Marine Biotechnology最新文献

{"title":"Histological and Transcriptomic Insights into the Ovary Development of Hemibarbus labeo Injected with Spawn-Inducing Hormones","authors":"Xinming Gao,&nbsp;Yaoping Lv,&nbsp;Qingmin Dai,&nbsp;Ling Zhu,&nbsp;Siqi Liu,&nbsp;Zehui Hu,&nbsp;Junkai Lu,&nbsp;Haidong Zhou,&nbsp;Zufei Mei","doi":"10.1007/s10126-024-10335-7","DOIUrl":"10.1007/s10126-024-10335-7","url":null,"abstract":"<div><p>Naturally, the ovaries of many farmed fish can only develop to stage IV (mainly including stage IV oocytes, known as full-grown postvitellogenic oocytes). Therefore, spawn-inducing hormone injections are used to promote ovary development and oocyte maturation, facilitating reproduction in the aquaculture industry. The study of spawn-inducing hormones and their underlying neuroendocrine mechanisms has been a recent focus in fish reproductive biology. However, the intra-ovarian regulatory mechanisms of ovary development and oocyte maturation after hormone injection require further investigation. In this study, we explored the histological and transcriptomic map of the ovary of <i>Hemibarbus labeo</i> after hormone injection to reveal changes in the ovary. The gonad index significantly increased after hormone injection for 5.5 h, after which no significant change was observed. Histological analysis showed that the nuclei had moved to one side of the oocytes at 5.5 h after hormone injection. Moreover, the volume of the oocytes increased and their yolk membranes thickened. Oocytes then underwent their first meiotic division at 5.5–11 h after hormone injection. Subsequently, the follicular membrane was ruptured, and ovulation was completed at 11–16.5 h after hormone injection. In addition, we identified 3189 differentially expressed genes (DEGs) on comparing the transcriptomes at different time points after hormone injection. These DEGs were significantly enriched in the GO terms of nervous system process, molecular transducer activity, and extracellular region, and the KEGG pathways of TNF signaling and cytokine–cytokine receptor interaction; these may play important roles in ovary development and oocyte maturation. Within these pathways, genes such as <i>apoe</i>, <i>creb3</i>, <i>jun</i>, <i>junb</i>, <i>il11</i>, and <i>il8</i> may play important roles in steroid hormone synthesis and ovulation. Conclusively, our results show detailed sequential dynamics of oocyte development and provide new insights into the intra-ovarian regulatory mechanisms of ovarian development and oocyte maturation in <i>H. labeo</i>. These findings may be important for research on improving egg quality and reproduction in aquaculture.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HcN57, A Novel Unusual Acidic Silk-Like Matrix Protein from Hyriopsis cumingii, Participates in Framework Construction and Nacre Nucleation During Nacreous Layer Formation","authors":"Can Jin,&nbsp;Fangmengjie Wei,&nbsp;Jiayi Zhang,&nbsp;Xiaoyang Tan,&nbsp;Taixia Fan,&nbsp;Wen Luo,&nbsp;Jiale Li","doi":"10.1007/s10126-024-10339-3","DOIUrl":"10.1007/s10126-024-10339-3","url":null,"abstract":"<div><p>In the classic molecular model of nacreous layer formation, unusual acidic matrix proteins rich in aspartic acid (Asp) residues are essential for nacre nucleation due to their great affinity for binding calcium. However, the acidic matrix proteins discovered in the nacreous layer so far have been weakly acidic with a high proportion of glutamate. In the present study, several silk-like matrix proteins, including the novel matrix protein HcN57, were identified in the ethylenediaminetetraacetic acid-soluble extracts of the nacreous layer of <i>Hyriopsis cumingii</i>. HcN57 is a highly repetitive protein that consists of a high proportion of alanine (Ala, 34.4%), glycine (Gly, 22.5%), and serine (Ser, 11.4%). It forms poly Ala blocks, Gly_nX repeats, an Ala-Gly repeat, and a Ser-Ala-rich region, exhibiting significant similarity to silk proteins found in spider species. The expression of HcN57 was specifically located in the dorsal epithelial cells of the mantle pallium and mantle center. Notably, expression of HcN57 was relatively high during nacreous layer regeneration and pearl nacre deposition, suggesting HcN57 is a silk matrix protein in the nacreous layer. Importantly, HcN57 also contains a certain content of Asp residues, making it an unusual acidic matrix protein present in the nacreous layer. These Asp residues are mainly distributed in three large hydrophilic acidic regions, which showed inhibitory activity against aragonite deposition and morphological regulation of calcite in vitro. Moreover, HcN57-dsRNA injection resulted in failure of nacre nucleation in vivo. Taken together, our results show that HcN57 is a bifunctional silk protein with poly Ala blocks and Gly-rich regions that serve as space fillers within the chitinous framework to prevent crystallization at unnecessary nucleation sites and Asp-rich regions that create a calcium ion supersaturated microenvironment for nucleation in the center of nacre tablets. These observations contribute to a better understanding of the mechanism by which silk proteins regulate framework construction and nacre nucleation during nacreous layer formation.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic Responses and Larval-Stage Growth of Protandrous Yellowfin Seabream (Acanthopagrus Latus) to Different Polyethylene Microplastics Exposure","authors":"Meng Xu,&nbsp;Wenyu Fang,&nbsp;Genmei Lin,&nbsp;Xiaoshan Zhu,&nbsp;Jianguo Lu","doi":"10.1007/s10126-024-10334-8","DOIUrl":"10.1007/s10126-024-10334-8","url":null,"abstract":"<div><p>Polyethylene microplastics (PE-MPs) were widespread in the marine environment; thus, their influences on marine hermaphroditic fish cannot be ignored. This study intends to evaluate the adverse biological effects of two different sources of PE, identified by Raman spectroscopy, on protandrous yellowfin seabream (<i>Acanthopagrus latus</i>) larvae. Growth retardation, brain lesions, head/body length ratio increase, and neuroendocrine system disorders were found, and growth and neuroendocrine regulation-related genes such as <i>sstr2</i>, <i>ghrb</i>, <i>irs1</i>, UGT2B15, UGT2C1, <i>drd4a</i>, <i>esr2b, hsd3b7</i>, and <i>hsd17b2</i> were identified. PE microbeads (100 μm) showed more severe tissue damage on fish, while environmental PE fibers (500–2500 μm) showed more imperceptible adverse effects. There were 218 DEGs up-regulated and 147 DEGs down-regulated in the environmental PE group, while 1284 (up) and 1267 (down) DEGs were identified in the virgin PE group. PE-MP stress influenced physiological processes like growth and neuroendocrine regulation and cholesterol-steroid metabolism, and caused tissue damage in the fish larvae. The study highlights the effects of environmental PE exposure on hermaphroditic protandrous fish.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Localization of Health-Promoting Peptides Derived from Fish Protein Hydrolyzates on Fish Muscle Proteins","authors":"Shugo Watabe,&nbsp;Nanami Mizusawa,&nbsp;Kenta Hosaka,&nbsp;Shoichiro Ishizaki,&nbsp;Lu Peng,&nbsp;Koji Nagata,&nbsp;Nobuhiko Ueki","doi":"10.1007/s10126-024-10331-x","DOIUrl":"10.1007/s10126-024-10331-x","url":null,"abstract":"<div><p>The four previously reported health-promoting dipeptides, valine-tyrosine, lysine-tryptophan, methionine-phenylalanine, and arginine-isoleucine, found in the fish muscle hydrolyzates, were mainly located in the myosin subfragment-1 heavy chain, whereas the health-promoting tripeptide, alanine-lysine-lysine, was found in the fibrous rod consisting of the myosin subfragment-2 and light meromyosin with a regular coiled-coil structure of α-helix, irrespective of the fish species. Furthermore, the localization of these peptides either in the random coil, β-sheet, or α-helix was also examined in the three-dimensional image, showing no specific tendency. Surprisingly, the same trend was observed even for the mammalian rabbit fast muscle myosin heavy chain. Since a trade-off between myofibrillar ATPase and structural stability has been reported for fish living at low environmental temperatures, it is speculated that fish muscle proteins, when ingested, are easily digested by various proteases in the human digestive tract and provide various health-promoting peptides also in vivo. While fish actin contained only two dipeptides, methionine-phenylalanine and valine-tyrosine, glyceraldehyde 3-phosphate dehydrogenase, one of the major components of fish muscle water-soluble protein, contained all of the four dipeptides and one tripeptide mentioned above.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accumulation and Phagocytosis of Fluorescently Visualized Macrophages Against Edwardsiella piscicida Infection in Established mpeg1.1-Transgenic Japanese Medaka Oryzias latipes","authors":"Juna Yamamoto,&nbsp;Hana Deguchi,&nbsp;Takechiyo Sumiyoshi,&nbsp;Kentaro Nakagami,&nbsp;Akatsuki Saito,&nbsp;Hiroshi Miyanishi,&nbsp;Masakazu Kondo,&nbsp;Tomoya Kono,&nbsp;Masahiro Sakai,&nbsp;Masato Kinoshita,&nbsp;Jun-ichi Hikima","doi":"10.1007/s10126-024-10333-9","DOIUrl":"10.1007/s10126-024-10333-9","url":null,"abstract":"<div><p>Intracellular bacteria such as those belonging to the genus <i>Edwardsiella</i> can survive and proliferate within macrophages. However, the detailed mechanisms underlying the host macrophage immune response and pathogen evasion strategies remain unknown. To advance the field of host macrophage research, we successfully established transgenic (Tg) Japanese medaka <i>Oryzias latipes</i> that possesses fluorescently visualized macrophages. As a macrophage marker, the macrophage-expressed gene 1.1 (<i>mpeg1.1</i>) was selected because of its predominant expression across various tissues in medaka. To validate the macrophage characteristics of the fluorescently labeled cells, May-Grünwald Giemsa staining and peroxidase staining were conducted. The labeled cells exhibited morphological features consistent with those of monocyte/macrophage-like cells and tested negative for peroxidase activity. Through co-localization studies, the fluorescently labeled cells co-localized with <i>E. piscicida</i> in the intestines and kidneys of infected medaka larvae, confirming the ingestion of bacteria through phagocytosis. In addition, the labeled cells expressed macrophage markers but lacked a neutrophil marker. These results suggested that the fluorescently labeled cells of Tg[<i>mpeg1.1</i>:mCherry/mAG] medaka were monocytes/macrophages, which will be useful for future studies aimed at understanding the mechanisms of macrophage-mediated bacterial infections.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141417185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of DNA Insertion-specific Markers Based on the Intergenic Region of Oplegnathus punctatus Cdkn1/srsf3 for Sex Identification","authors":"Yuting Ma,&nbsp;Yongshuang Xiao,&nbsp;Zhizhong Xiao,&nbsp;Jun Li","doi":"10.1007/s10126-024-10336-6","DOIUrl":"10.1007/s10126-024-10336-6","url":null,"abstract":"<div><p>Spotted knifejaw (<i>Oplegnathus punctatus</i>) is a marine economic fish with high food and ecological value, and its growth process has obvious male and female sexual dimorphism, with males growing significantly faster than females. However, the current sex identification technology is not yet mature, which will limit the growth rate of <i>O. punctatus</i> aquaculture and the efficiency of separate sex breeding, so the development of efficient sex molecular markers is imperative. This study identified a 926 bp DNA insertion fragment in the <i>cdkn1</i>/<i>srsf3</i> intergenic region of <i>O. punctatus</i> males through whole-genome scanning, comparative genomics, and structural variant analysis. A pair of primers was designed based on the insertion information of the Y chromosome intergenic region in male individuals. Agarose gel electrophoresis revealed the amplification of two DNA fragments, 1118 bp and 192 bp, in male <i>O. punctatus</i> individuals. The 926 bp fragment was identified as the insertion in the intergenic region of <i>cdkn1</i>/<i>srsf3</i> in males, while only a single 192 bp DNA fragment was amplified in females. The biological sex of the individuals identified in this manner was consistent with their known phenotypic sex. In this study, we developed a method to detect DNA insertion variants in the intergenic region of <i>O. punctatus</i>. Additionally, we introduced a new DNA marker for the rapid identification of the sex of <i>O. punctatus</i>, which enhances detection efficiency. The text has important reference significance and application value in sex identification, all-male breeding, and lineage selection. It provides new insights into the regulation of variation in the intergenic region of <i>cdkn1</i>/<i>srsf3</i> genes and the study of RNA shearing.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shotgun Metagenomics Reveals Taxonomic and Functional Patterns of the Microbiome Associated with Barbour’s Seahorse (Hippocampus barbouri)","authors":"Rose Chinly Mae H. Ortega-Kindica,&nbsp;Chinee S. Padasas-Adalla,&nbsp;Sharon Rose M. Tabugo,&nbsp;Joey Genevieve T. Martinez,&nbsp;Olive A. Amparado,&nbsp;Carlo Stephen O. Moneva,&nbsp;Rodelyn Dalayap,&nbsp;Carlos O. Lomeli-Ortega,&nbsp;Jose Luis Balcazar","doi":"10.1007/s10126-024-10330-y","DOIUrl":"10.1007/s10126-024-10330-y","url":null,"abstract":"<div><p>This study aimed to investigate the taxonomic and functional patterns of the microbiome associated with Barbour’s seahorse (<i>Hippocampus barbouri</i>) using a combination of shotgun metagenomics and bioinformatics. The analyses revealed that Pseudomonadota and Bacillota were the dominant phyla in the seahorse skin microbiome, whereas Pseudomonadota and, to a lesser extent, Bacillota and Bacteroidota were the dominant phyla in the seahorse gut microbiome. Several metabolic pathway categories were found to be enriched in the skin microbiome, including amino acid metabolism, carbohydrate metabolism, cofactor and vitamin metabolism, energy metabolism, nucleotide metabolism, as well as membrane transport, signal transduction, and cellular community-prokaryotes. In contrast, the gut microbiome exhibited enrichment in metabolic pathways associated with the metabolism of terpenoids and polyketides, biosynthesis of other secondary metabolites, xenobiotics biodegradation and metabolism, and quorum sensing. Additionally, although the relative abundance of bacteriocins in the skin and gut was slightly similar, notable differences were observed at the class level. Specifically, class I bacteriocins were found to be more abundant in the skin microbiome, whereas class III bacteriocins were more abundant in the gut microbiome. To the best of our knowledge, this study represents the first comprehensive examination of the taxonomic and functional patterns of the skin and gut microbiome in Barbour’s seahorse. These findings can greatly contribute to a deeper understanding of the seahorse-associated microbiome, which can play a pivotal role in predicting and controlling bacterial infections, thereby contributing to the success of aquaculture and health-promoting initiatives.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The New Roles of traf6 Gene Involved in the Development of Zebrafish Liver and Gonads","authors":"Hongyan Xu,&nbsp;Wenzhuo Ban,&nbsp;Jiaming Tian,&nbsp;Jianfei Xu,&nbsp;Zhimin Tan,&nbsp;Sendong Li,&nbsp;Kaili Chen,&nbsp;Mi Ou,&nbsp;Kaibin Li","doi":"10.1007/s10126-024-10329-5","DOIUrl":"10.1007/s10126-024-10329-5","url":null,"abstract":"<div><p>Traf6, an adaptor protein, exhibits non-conventional E3 ubiquitin ligase activity and was well studied as an important factor in immune systems and cancerogenesis. In mice, the traf6-null caused a perinatal death, so that the underlying pathophysiology of <i>traf6</i>-defeciency is still largely unclear in animals. Here, in the present study, a <i>traf6</i> knockout zebrafish line (<i>traf6</i>^{<i>−/−</i>}) was generated and could survive until adulthood, providing a unique opportunity to demonstrate the functions of <i>traf6</i> gene in animals’ organogenesis beyond the mouse model. The body of <i>traf6</i>^{<i>−/−</i>} fish was found to be significantly shorter than that of the wildtype (WT). Likewise, a comparative transcriptome analysis showed that 866 transcripts were significantly altered in the <i>traf6</i>^{<i>−/−</i>} liver, mainly involved in the immune system, metabolic pathways, and progesterone-mediated oocyte maturation. Especially, the mRNA expression of the pancreas duodenum homeobox protein 1 (<i>pdx1</i>), glucose-6-phosphatase (<i>g6pcb</i>), and the vitellogenesis genes (<i>vtgs</i>) were significantly decreased in the <i>traf6</i>^{<i>−/−</i>} liver. Subsequently, the glucose was found to be accumulated in the <i>traf6</i>^{<i>−/−</i>} liver tissues, and the meiotic germ cell was barely detected in <i>traf6</i>^{<i>−/−</i>} testis or ovary. The findings of this study firstly implied the pivotal functions of <i>traf6</i> gene in the liver and gonads’ development in fish species.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141299614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tissue Localization of Tetrodotoxin in the Flatworm Planocera multitentaculata (Platyhelminthes: Polycladida)","authors":"Ryo Yonezawa,&nbsp;Kentaro Hayashi,&nbsp;Hikaru Oyama,&nbsp;Kazutoshi Yoshitake,&nbsp;Soshi Sato,&nbsp;Jayan Duminda M. Senevirathna,&nbsp;Ashley R. Smith,&nbsp;Taiki Okabe,&nbsp;Rei Suo,&nbsp;Shigeharu Kinoshita,&nbsp;Tomohiro Takatani,&nbsp;Osamu Arakawa,&nbsp;Shuichi Asakawa,&nbsp;Shiro Itoi","doi":"10.1007/s10126-024-10332-w","DOIUrl":"10.1007/s10126-024-10332-w","url":null,"abstract":"<div><p>Tetrodotoxin (TTX), a pufferfish toxin, is a highly potent neurotoxin that has been found in a wide variety of animals. The TTX-bearing flatworm <i>Planocera multitentaculata</i> possesses a large amount of TTX and is considered responsible for the toxification of TTX-bearing animals such as pufferfish (<i>Takifugu</i> and <i>Chelonodon</i>) and the toxic goby <i>Yongeichthys criniger</i>. However, the mechanism underlying TTX accumulation in flatworms remains unclear. Previous studies have been limited to identifying the distribution of TTX in multiple organs, such as the digestive organs, genital parts, and the remaining tissues of flatworms. Here, we performed liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis and immunohistochemical staining using a monoclonal anti-TTX antibody to elucidate the detailed localization of TTX in the tissues and organs of the flatworm <i>P. multitentaculata</i>. Immunohistochemical staining for <i>P. multitentaculata</i> showed that TTX-specific signals were detected not only in the ovaries and pharynx but also in many other tissues and organs, whereas no signal was detected in the brain, Lang’s vesicle, and genitalia. In addition, combined with LC–MS/MS analysis, it was revealed for the first time that TTX accumulates in high concentrations in the basement membrane and epidermis. These findings robustly support the hypotheses of “TTX utilization protection from predators.”</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141299615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family","authors":"Samuel Mwakisha Mwamburi,&nbsp;Satoshi Kawato,&nbsp;Miho Furukawa,&nbsp;Kayo Konishi,&nbsp;Reiko Nozaki,&nbsp;Ikuo Hirono,&nbsp;Hidehiro Kondo","doi":"10.1007/s10126-024-10325-9","DOIUrl":"10.1007/s10126-024-10325-9","url":null,"abstract":"<div><p>This study presents the first draft genome of <i>Siganus fuscescens</i>, and thereby establishes the first whole-genome sequence for a species in the Siganidae family. Leveraging both long and short read sequencing technologies, i.e., Oxford Nanopore and Illumina sequencing, we successfully assembled a mitogenome spanning 16.494 Kb and a first haploid genome encompassing 498 Mb. The assembled genome accounted for a 99.6% of the estimated genome size and was organized into 164 contigs with an N50 of 7.2 Mb. This genome assembly showed a GC content of 42.9% and a high Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness score of 99.5% using actinopterygii_odb10 lineage, thereby meeting stringent quality standards. In addition to its structural aspects, our study also examined the functional genomics of this species, including the intricate capacity to biosynthesize long-chain polyunsaturated fatty acids (LC-PUFAs) and secrete venom. Notably, our analyses revealed various repeats elements, which collectively constituted 17.43% of the genome. Moreover, annotation of 28,351 genes uncovered both shared genetic signatures and those that are unique to <i>S. fuscescens</i>. Our assembled genome also displayed a moderate prevalence of gene duplication compared to other fish species, which suggests that this species has a distinctive evolutionary trajectory and potentially unique functional constraints. Taken altogether, this genomic resource establishes a robust foundation for future research on the biology, evolution, and the aquaculture potential of <i>S. fuscescens</i>.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141292992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}