 5). Gamelia bennetti sp. nov. is segregated as BIN BOLD:ADW6987. Variability. Based on the limited observations from Trinidad (two specimens and two photographic records), the male seems to be rather variable with regard to the ground colour, or it occurs in two colour forms, the holotype (Fig. 2 left) being of a dark blackish brown form and the paratype (Fig. 2 right) a paler brown form. The dark blackish brown form is seen in the unvouchered images of living males (e.g. Fig. 6), and so the specimen of this form was chosen as the holotype. The image of putative females from Trinidad (e.g. Fig. 4 left) indicates a degree of sexual dimorphism in addition. More observations are needed to assess the variation in this species. Lemaire (2002) states that G. lichyi is more variable than G. rubriluna and notes that the lightest males have a bright yellow underside, so it seems likely that G. bennetti sp. nov. will prove to be continuously variable. An additional photograph of a female from Tobago was located (Davis 2014, Fig. 4 right). This individual is dark blackish brown, there is a single distinct discal spot, the inner margin of the post median line is pale, and there is a distinct pale subapical patch on the costa. This is likely to be G. bennetti sp. nov., suggesting that the female is also variable, but without a specimen from Tobago to examine, we do not make this assumption. Nevertheless, in almost all cases, the Lepidoptera of Tobago are a subset of the species found in Trinidad, and there are just a few examples of species found in Tobago but not yet in Trinidad, or where Trinidad and Tobago have different subspecies of the same species (Cock 2017a, 2017b). Distribution (Fig. 7). Trinidad and Tobago, Trinidad: W.I., Brigand Hill lighthouse (type series), Bush Bush, Cunaripa, Inniss Field, Rampanalgas (unvouchered photographic records as listed below). TRINIDAD: Bush Bush: &male; 18 October 2014 (K. Sookdeo photo) (Fig. 6), &male; 18 October 2014 (R. Rutherford photo) [iNaturalist observation 38318126] (these two observations are of the same individual); East of Cunaripa, Bedes Buxoo Trace, by night: &female; 30 May 2020 (R. Deo photo) [iNaturalist observation 48063102] (Fig. 4 left); Inniss Field, 10.17N 61.27W, by night: &female; 24 December 2020 (R. Deo photo) [iNaturalist observation 67114868] (not shown); NE of Rampanalgas on Toco Main Road, at light &male; 26 October 2019 (laurababoolal photo) [iNaturalist observation 34905707] (not shown). The single photographic record from Tobago (Davis 2014) probably represents this species, but this needs confirmation: TOBAGO: Near Speyside, + 11.301N, - 60.534W, at light: &female; 29 November 2014 (P. Davis photo) (Fig. 4 right). Etymology. This species is named with thanks and appreciation after Dr Fred D. Bennett (Frank 2019), who was director of the Commonwealth Institute of Biological Control (now integrated within CABI) in Trinidad, during the five years that the first author was based there. Fred’s support, encouragement and help with the study the insects of Trinidad has contributed to the first author’s subsequent four decades long interest in the Lepidoptera of Trinidad and Tobago. Remarks. This is a rarely seen species in Trinidad, with two collection records and three photographic records, all from the less collected eastern side of the island. The months of capture or observation are January, March, May, October (2) and December in Trinidad, i.e. in both the dry season (January to early May) and the wet season (mid-May to December, often with a short break mid-September to mid-October).Published as part of Cock, Matthew J. W. & Rougerie, Rodolphe, 2021, Gamelia bennetti sp. nov., a new Saturniidae species from Trinidad and Tobago (Lepidoptera: Bombycoidea), pp. 339-350 in Zootaxa 4942 (3) on pages 343-348, DOI: 10.11646/zootaxa.4942.3.2, <a href="http://zenodo.org/record/4604304">http://zenodo.org/record/4604304</a&gt

ZENODO

Analyse évolutive et fonctionnelle des gènes du cycle de vie des algues brunes

Author: Ratchinski Pélagie
Publication venue
Publication date: 16/12/2024
Field of study

Les Phaeophyceae (algues brunes) forment un clade d'organismes photosynthétiques eucaryotes multicellulaires, phylogénétiquement éloignés de la lignée verte. Le cycle de la plupart des espèces d'algues brunes alterne entre une phase sporophytique diploïde et une phase gamétophytique haploïde. Des études antérieures sur l'espèce modèle Ectocarpus ont identifié deux facteurs de transcription clés à homéodomaine TALE, OUROBOROS (ORO) et SAMSARA (SAM), qui contrôlent le programme de développement du sporophyte. Cette thèse fournit une analyse multi-échelle de la dynamique de l'expression des gènes au cours du cycle de vie des algues brunes, allant de la transcriptomique comparative sur diverses espèces à la caractérisation plus approfondie des premiers stades du développement du sporophyte. Tout d'abord, nous avons comparé les profils d'expression des gènes entre le sporophyte et le gamétophyte chez dix espèces d'algues brunes. Bien que la majorité des gènes soit exprimée par les deux générations dans chaque espèce, la proportion de gènes différentiellement exprimés entre les deux générations peut varier d'une espèce à l'autre. Nous avons été en mesure d'identifier des fonctions biaisées de manière conservée entre les différentes espèces étudiées, suggérant une identité transcriptionnelle partagée pour chaque génération. Nous avons ensuite analysé la dynamique de co-expression des gènes tout au long du cycle de vie chez l'espèce modèle Ectocarpus, en générant notamment un nouveau jeu de données capturant les premiers stades du développement du sporophyte. Cela nous a permis d'identifier des groupes de gènes co-exprimés impliqués dans des processus comme la transcription et la traduction, qui sont activés au début du programme du sporophyte. De plus, nous avons comparé la co-expression de groupes de gènes entre Ectocarpus et l'espèce plus distante Dictyota (divergence il y a environ 225 million d'années), ce qui nous a permis de montrer la conservation de co-expression de groupes de gènes entre ces deux espèces. Enfin, nous avons étudié les mécanismes moléculaires par lesquels ORO et SAM régulent l'expression des gènes. Une analyse in silico a suggéré des motifs de liaison potentiels d'ORO/SAM associés à des nucléosomes dont la position serait spatialement contrainte, mais la fixation in vivo d'ORO et/ou SAM à ces motifs reste à confirmer. Nous avons également caractérisé des mutants pour une protéine interagissant potentiellement avec ORO, BLZ1, et un troisième facteur à homéodomaine TALE, THD3, mais n'avons pas observé de phénotypes clairs liés au cycle de vie ou au développement. Dans l'ensemble, cette thèse fournit de nouvelles perspectives sur les fondements transcriptionnels de l'alternance du cycle de vie des algues brunes, des tendances évolutives générales aux événements de développement spécifiques contrôlés par des facteurs de régulation clés.Phaeophyceae (brown algae) are a clade of multicellular eukaryotic photosynthetic organisms phylogenetically distant from the well-studied green lineage. Most brown algal species alternate between a diploid sporophytic and a haploid gametophytic phase during their life cycle. Previous studies in the model species Ectocarpus have identified key TALE-homeodomain transcription factors, OUROBOROS (ORO) and SAMSARA (SAM), that control the sporophyte developmental program. This thesis provides a multi-scale analysis of gene expression dynamics during the brown algal life cycle, from comparative transcriptomics across diverse species to in-depth characterization of early sporophyte development. First, we compared gene expression patterns between the sporophyte and gametophyte generations in ten brown algal species. While there was a significant overlap in the genes expressed by both generations, the two generations exhibited distinct expression profiles and proportions of differentially expressed genes. Importantly, we were able to identify conserved generation-biased functions across species, suggesting a shared transcriptional identity for each generation independent of morphological differences. Building on this first study, we analysed gene co-expression dynamics throughout the life cycle in the model species Ectocarpus, including a new dataset capturing early stages of sporophyte development. This allowed us to identify key groups of co-expressed genes involved in processes such as transcription and translation that are activated at the onset of the sporophyte program. Furthermore, we performed a comparative co-expression analysis between Ectocarpus and the more distantly related species Dictyota (diverged ~225 million years ago), identifying conserved patterns of co-expressed gene modules across these two brown algal species. Finally, we investigated the molecular mechanisms by which ORO and SAM regulate gene expression. In silico analysis suggested putative ORO/SAM binding motifs associated with positioned nucleosomes, but the in vivo binding and functional impact of these motifs remains to be confirmed. We also used a mutant approach to characterize a potential ORO-interacting protein, BLZ1, and a third TALE-homeodomain factor, THD3, but found no clear life cycle or developmental phenotypes associated with these genes. Overall, this thesis provides novel insights into the transcriptional underpinnings of brown algal life cycle alternation, from broad evolutionary patterns to the specific developmental events controlled by key regulatory factors

Theses.fr

Predicting adherence to antiretroviral therapy and retention to HIV care : effects of baseline biopsychosocial status and neuropsychological functioning

Author: Mark Daniella
Publication venue
Publication date: 01/01/2011
Field of study

These drugs have demonstrated efficacy in improving immune function and reducing HIV-related morbidity and mortality, and while a cure is not available, patients on treatment may live longer, healthier lives. However, early optimism has been tempered by the growing recognition that meticulous adherence is a prerequisite for optimal clinical response and prevention of drug resistance

Cape Town University OpenUCT

Sex determination and differentiation in the brown alga Ectocarpus

Author: Luthringer Rémy
Publication venue
Publication date: 17/12/2014
Field of study

Le déterminisme génétique du sexe nécessite souvent l’évolution d’une région non-recombinante (NR) formant ainsi paire de chromosomes sexuels. Bien que la reproduction sexuée ait une origine commune à tous les eucaryotes, l’évolution des chromosomes sexuels s’est quant à elle effectuée de manière répétée et indépendante. Les chromosomes du sexe ont été particulièrement étudiés dans les systèmes diploïdes (chromosomes sexuels XY et ZW) des plantes et animaux. Le récent séquençage du génome d’Ectocarpus, modèle d’étude des algues brunes, donne non seulement une chance unique d’analyser les chromosomes sexuels dans un groupe phylogénétiquement distant des opisthocontes et de la lignée verte ; mais il donne aussi l’opportunité d’examiner un système haploïde de chromosomes sexuels (système UV). Chez Ectocarpus l’expression du sexe a lieu pendant la phase haploïde du cycle de vie, avec les chromosomes U et V, respectivement spécifiques aux femelles et aux mâles. L’analyse des chromosomes sexuels chez Ectocarpus a montré que la taille de la région NR est restée modeste pour un système vieux de plus de 70 millions d’années. Une analyse des dimorphismes sexuels a été effectuée ainsi que l’étude comparative des transcriptomes mâle et femelle d’Ectocarpus. Le développement parthénogénétique est, dans certaines populations d’Ectocarpus, un dimorphisme sexuel. Le lien génétique entre parthénogenèse et sexe a été analysé et suggère qu’un locus contrôlant la parthénogenèse est localisé au niveau de la partie recombinante du chromosome sexuel d’Ectocarpus. De plus, une analyse de fitness indique que le locus de la parthénogenèse est soumis à une sélection antagoniste entre les deux sexes.Genetic sex determination is usually controlled by sex chromosomes carrying a non-recombining sex-determining region (SDR). Despite the common origin of sex (meiosis) in Eukaryotes, the evolution of sex chromosomes has evolved repeatedly and independently. Our knowledge in sex chromosomes comes mainly from the analysis of diploid systems (XY and ZW sex chromosomes) in animals and land plants. However the recent genome sequencing of the brown alga Ectocarpus, not only opens up the possibility of studying sex chromosomes in a phylogenetic distant group but also of analysing a haploid sex chromosome system (UV sex chromosomes). Indeed in Ectocarpus sex is expressed during the haploid phase of the life cycle, where U and V sex chromosomes are restricted to female and male, respectively. The Ectocarpus sex chromosomes have some unusual evolutionary features such as the size of the non-recombining region, which is surprisingly small for a 70 million year old system. Also the evolutionary aspect of sexual dimorphism was studied by analyzing male and female transcriptomes and by identifying several subtle sexual dimorphic traits. Parthenogenetic capacity is a sexual dimorphic trait in some populations of Ectocarpus. The genetic link between parthenogenesis and sex was analysed and a locus that controls parthenogenetic was located to the Ectocarpus sex chromosome, in the recombining pseudoautosomal region. Fitness analysis strongly suggested that the parthenogenetic locus is a sexual antagonistic locu

Theses.fr

The brown alga model for functional and evolutionary analysis of sex determination

Author: Cormier Alexandre
Publication venue
Publication date: 16/11/2015
Field of study

Les mécanismes de détermination génétique du sexe, qui requièrent la présence de régions chromosomiques non recombinantes ou bien de chromosomes sexuels, ont émergé de manière indépendante et répétée au sein de plusieurs lignées d'eucaryotes. La plupart des connaissances acquises dans ce domaine portent sur un nombre limité de groupes d'eucaryotes. La disponibilité d'une espèce modèle pour le groupe des algues brunes, Ectocarpus siliculosus, dont le génome a été séquencé, permet de disposer des outils nécessaires pour étudier ces mécanismes au sein d'une lignée phylogénétiquement éloignée des modèles classiquement étudiés. L'un des premiers défis a été d'identifier les chromosomes sexuels dans le génome d'E. siliculosus et de réaliser l'analyse comparative de ces structures. Par la suite, l'analyse de l'expression des gènes entre individus mâles et femelles à différents stades du cycle de vie a permis d'identifier les gènes différentiellement exprimés, de caractériser leurs fonctions et d'analyser leur évolution moléculaire. Les nombreuses données générées afin de réaliser ces différentes analyses ont permis de proposer une nouvelle version de l'assemblage du génome et de l'annotation structurale et fonctionnelle de l'ensemble des gènes codants et non-codants d'E. siliculosus. Ces différents travaux ont permis d'apporter une importante contribution sur les connaissances dans le domaine de l'analyse fonctionnelle et évolutive du déterminisme sexuel chez les algues brunes ainsi qu'une importante actualisation des ressources génomiques du modèle Ectocarpus.Genetically determined sex determination mechanisms, which are controlled by non-recombinant chromosome regions or sex chromosomes, have emerged independently and repeatedly across several eukaryotic lineages. Most of the knowledge acquired in this area has been obtained for a limited number of eukaryotic groups. The availability of a model organism for the brown algae, Ectocarpus, whose genome has been sequenced, allows the development of tools to study these mechanisms in a lineage that is phylogenetically distant from classically studied models. One of the first challenges was to identify the sex chromosomes in Ectocarpus and to carry out a comparative analysis of these genomic structures. Analysis of gene expression in males and females at different stages of the life cycle then allowed the identification of differentially expressed genes. The functions and molecular evolution of these sex-biased genes was then studied. The large amount of data generated during the course of these analyses allowed the establishment of a new version of the genome assembly and refined structural and functional annotation of both coding and non-coding genes in Ectocarpus. This work helped made a significant contribution to knowledge in the field of functional and evolutionary analysis of sex determination in brown algae and a significantly updated the genomic resources available for the model organism Ectocarpus

Theses.fr

Genetic and epigenetic control of life cycle transitions in the brown alga Ectocarpus sp.

Author: Bourdareau Simon
Publication venue
Publication date: 27/03/2018
Field of study

L’algue brune Ectocarpus présente un cycle de vie haplo-diploïde avec l’alternance de deux générations multicellulaires : un gamétophyte haploïde et un sporophyte diploïde. Deux mutants présentent un changement homéotique entre les programmes de développement des générations sporophyte et gamétophyte. Les mutants réitèrent le programme de développement du gamétophyte à la place du sporophyte. Ces mutants, appelés ouroboros (oro) et samsara (sam), sont affectés dans deux gènes différents codant pour des facteurs de transcription à homéodomaine de classe TALE. Ma thèse porte sur la caractérisation des deux facteurs de transcription ORO et SAM ainsi que sur les dynamiques chromatiniennes sous-jacentes. Cette thèse présente les phénotypes des deux mutants oro et sam ainsi qu’une comparaison du transcriptome des mutants avec celui du gamétophyte et sporophyte. L’interaction entre ORO et SAM a été également testée et a lieu au niveau de chaque homéodomaine. Les préférences de liaison à l’ADN des deux facteurs de transcription ont été évaluées in vitro. Un criblage par double-hybride de levure a permis d’identifier deux sous-unités C de la famille de facteurs de transcription Nuclear Factor Y interagissant avec ORO. Cette thèse a également permis des avancées importantes dans l’étude de la régulation de la chromatine notamment en mettant au point un protocole d’immunoprécipitation de la chromatine. Ainsi, les profils de six modifications post-traductionnelles d’histones sur l’ensemble du génome ont été établis. Ce travail est pionnier dans la compréhension de la reprogrammation de la chromatine et la régulation de voies de développement majeures chez les algues brunes.The brown alga Ectocarpus exhibits a haploid-diploid life cycle with an alternation between two multicellular generations : a haploid gametophyte and a diploid sporophyte. Two mutants exhibit homeotic switching between the sporophyte and gametophyte programs, reiterating the gametophyte program instead of switching to the sporophyte. These mutants, called ouroboros (oro) et samsara (sam), carry mutations into two different genes that code for TALE homeodomain transcription factors. This thesis aimed to characterize these two transcription factors and the chromatin dynamics associated with the alternation of generation in Ectocarpus. This thesis presents the characterisation of the oro and sam mutants and a transcriptomic comparison of the mutants with the sporophyte and gametophyte. DNA-binding preferences of the two transcription factors were evaluated using in vitro methods. ORO and SAM are able to heterodimerise via their respective homeodomains and a yeast two-hybrid screen showed that two C subunits of the Nuclear Factor Y family are able to interacting with ORO. This thesis also presents major advances in the study of chromatin regulation in the brown alga. A chromatin immunoprecipitation protocol was established and used to obtain genome-wide profiles for six histone modifications. Taken together, the data presented here suggests that ORO and SAM may be involved directly in chromatin reprogramming at generation-biased genes via an association with the NF-Y complex. The work presented represents a pioneer analysis of brown algal transcription factors and chromatin reprogramming events involved in the regulation of developmental pathways

Theses.fr

Evolution of Multicellularity

Author: Cock J. Mark
J. Mark Cock
Publication venue
Publication date: 28/09/2021
Field of study

The emergence of multicellular organisms was, perhaps, the most spectacular of the major transitions during the evolutionary history of life on this planet [...

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Genetic and cellular characterisation of parthenogenesis in the brown alga Ectocarpus sp.

Author: Mignerot Laure
Publication venue
Publication date: 14/12/2018
Field of study

Bien que la reproduction sexuée soit prédominante chez les eucaryotes, plusieurs centaines d’organismes ont opéré une transition vers la reproduction asexuée. Les transitions entre reproduction sexuée et asexuée peuvent avoir une importance et des conséquences évolutives mais elles restent largement peu décrites au niveau écologique, moléculaire, génétique ou cytologique. La reproduction asexuée par parthénogenèse correspond au développement d’un organisme à partir de gamètes sans fécondation. Bien que beaucoup d’eucaryotes soient parthénogénétiques, nous connaissons très peu les bases génétiques, les causes et les conséquences évolutives conduisant à ce mode de reproduction asexuée. Les algues brunes sont un groupe d’eucaryotes multicellulaires qui présentent une incroyable diversité en termes de cycle de vie, de systèmes sexués ou mode de reproduction. Elles représentent d’excellents modèles pour étudier l’origine, l’évolution et les mécanismes de la parthénogenèse. Dans cette thèse, les nombreux outils génétiques et cellulaires développés pour l’algue brune modèle Ectocarpus ont permis de caractériser les loci impliqués dans la parthénogenèse et de mettre en lumière les causes et les conséquences de ce développement à l’échelle de l’organisme. Nos résultats soulignent le rôle clé des chromosomes sexuels en tant que régulateur majeur de la reproduction asexuée, ainsi que deux loci autosomaux. Des effets négatifs de la parthénogenèse sur la fitness des mâles ont été identifiés ainsi que des effets sur la fitness des générations du cycle de vie. Ces résultats indiquent que la parthénogenèse pourrait être à la fois sous sélection sexuelle et sous sélection antagoniste par rapport aux générations (polyploidallie) (Chapitre 2). La croissance des zygotes est significativement affectée par la capacité parthénogénétique des parents mâles et la transmission des mitochondries a été suivie afin de caractériser les retards de croissances observés (Chapitre 2 et 3). En parallèle, la transmission mitochondriale chez Ectocarpus sp.7 s’est révélé être non usuelle (Chapitre 3). Enfin, la carte génétique générée (Chapitre 2) pour l’espèce Ectocarpus siliculosus a été comparée à celle d’Ectocarpus sp.7 (génome de référence séquencé en 2010) et a révélé une synténie fortement conservé entre les deux espèces (Chapitre 4). En étudiant la parthénogenèse chez un organisme multicellulaire qui a évolué indépendamment des plantes et des animaux, ce travail a participé à approfondir les connaissances sur les mécanismes évolutifs conduisant à la parthénogenèse.Although sexual reproduction predominates in eukaryotes, several hundred lineages have undergone the transition from sexuality to asexuality. Transitions between sexual and asexual reproduction are believed to have important evolutionary and ecological consequences, yet the molecular, genetic, and cytological foundations of such transitions remain elusive. One type of asexual reproduction is parthenogenesis, i.e., the development of an adult organism directly from gametes in the absence of fertilisation. Although many eukaryotes are capable of reproducing by parthenogenesis, we know very little about its genetic basis, and the evolutionary causes and consequences of transitions to asexuality are poorly understood. The brown algae are a group of multicellular eukaryotes, that show an extraordinary diversity of types of life cycle, sexual systems, modes of reproduction, and they provide excellent models to look at the origins, evolution and mechanisms underlying parthenogenesis. In this thesis, we have used a wide array of genomic and cell biology tools available for the model brown alga Ectocarpus to identify and characterize loci involved in parthenogenesis, shedding light on the causes and consequences of parthenogenesis at the organism level. Our results highlight the key role of the sex chromosome as a major regulator of asexual reproduction, together with two autosomal loci. Importantly, we identify several negative effects of parthenogenesis on male fitness, but also different fitness effects between parthenogenesis and life cycle generations, supporting the idea that parthenogenesis may be under both sexual selection and generation/ploidally-antagonistic selection (Chapter 2). Zygotic growth was significantly affected by the parthenogenetic capacity of the male parent and the putative role of mitochondrial inheritance patterns on the fitness of sporophytes was also investigated (Chapter 2 and 3). This work revealed an unusual transmission pattern of mitochondria specifically in Ectocarpus species 7 (Chapter 3). Finally, the QTL analysis (Chapter 2) required the construction of a genetic map for Ectocarpus siliculosus and a comparison with Ectocarpus species 7 genetic map (reference genome sequenced in 2010) showed that the synteny was highly conserved between the two species (Chapter 4). By investigating parthenogenesis in a multicellular organism that has independently evolved from plants and animals, the work presented in this thesis has helped to assess the diversity of evolutionary mechanisms that lead to parthenogenesis

Theses.fr