Academic literature on the topic 'Holocentrique'

To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507–16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, nad6 was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except cox1, which begins with the codon GTG. By examining their phylogeny, Sargocentron and Neoniphon were verified to be closely related and to belong to the same subfamily Holocentrinae, while Myripristis and Ostichthys belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.

Holocentrinae and Myripristinae (Holocentridae) are among the most apparent species in the nocturnal reef fish community. However, there is no clear assent regarding their phylogenetic relations, which is reported in their complicated taxonomic history. In this study, Sargocentron spinosissimum (Temminck et Schlegel, 1843) and Sargocentron tiereoides (Bleeker, 1853) were reported from the Mediterranean coast of Egypt (Damietta coast). This is the first record of these species which is greatly distributed across Indo-Pacific regions and eastern Africa showed the success of these species to migrate to the Mediterranean water with a good adaptation to the new habitats. In the presently reported study, 26 morphometric measurements were recorded and cytochrome c oxidase subunit I (COI) barcodes were recovered for a total of 20 specimens (8 from S. spinosissimum and 12 from S. tiereoides). The specimens from the Damietta coast, Egypt show character states diagnostic of S. spinosissimum: Head is curved. Spinous dorsal fin base straight. Soft dorsal fin base slightly raised. Spinous dorsal fin membranes red. Anterior margin of pelvic and anal fins white. Other fin rays are red. While character states diagnostic of S. tiereoides: Head is straight and pointed. Spinous dorsal fin base almost straight. Soft dorsal fin base not raised and spinous dorsal fin membranes vaguely red. Sequences of both species were submitted to the GenBank and Barcode of Life Database (BOLD) publication database which displayed 99%–100% similarity value S. tiereoides from GenBank and BOLD databases but, S. spinosissimum has not any deposited sequences from GenBank or BOLD. DNA barcoding based on COI gene was demonstrated as a powerful and useful molecular marker in the identification and differentiation of S. spinosissimum and S. tiereoides fish species.

Title (Bahasa Indonesia):Kontaminasi merkuri (Hg) di Teluk Manado, Sulawesi Utara, IndonesiaArtisanal gold minings, which are situated in the highlands of the northern part of Sulawesi Island,use mercury (Hg) to extract gold and dischargetheirs tailings into rivers; one of the rivers(Bailang River) is connected to Manado Bay. This could cause Hg contamination into the bay. This study aimed to assess the contamination of Hg in the aquatic ecosystem of the bay. For the assessment, the bay was divided into 2 parts, namely the North and the South, and the contamination was assessed by measuring the total Hg concentration in sediments and fishes. Determination of Hg concentration refers to the Indonesian National Standard (SNI) 01-2896-1992 and Guidance of Balai Riset dan Standarisasi Industri Manado. The results showed that the range of Hg concentrations in fish varied by species; in the northern part of the bay: Holocentridae (0.1144-0.1151 ppm), Siganidae (0.0020-0.0034 ppm), Apogonidae (0.0461-0.050 ppm), and Nemipterus (0.0142-0.0144 ppm ). While in the southern part of the bay: Holocentridae (0.1090-0.1104 ppm), Siganidae (0.160-0.164 ppm), Apogonidae (0.1280-0.1291 ppm), Nemipterus (0.0522-0.0530 ppm) , and Priacanthus sp. (0.0194-0.0210 ppm). The average concentration of Hg in sediments of the bay around river mouths varied based on location, i.e. Bailang River was 0.0502 ppm, Sario River was 0.0270 ppm, Bahu River was 0.0615 ppm, and Malalayang River was 0.0143 ppm.Pertambangan emas rakyat menggunakan merkuri (Hg), yang berada di daerah dataran tinggi bagian Utara Pulau Sulawesi, membuang limbah tailing ke sungai menuju ke laut; satu dari sungai tersebut (Sungai Bailang) bermuara ke Teluk Manado. Hal ini dapat menyebabkan kontaminasi Hg ke lingkungan perairan teluk. Penelitian ini bertujuan untuk menilai kontaminasi Hg di ekosistem perairan teluk tersebut. Untuk penilaian, perairan teluk dibagi 2 bagian, yaitu bagian Utara dan Selatan, dan kontaminasi dinilai dengan cara mengukur konsentrasi Hg total pada sedimen dan ikan. Penentuan konsentrasi Hg mengacu Standar Nasional Indonesia (SNI) 01-2896-1992 dan Panduan Balai Riset dan Standarisasi Industri Manado. Hasil penelitian menunjukkan, bahwa kisaran konsentrasi Hg dalam ikan bervariasi berdasarkan jenis; dibagian Utara teluk: Holocentridae(0,1144-0,1151 ppm), Siganidae (0,0020-0,0034 ppm), Apogonidae (0,0461-0,050 ppm), dan Nemipterus (0,0142-0,0144 ppm).Sedangkandi perairan bagian Selatan teluk: Holocentridae (0,1090-0,1104 ppm), Siganidae (0,160-0,164 ppm), Apogonidae (0,1280-0,1291 ppm), Nemipterus (0,0522-0,0530 ppm),dan Priacanthus sp.(0,0194-0,0210 ppm). Konsentrasi rata-rata Hg di sedimen perairan teluk sekitar muara Sungai Bailang sebesar 0,0502 ppm, muara Sungai Sario sebesar 0,0270 ppm, muara Sungai Bahu sebesar 0,0615 ppm, dan muara Sungai Malalayang sebesar 0,0143 ppm.

Mesophotic coral ecosystems (MCEs: ~30 to 100+ m depth) may be older and more stable than shallow coral ecosystems that are more prone to disturbances in both the long term (glacial sea level cycles) and short term (heavy weather and anthropogenic activities). Here, we assess the phylogeography of two MCE fishes, the soldierfish Myripristis chryseres (N = 85) and the squirrelfish Neoniphon aurolineatus (N = 74), with mtDNA cytochrome oxidase C subunit I. Our goal is to resolve population genetic diversity across the Central and West Pacific and compare these patterns to three shallow-reef species in the same taxonomic family (Holocentridae). Significant population structure (ΦST = 0.148, p = 0.01) was observed in N. aurolineatus, while no structure was detected in M. chryseres (ΦST = −0.031, p = 0.83), a finding that matches the shallow-water congener M. berndti (ΦST = −0.007, p = 0.63) across the same range. Nucleotide diversity in the MCE fishes was low (π = 0.0024–0.0028) compared to shallow counterparts (π = 0.003–0.006). Coalescence times calculated for M. chryseres (~272,000 years) and N. aurolineatus (~284,000 years) are more recent or comparable to the shallow-water holocentrids (~220,000–916,000 years). We conclude that the shallow genetic coalescence characteristic of shallow-water marine fishes cannot be attributed to frequent disturbance. We see no evidence from holocentrid species that MCEs are older or more stable habitats.

Chez les eucaryotes, l’ADN est empaqueté dans des complexes protéiques d’histones nommés nucléosomes qui assurent sa conformation. Cet arrangement est hétérogène à travers le génome et peut être dynamiquement modifié. La régulation de l’architecture chromatinienne joue un rôle essentiel dans la stabilité des génomes ainsi que la dynamique transcriptionnelle. Certaines régions qualifiées d’ ‘’heterochromatine constitutive’’ sont toutefois connues pour être maintenues à l’état condensé. Régionalisées aux extrémités et centres des chromosomes, l’hétérochromatine constitutive participe des fonctions télomériques et centromériques.Spodoptera frugiperda (S.fru, Lépidoptère, Noctuelle) est un ravageur de culture endémique du continent américain, récemment invasif dans le continent africain. Comme tous les Lépidoptères, S.fru est une espèce holocentrique dont le centromère est réparti le long des chromosomes et non restreint en un point unique. Cette disposition interroge sur l’établissement, la distribution ainsi que la fonction conservée de l’HC puisque cette dernière est principalement décrite pour être majoritairement localisée dans de larges régions péricentriques. Comprendre l’architecture chromatinienne chez S.fru peut avoir un intérêt en lutte biologique mais également permettre d’approfondir les connaissances en épigénétique chez un organisme non-modèle.Dans le cadre de la thèse, nous nous sommes demandés si la diméthylation de la lysine 9 de l’histone 3 (H3K9me2), marqueur de l’hétérochromatine constitutive, possédait un rôle conservé chez S.fru. Pour ce faire, nous avons comparé des données de ChIP-seq d’H3K9me2 sur cellules et larves entières après avoir annoté les gènes et l’ensemble des éléments répétés du génome, susceptibles d’être enrichis par cette marque. Parallèlement, des échantillons d’ARN-seq ont été étudiés afin de questionner le statut répressif de l’hétérochromatine constitutive. Nos résultats suggèrent un invariable maintien d’H3K9me2 dans les régions (sub)télomériques transcriptionnellement inactives ainsi qu’une forte association aux locus répétés d'ADN ribosomal (rDNA). Ces séquences ne constituent toutefois qu’une minorité des régions enrichies, le reste étant retrouvé dans des séquences répétées ainsi que dans le corps des gènes, indifféremment de leur état transcriptionnel. La persistante association d’H3K9me2 aux télomères et rDNA présagerait d’un maintien de la marque à proximité des centromères dont nous proposons un modèle d’établissement.La disposition de l’hétérochromatine constitutive questionne celle des régions euchromatiniennes, pauvres en nucléosomes, transcriptionnellement active et dynamiquement modifiées au cours du développement, du cycle cellulaire et des conditions environnementales. Afin de tester l’antagonisme de ces conformations, nous avons respectivement étudié la répartition des zones ouvertes et fermées du génome de la larve au stade L4 par approches de FAIRE-seq et de MAINE-seq. Ces structures ont été décrites dans la littérature pour être enrichies par de spécifiques modifications d’histones. Ainsi nous avons mis au point le protocole de native ChIP-seq d’H3K4me3 (marque active) et H3K9me2, H3K9me3, H3K27me3 (marques répressives). L’analyse en cours de l’ensemble de ces données de séquençages permettra d’avoir une vue intégrée de l’architecture chromatinienne au stade ravageur
In eukaryotes, DNA is arranged in histones proteins complexes called nucleosomes that shape its conformation. This arrangement is heterogeneous across genomes and can be dynamically modified. Regulation of chromatin architecture plays an essential role in genome stability and transcription dynamics. Some regions named ‘’constitutive heterochromatin’’ are nonetheless known to remain highly condensed, regardless of conditions. Regionalized at extremities and chromosomes centers, constitutive heterochromatin contributes to telomeric and centromeric functions.Spodoptera frugiperda (S.fru, Lepidoptera, Noctuidae) is major crop pest in the Americas that recently invaded Africa. Like all Lepidopteran, S.fru is holocentric which means that its centromere is spread along chromosome and not restricted to a uniq point. This disposition question about establishment, distribution but also conserved function of constitutive heterochromatin since its usually and mainly localized in large pericentric regions.Deciphering chromatinian architecture in S.fru can be of interest in biological control but also allow to deepen epigenetic knowledge in a non-model organism.During my phD, we questionned the role of histone 3 lysine 9 demethylated (H3K9me2) in S.fru, a histone modification known in other yet described organisms to be a constitutive constitutive heterochromatinian hallmark.We compared H3K9me2 ChIP-seq data on cells and larvae after overall genomic functional annotation, potentially enriched for this mark. In parallel, RNA-seq samples were analyzed to question the putative repressive status of constitutive heterochromatin.Our results suggest an invariant retention of H3K9me2 in (sub)telomeric regions transcriptionally inactive but also a strong association of this mark in repeated ribosomal DNA locus (rDNA).These sequences constitutes nonetheless a minority of enriched regions since most of them regionalize in repeated sequences like transposons and tandem array but also gene bodies, independently of their transcriptional states.Persistent H3K9me2 association to telomeres and rDNA could predict of the conserved expression of this mark near centromeres. Based on literature and bioinformatics analysis, we proposed a model for S.fru holocentromeres.Constitutive heterochromatin questions euchromatin arrangement, described to be nucleosome poor, transcriptionally active and dynamically modified across development, cell cycle and environmental conditions. In order to test these structural antagonisms, we respectively studied open and closed genome conformations by FAIRE-seq and MAINE in larvae. These structures are reported to be associated to specific histones marks. We developed a native ChIP-seq protocol on H3K4me3 (active mark) and H3K9me2, H3K9me3, H3K27me3 (repressives marks). Overall analysis of these NGS data would help to picture an integrative view of chromatin architecture during larval pest stage

The squirrelfishes and soldierfishes, family Holocentridae, show site fidelity to their diurnal refuges on coral reefs. Species feeding at night on benthic crustaceans partition food and foraging habitats. However, it is not known whether holocentrids also partition diurnal resting habitats and refuge sites or how their density and size vary with habitat and refuge characteristics. I examined the diurnal distribution, density and size of holocentrids on the west coast of Barbados, West Indies, to determine how they are influenced by the habitat at three spatial scales. At the meso-scale, I surveyed 42 transects on seven sites located in five different zones of three different reefs. I recorded six holocentrid species that varied in density among sites and were strongly associated with habitat characteristics, although sites alone explained most of the variation. At the micro-scale, I recorded the presence of species and characterized substratum composition and topography of 5 quadrats (4 x 4 m) within each transect, but little of the variation in community composition was explained by habitat at this scale. At the refuge scale, four species common enough to analyze occupied 248 holes and spaces under ledges that varied in their volume, orientation, light intensity and presence of cleaner fish. Refuge volume was an important determinant of the biomass of the fishes it contained, due to positive relationships with both the number and size of the occupants, even though holocentrids were usually considerably smaller than the refuge they occupied. Species differed in social organizations and different species and social organizations occupied refuges of different sizes. This thesis provides the first detailed examination of diurnal habitat use in the Holocentridae and shows that their density, biomass and social organization is related to habitat and differs among species at some scales but not others.
Les poissons écureuils et poissons soldats, de la famille des Holocentridae, sont fidèles à leurs refuges diurnes sur les récifs coralliens. Il est suggéré que les espèces qui se nourrissent la nuit de crustacés benthiques se partagent la nourriture et la niche alimentaire. Cependant, il subsiste peu d'information sur comment les poissons Holocentridae se partagent les habitats de repos diurnes et les sites de refuges. Nous ignorons également comment la densité et la taille de ces poissons peuvent varier en fonction de l'habitat et des caractéristiques des refuges. J'ai examiné la distribution diurne, la densité et la taille des poissons Holocentridae sur deux récifs frangeants et une section d'un banc de coraux bordant la côte ouest de la Barbade, Inde Occidentale, afin de déterminer comment la distribution, la densité et la taille des poissons Holocentridae sont influencés par l'habitat à trois échelles spatiales. À l'échelle intermédiaire des sites, j'ai recensé les poissons Holocentridae dans 42 transects distribués sur sept sites situés dans cinq zones différentes sur trois récifs différents. J'ai observé six espèces de poissons Holocentridae dont les densités variaient entre les sites et étaient fortement associées avec les caractéristiques de l'habitat, même si les sites à eux seuls expliquaient la majorité de la variation du système. À plus petite échelle, j'ai recensé la présence d'espèces de poissons Holocentridae dans 5 quadrats (4 x 4 m) à l'intérieur de chaque transect et j'ai caractérisé la composition du substrat et la topographie. À cette échelle, même après avoir contrôlé l'effet des sites et des transects, seulement une très petite portion de la variation dans la composition de la communauté des poissons Holocentridae était expliquée par l'habitat. À une échelle encore plus petite, celle des refuges occupés par les poissons Holocentridae, quatre espèces étaient suffisamment abondante

碩士
國立中山大學
海下技術研究所
94
Taiwan is surrounded by sea, there are coral reefs at both south and north ends, and also at off-shore islands. Coral reef offers habitat and resources for marine animals, that are attracted to in numbers, however due to the limited resources, competitions and conflicts are common among animals. In order to defend the territory on intimidate intruder, some fishes develop vocal mechanism that certain sounds are generated at encounter. The sounds of common Holocendridae fishes at coral reef were studied before, but the sound characteristics of sound were not fully investigated. In this research, sound samples were recorded from Neoniphon sammara, Myripristis murdjan, and Sargocentron spinosissimum(Holocentridae) in an indoor water tank, to understand more about their specific features of sounds generated at disturbance. The identification system of this study was based on Matlab, which extracted the characteristic parameters from the sounds, so the database for comparison can be formed. The sounds can be classified into single pulse and pulse train, and the parameters used are dominant frequency, band width, duration, and pulse repetition rate. As the result, Neoniphon sammara has single pulse frequency of 428.0±95.0 Hz (mean ± standard deviation), pulse train frequency of 449.8±92.4 Hz, Myripristis murdjan has single pulse and pulse train frequency of 375.2±96.3 Hz and 369.2±96.0 Hz, and Sargocentron spinosissimum has single pulse and pulse train frequency of 377.6±93.5 Hz and 387.8±97.1 Hz. The similarity of sounds between Neoniphon sammara and Myripristis murdjan is 81.3%, between Myripristis murdjan and Sargocentron spinosissimum is 83.6%, and between Neoniphon sammara and Sargocentron spinosissimum is 90.3%. Finally, the identification accuracy of Neoniphon sammara is 78.9%, Myripristis murdjan is 71.4%, and Sargocentron spinosissimum is 38.4%. The low identification accuracy of Sargocentron spinosissimum is due to the high similarity of sounds with Myripristis murdjan, and the number of sound samples is not sufficient.