Marine Biotechnology最新文献

{"title":"Regulatory Genes in Eyespot Formation and Function of Mytilus coruscus","authors":"Minhui Xu,&nbsp;Jiji Li,&nbsp;Hongfei Li,&nbsp;Pengzhi Qi,&nbsp;Yingying Ye,&nbsp;Xiaojun Yan","doi":"10.1007/s10126-024-10396-8","DOIUrl":"10.1007/s10126-024-10396-8","url":null,"abstract":"<div><p>Light sensitivity is important for marine benthic invertebrates, and it plays a vital role in the marine bivalves settling. Animal visual systems are enormously diverse; their development appears to be controlled by a set of conserved retinal determination genes (RDGs). Eyespots, as the simplest animal eyes, their appearance indicates the important effect on mussel larvae attachment. Nevertheless, the molecular mechanism of the eyespot’s development in <i>Mytilus coruscus</i> larvae is not clear. In this study, we identified 11 genes which play a regulatory role in the visual system (i.e. <i>Pax1/9</i>, <i>Pax2/5/8</i>, <i>Pax6</i>, <i>Pax3/7</i>, <i>Six1/2, Six3/6</i>, <i>Six4/5</i>, <i>Dach</i>, <i>Eya</i>, <i>Brn</i> and <i>Tbx2</i>) from transcriptome data and the whole genome sequence of <i>M. coruscus</i>. The results of chromosome localization showed that 11 genes were distributed on different chromosomes. Subcellular mapping revealed that all the proteins except <i>Brn</i> were located in the nucleus. Phylogeny and gene structure analyses revealed that the <i>Pax</i> members were divided into four subfamilies, the <i>Six</i> members were divided into three subfamilies and structures within the same subfamily were relatively conserved. Quantitative real-time PCR (qPCR) showed that <i>Dach</i>, <i>Pax6</i>, <i>Pax3/7</i>, <i>Six1/2</i> and <i>Six4/5</i> were expressed at high levels during the pediveliger stage. Moreover, <i>Six1/2</i> and <i>Six4/5</i> were highly expressed in mantle tissues. Subsequent overall in situ hybridization experiments in the planktonic larval stage revealed that <i>Pax6</i>, <i>Six1/2</i> and <i>Six4/5</i> detected signals in the region of the eyespot. Based on these analyses, we suggested that the development of vision in <i>M. coruscus</i> not only depended on the expression pattern of <i>Pax6</i>, but perhaps also related to <i>Six1/2</i> and <i>Six4/5</i> in the planktonic larval stage, while <i>Six1/2</i> and <i>Six4/5</i> were the dominant genes for visual function in the adult mussel. This study made a comprehensive analysis of the visual function of <i>M. coruscus</i> at the genome level, which helps us to understand the intrinsic mechanism of the visual system of marine bivalves, and also provides a molecular basis for improving the attachment and metamorphosis rate of <i>M. coruscus</i> larvae.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724593","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":"A Zinc Uptake Transporter ZIP1-II Is Involved in Zinc Accumulation in the Hepatopancreas of Pacific Oyster Crassostrea gigas","authors":"Ning Kong,&nbsp;Cong Luo,&nbsp;Mengjia Wang,&nbsp;Junyan Zhao,&nbsp;Xiang Li,&nbsp;Lingling Wang,&nbsp;Linsheng Song","doi":"10.1007/s10126-024-10379-9","DOIUrl":"10.1007/s10126-024-10379-9","url":null,"abstract":"<div><p>The Pacific oyster <i>Crassostrea gigas</i> is known to have an exceptional ability to accumulate zinc, which endows it with robust resistance to pathogens and makes it an excellent source of dietary zinc. ZIP1 has been identified as an important zinc uptake protein in other species, but its role in oysters remains unclear. In the present study, a ZIP1 homologue (<i>Cg</i>ZIP1-II) of the Zrt/Irt-like protein (ZIP) family was identified in <i>C</i>. <i>gigas</i>. The mRNA transcripts of <i>Cg</i>ZIP1-II were constitutively expressed in examined tissues of <i>C. gigas</i>, with higher levels in the hepatopancreas and gill. After zinc exposure, the mRNA transcripts of <i>Cg</i>ZIP1-II in the hepatopancreas showed a significant decline from 12 h to 14 d, while those in the gill significantly decreased at 72 h, followed by a recovery to basal level at 7 to 14 d. Immunocytochemical analysis revealed that the <i>Cg</i>ZIP1-II protein was mainly located at the plasma membrane of oyster hemocytes. Compared to the control cells, overexpression of <i>Cg</i>ZIP1-II in the transfected HEK293 cells resulted in a 2.44-fold (<i>p</i> &lt; 0.05) increase in zinc content after incubation with 100 μM zinc for 24 h. Inhibition of endogenous <i>Cg</i>ZIP1-II expression with siRNAs led to a 42% reduction in zinc content in the hepatopancreas of oysters. Similarly, in vivo blocking of <i>Cg</i>ZIP1-II with anti-<i>Cg</i>ZIP1-II antibody caused a 43% decrease in zinc content in the hepatopancreas. These results collectively indicated that <i>Cg</i>ZIP1-II functioned as a zinc uptake transporter in <i>C. gigas</i> and played a certain role in zinc accumulation.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724591","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":"Identification of Key Genes Correlated with Economic Trait Superiorities and Their SNP Screening Through Transcriptome Comparisons, WGCNA and Pearson Correlation Coefficient in the Sea Cucumber Apostichopus Japonicus","authors":"Jingxian Sun,&nbsp;Haolin Wang,&nbsp;Yaoyao Zhan,&nbsp;Tanjun Zhao,&nbsp;Chengda Li,&nbsp;Cao Cheng,&nbsp;Zengdong Wang,&nbsp;Ange Zou,&nbsp;Yaqing Chang","doi":"10.1007/s10126-024-10384-y","DOIUrl":"10.1007/s10126-024-10384-y","url":null,"abstract":"<div><p>Variation in morphology-driven economic traits is a common issue hindering the development of the sea cucumber aquaculture industry. In this study, transcriptome comparisons, weighted gene correlation network analysis (WGCNA) and Pearson correlation coefficient (PCC) were first employed to identify key genes correlated with morphological variation in the sea cucumber <i>Apostichopus japonicus</i>, after which the relationship between identified key genes (relative expression and genotype) and economic trait phenotypes was investigated to screen potential biomarker targets for molecular-assisted breeding. The results showed that three genes (<i>putative ficolin–2</i>,<i> fibrinogen c domain–containing protein 1</i>, and <i>angiopoietin–4</i>) were closely associated with economic trait superiorities. Two single nucleotide polymorphisms (SNPs) were identified in the <i>putative ficolin–2</i> gene as having a strong correlation with body weight and papilla number. The findings from this study will enrich breeding biomarker resources and benefit the development of molecular-assisted breeding techniques in sea cucumber aquaculture.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724592","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":"Long-Read Sequencing Revealing the Effectiveness of Captive Breeding Strategy for Improving the Gut Microbiota of Spotted Seal (Phoca largha)","authors":"Jing Du,&nbsp;Zhen Wang,&nbsp;Yankuo Xing,&nbsp;Xianggang Gao,&nbsp;Zhichuang Lu,&nbsp;Duohui Li,&nbsp;Jiashen Tian","doi":"10.1007/s10126-024-10397-7","DOIUrl":"10.1007/s10126-024-10397-7","url":null,"abstract":"<div><p>The spotted seal (<i>Phoca largha</i>) is the sole pinniped species that can reproduce in China and has been classified as the First-Grade State Protection animal. The conventional method for the protection and maintenance of the spotted seal population is the captive maintenance of the species in artificially controlled environments. Nevertheless, the efficacy of the captive strategy remains uncertain, with the potential to impact the health of spotted seals through alterations in gut microbiota. In this study, PacBio sequencing based on the full-length of the bacterial 16S rRNA gene was applied to faeces from captive and wild spotted seals, thereby providing a first reference for the gut microbiota profile of spotted seals at the species scale. The gut microbiota of captive spotted seals was found to be more diverse than that of the wild population. The gut microbiota of spotted seals exhibited notable variation due to captive breeding, with an enrichment of Firmicutes and a reduction in Proteobacteria. The results of the co-occurrence network analysis indicated that the gut microbiota of captive spotted seals exhibited a greater degree of complexity and stability in comparison to that observed in their wild counterparts. The analysis of community assembly mechanisms revealed an increased determinism for the gut microbiota of captive individuals, with a concomitant decrease in the contribution of drift. Furthermore, the results of the predicted functions indicated a reduction in stress responses and an enhanced ability to metabolise sugars in the gut microbiota of captive spotted seals. In conclusion, the results of this study provide evidence that the current captive breeding strategy is an effective approach for improving the gut microbiota of spotted seals. Furthermore, this study demonstrates the potential of monitoring the gut microbiota to assess the health of marine mammals and inform conservation strategies for endangered species.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714189","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":"SNP Fingerprinting for Germplasm Identification of the Fast-Growing Pacific oyster (Crassostrea gigas) “Haida No. 1” Variety","authors":"Zihao Zhang,&nbsp;Ben Yang,&nbsp;Liting Ren,&nbsp;Qi Li,&nbsp;Shikai Liu","doi":"10.1007/s10126-024-10392-y","DOIUrl":"10.1007/s10126-024-10392-y","url":null,"abstract":"<div><p>The Pacific oyster (<i>Crassostrea gigas</i>) is a global aquaculture species of economic significance. Selective breeding programs have been conducted to produce multiple strains with fast growth as well as other desirable traits. However, due to the phenotypic plasticity of oysters, challenges existed for precise germplasm identification among selectively bred strains. In this work, we identified selection signatures of three fast-growing Pacific oyster strains originated from wild populations collected from China, Japan, and Korea, respectively, which were used for development of SNP-based molecular fingerprinting for precise identification of germplasm. We performed whole-genome resequencing of 59 oysters from three selectively bred strains and a wild population for genome-wide SNP analyses. Population structure analysis with these SNPs revealed significant genetic differentiation among the selectively bred strains. Based on the <i>F</i>_ST index, we identified 41, 49, and 36 strain-specific SNPs from the three selectively bred strains. Taking into account the “hitch-hiking effect” that occurs in the genome during positive selection, we identified two, three, and two molecular fingerprints for the three strains, respectively. We validated the molecular fingerprints of the China selectively bred strain (i.e., “Haida No. 1” variety) with a separate population of 42 oysters with diverse genetic background, demonstrating the accuracy of germplasm identification of over 96%. This work provides a reliable tool for precise germplasm identification of the \"Haida No. 1\" variety as well as other two selectively bred strains, which is valuable in germplasm conservation and breeding design in the <i>C. gigas</i>.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714188","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":"An Improved RNA Extraction Method for Octocorals and Its Application in Transcriptome Analysis of Dark-Induced Bleaching Octocoral","authors":"Jing-Wen Michelle Wong,&nbsp;An-Chi Liu,&nbsp;Hsuan-Tung Lin,&nbsp;Chuya Shinzato,&nbsp;Sung-Yin Yang,&nbsp;Shan-Hua Yang","doi":"10.1007/s10126-024-10391-z","DOIUrl":"10.1007/s10126-024-10391-z","url":null,"abstract":"<div><p>Octocorals, vital components of reef ecosystems, inhabit various marine environments across diverse climate zones, spanning from tropical shallows to frigid deep-sea regions. Certain octocoral species, notably <i>Lobophytum</i> and <i>Sinularia</i>, are particularly intriguing due to their production of diverse metabolites, warranting continuous investigation. Although octocorals played the roles in coral ecosystems, the studies are rare in comparison to scleractinian corals, especially in transcriptomic and genomic data. However, RNA extraction was massively interfered by the polysaccharides and secondary metabolites produced from octocoral holobiont. For this purpose, five lysis buffer systems and two extraction processes were examined for the RNA extraction efficiency in octocorals. We found CTAB/10%SDS as a new method for RNA extraction from six different octocoral genera. Furthermore, our new method is enable to extract RNA with good quality for downstream application such as quantitative PCR and RNA sequencing. Finally, comparative transcriptomic analysis between healthy octocorals and those dark-induced bleaching corals in <i>Lobophytum hsiehi</i> revealed extracellular matrix and immunity-related genes may play the important roles in coral-symbiodinium symbiosis. We believe that this study’s findings and the developed RNA extraction method will serve as valuable references for future research, particularly in octocorals.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714187","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":"Analysis of Gut Microbiota Associated with WSSV Resistance in Litopenaeus vannamei","authors":"Warapond Wanna,&nbsp;Chitchanok Aucharean,&nbsp;Nittaya Jaeram","doi":"10.1007/s10126-024-10381-1","DOIUrl":"10.1007/s10126-024-10381-1","url":null,"abstract":"<div><p>Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families <i>Rhodobacteraceae</i> and <i>Flavobacteriaceae</i>, and the genus <i>Nautella</i>, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714569","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":"Hydin as the Candidate Master Sex Determination Gene in Channel Catfish (Ictalurus punctatus) and Its Epigenetic Regulation","authors":"Zhanjiang Liu,&nbsp;Dongya Gao","doi":"10.1007/s10126-024-10387-9","DOIUrl":"10.1007/s10126-024-10387-9","url":null,"abstract":"<div><p>Sex determination is a fascinating area of research. To date, more than 20 master sex determination (SD) genes have been reported from vertebrate animals. With channel catfish (<i>Ictalurus punctatus</i>), much work has been conducted to determine its master SD gene, ranging from genetic linkage mapping, genome-wide association (GWA) analysis, genome sequencing, comparative genome analysis, epigenomic analysis, transcriptome analysis, and functional studies. Here in this mini review, we provide positional, expression, regulatory, and functional evidence supporting hydin (hydrocephalus-inducing protein or HYDIN axonemal central pair apparatus protein-like) as a master SD gene in channel catfish. Hydin is located within the sex determination region (SDR) within a mapped 8.9-Mb non-recombinational segment on chromosome 4 of channel catfish. It is highly expressed in genetic males, but not in genetic females. The alleles of X and Y are highly differentially methylated with the X chromosome being hypermethylated and the Y chromosome hypomethylated. The hypomethylated Y allele of hydin is expressed while the hypermethylated X allele is not expressed. Such allelic expression fits well with the XY sex determination system of channel catfish. Functional analysis using a methylation blocker, 5-aza-dC, demonstrated that demethylation, especially within the SDR, is accompanied with increased expression of hydin, which led to sex reversal of genetic females into phenotypic males. These evidences support the candidacy of hydin as a master SD gene in channel catfish. Future knockout and analysis of affected genes after hydin knockout should provide insights into how hydin functions as a master SD gene.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142691848","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":"Histone Modifications in the Anoxic Northern Crayfish, Faxonius virilis","authors":"Imane Rhzali,&nbsp;Kenneth B. Storey","doi":"10.1007/s10126-024-10394-w","DOIUrl":"10.1007/s10126-024-10394-w","url":null,"abstract":"<div><p>Northern Crayfish, <i>Faxonius virilis</i>, displays various strategies that allow them to survive extended periods of oxygen deprivation. However, certain epigenetic adaptations that these crayfish use have not been studied in detail, and the role of specific mechanisms used such as histone modifications remain unknown. Epigenetic studies offer a new perspective on how crayfish can regulate gene expression to redirect energy to essential functions needed for survival. This study investigates the regulation of histone modifications of proteins including acetylation and deacetylation in <i>F. virilis</i> in response to 20-h anoxia exposure. These histone modifications were studied via analysis of writer, reader, and eraser proteins such as lysine acetyltransferases (KATs), bromodomain proteins (BRDs), histone deacetylases (HDAC), and sirtuin proteins (SIRTs). Significant upregulation was seen in one histone protein and one lysine acetyltransferase: H3K14Ac and KAT2A. These proteins are known to be regulated by BRD2; a protein that specifically reads and targets H3K14Ac. In response to anoxia, a larger number of histone deacetylases and sirtuin proteins were upregulated in comparison to lysine acetyltransferases suggesting a focus on suppression of gene expression. The histone deacetylases and sirtuin proteins with significant upregulation were HDAC2, HDAC3, SIRT2, SIRT3, and SIRT6. These proteins have also all been implicated in DNA damage regulation which further suggests that crayfish focus limited energy on ensuring cell survival. This study provides an understanding of how histone acetylation and deacetylation are regulated in crayfish as a component of metabolic rate suppression under anoxia.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142679841","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":"Correlation Between Effector Gene Expression Targeted by lncRNAs in the Oomycete Fish Pathogen, Saprolegnia parasitica","authors":"Lijuan Liao,&nbsp;Zihao Zhao,&nbsp;Ruoxiao Zhang,&nbsp;Chaoqun Luo,&nbsp;Yibo Hu,&nbsp;Ziquan Yu,&nbsp;Jun Cui","doi":"10.1007/s10126-024-10385-x","DOIUrl":"10.1007/s10126-024-10385-x","url":null,"abstract":"<div><p>Saprolegniasis caused by <i>Saprolegnia parasitica</i> leads to significant economic losses in the aquaculture industry worldwide. Effector proteins secreted by pathogens are key molecules involved in their pathogenicity and long non-coding lncRNAs (lncRNAs) act as regulators in these processes. However, little is known about the lncRNAs and effector proteins in <i>S. parasitica</i>. Here, we first identified 1027 lncRNAs during the developmental stages and infection process of <i>S. parasitica</i>. Compared with mRNAs, these lncRNAs had shorter sequences and exon lengths and lower expression levels. In addition, their sequence conservation among other oomycete species was also low. The <i>S. parasitica</i> lncRNAs were characterized according to developmental stage and infection time point. We also identified effector proteins using a computational pipeline. In total, 131 <i>S. parasitica</i> effector proteins were identified and classified into 34 families. The 47 genes encoding effector genes were neighbors of 39 lncRNAs, and there was a correlation between the transcription level of lncRNAs and their neighboring genes. Gain- and loss-of-function experiments revealed that lncRNA8375.2 promoted the expression of a neighboring effector gene, <i>SpCAP</i>. Our results provide new data on <i>S. parasitica</i> lncRNAs and effector proteins, and provide insights into the lncRNA-effector module involved in <i>S. parasitica</i>.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142679840","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}