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The micronuclear histone H3 clipping in the unicellular eukaryote Tetrahymena thermophila. 单细胞真核生物嗜热四膜虫的微核组蛋白H3剪切。
IF 5.8 2区 生物学
Marine Life Science & Technology Pub Date : 2022-11-24 eCollection Date: 2022-11-01 DOI: 10.1007/s42995-022-00151-0
Fan Wei, Bo Pan, Jinghan Diao, Yuanyuan Wang, Yalan Sheng, Shan Gao
{"title":"The micronuclear histone H3 clipping in the unicellular eukaryote <i>Tetrahymena thermophila</i>.","authors":"Fan Wei, Bo Pan, Jinghan Diao, Yuanyuan Wang, Yalan Sheng, Shan Gao","doi":"10.1007/s42995-022-00151-0","DOIUrl":"10.1007/s42995-022-00151-0","url":null,"abstract":"<p><p>Clipping of the histone H3 N-terminal tail has been implicated in multiple fundamental biological processes for a growing list of eukaryotes. H3 clipping, serving as an irreversible process to permanently remove some post-translational modifications (PTMs), may lead to noticeable changes in chromatin dynamics or gene expression. The eukaryotic model organism <i>Tetrahymena thermophila</i> is among the first few eukaryotes that exhibits H3 clipping activity, wherein the first six amino acids of H3 are cleaved off during vegetative growth. Clipping only occurs in the transcriptionally silent micronucleus of the binucleated <i>T. thermophila</i>, thus offering a unique opportunity to reveal the role of H3 clipping in epigenetic regulation. However, the physiological functions of the truncated H3 and its protease(s) for clipping remain elusive. Here, we review the major findings of H3 clipping in <i>T. thermophila</i> and highlight its association with histone modifications and cell cycle regulation. We also summarize the functions and mechanisms of H3 clipping in other eukaryotes, focusing on the high diversity in terms of protease families and cleavage sites. Finally, we predict several protease candidates in <i>T. thermophila</i> and provide insights for future studies.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00151-0.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 4","pages":"584-594"},"PeriodicalIF":5.8,"publicationDate":"2022-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9378198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ultrastructure of Diophrys appendiculata and new systematic consideration of the euplotid family Uronychiidae (Protista, Ciliophora). 尾棘棘龙的超微结构及整倍体棘龙科(原生目,纤毛虫目)的系统新认识。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2022-11-24 eCollection Date: 2022-11-01 DOI: 10.1007/s42995-022-00153-y
Jingyi Dong, Yujie Liu, Jiyang Ma, Honggang Ma, Thorsten Stoeck, Xinpeng Fan
{"title":"Ultrastructure of <i>Diophrys appendiculata</i> and new systematic consideration of the euplotid family Uronychiidae (Protista, Ciliophora).","authors":"Jingyi Dong, Yujie Liu, Jiyang Ma, Honggang Ma, Thorsten Stoeck, Xinpeng Fan","doi":"10.1007/s42995-022-00153-y","DOIUrl":"10.1007/s42995-022-00153-y","url":null,"abstract":"<p><p>The ultrastructure of ciliates carries important cytological, taxonomical, and evolutionary signals for these single-celled eukaryotic organisms. However, little ultrastructural data have been accumulated for most ciliate groups with systematic problems. In the present work, a well-known marine uronychiid, <i>Diophrys appendiculata</i>, was investigated using electron microscopy and a comparison with, and a discussion considering, phylogenetic analyses were made. The new findings primarily show that: (i) this species lacks the typical alveolar plate, bears cortical ampule-like extrusomes, and has microtubular triads in the dorsal pellicle, and thus exhibits some ultrastructural features in common with most of its previously studied congeners; (ii) each adoral membranelle before the level of frontal cirrus II/2 contains three rows of kinetosomes and each membranelle after the level of frontal cirrus II/2 contains four rows, which might be related with morphogenesis and could be considered as a distinctive character of <i>Diophrys</i>; (iii) some structural details of the buccal field, such as the extra-pellicular fibrils, pellicle, pharyngeal disks and microtubular sheet, were documented. In addition, based on the ultrastructural comparison of representatives, we discuss the differentiation between the subfamilies Diophryinae and Uronychiinae. A hypothetical systematic relationship of members in the order Euplotida based on a wide range of data is also provided.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 4","pages":"551-568"},"PeriodicalIF":5.7,"publicationDate":"2022-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
A practical reference for studying meiosis in the model ciliate Tetrahymena thermophila. 为研究模式纤毛虫嗜热四膜虫减数分裂提供实用参考。
IF 5.8 2区 生物学
Marine Life Science & Technology Pub Date : 2022-11-22 eCollection Date: 2022-11-01 DOI: 10.1007/s42995-022-00149-8
Miao Tian, Xia Cai, Yujie Liu, Mingmei Liucong, Rachel Howard-Till
{"title":"A practical reference for studying meiosis in the model ciliate <i>Tetrahymena thermophila</i>.","authors":"Miao Tian, Xia Cai, Yujie Liu, Mingmei Liucong, Rachel Howard-Till","doi":"10.1007/s42995-022-00149-8","DOIUrl":"10.1007/s42995-022-00149-8","url":null,"abstract":"<p><p>Meiosis is a critical cell division program that produces haploid gametes for sexual reproduction. Abnormalities in meiosis are often causes of infertility and birth defects (e.g., Down syndrome). Most organisms use a highly specialized zipper-like protein complex, the synaptonemal complex (SC), to guide and stabilize pairing of homologous chromosomes in meiosis. Although the SC is critical for meiosis in many eukaryotes, there are organisms that perform meiosis without a functional SC. However, such SC-less meiosis is poorly characterized. To understand the features of SC-less meiosis and its adaptive significance, the ciliated protozoan <i>Tetrahymena</i> was selected as a model. Meiosis research in <i>Tetrahymena</i> has revealed intriguing aspects of the regulatory programs utilized in its SC-less meiosis, yet additional efforts are needed for obtaining an in-depth comprehension of mechanisms that are associated with the absence of SC. Here, aiming at promoting a wider application of <i>Tetrahymena</i> for meiosis research, we introduce basic concepts and core techniques for studying meiosis in <i>Tetrahymena</i> and then suggest future directions for expanding the current <i>Tetrahymena</i> meiosis research toolbox. These methodologies could be adopted for dissecting meiosis in poorly characterized ciliates that might reveal novel features. Such data will hopefully provide insights into the function of the SC and the evolution of meiosis from a unique perspective.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00149-8.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 4","pages":"595-608"},"PeriodicalIF":5.8,"publicationDate":"2022-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9378203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Group-specific functional patterns of mitochondrion-related organelles shed light on their multiple transitions from mitochondria in ciliated protists. 线粒体相关细胞器的群体特异性功能模式揭示了纤毛原生生物线粒体的多重转变。
IF 5.8 2区 生物学
Marine Life Science & Technology Pub Date : 2022-11-21 eCollection Date: 2022-11-01 DOI: 10.1007/s42995-022-00147-w
Zhicheng Chen, Jia Li, Dayana E Salas-Leiva, Miaoying Chen, Shilong Chen, Senru Li, Yanyan Wu, Zhenzhen Yi
{"title":"Group-specific functional patterns of mitochondrion-related organelles shed light on their multiple transitions from mitochondria in ciliated protists.","authors":"Zhicheng Chen, Jia Li, Dayana E Salas-Leiva, Miaoying Chen, Shilong Chen, Senru Li, Yanyan Wu, Zhenzhen Yi","doi":"10.1007/s42995-022-00147-w","DOIUrl":"10.1007/s42995-022-00147-w","url":null,"abstract":"<p><p>Adaptations of ciliates to hypoxic environments have arisen independently several times. Studies on mitochondrion-related organelle (MRO) metabolisms from distinct anaerobic ciliate groups provide evidence for understanding the transitions from mitochondria to MROs within eukaryotes. To deepen our knowledge about the evolutionary patterns of ciliate anaerobiosis, mass-culture and single-cell transcriptomes of two anaerobic species, <i>Metopus laminarius</i> (class Armophorea) and <i>Plagiopyla</i> cf. <i>narasimhamurtii</i> (class Plagiopylea), were sequenced and their MRO metabolic maps were compared. In addition, we carried out comparisons using publicly available predicted MRO proteomes from other ciliate classes (i.e., Armophorea, Litostomatea, Muranotrichea, Oligohymenophorea, Parablepharismea and Plagiopylea). We found that single-cell transcriptomes were similarly comparable to their mass-culture counterparts in predicting MRO metabolic pathways of ciliates. The patterns of the components of the MRO metabolic pathways might be divergent among anaerobic ciliates, even among closely related species. Notably, our findings indicate the existence of group-specific functional relics of electron transport chains (ETCs). Detailed group-specific ETC functional patterns are as follows: full oxidative phosphorylation in Oligohymenophorea and Muranotrichea; only electron-transfer machinery in Armophorea; either of these functional types in Parablepharismea; and ETC functional absence in Litostomatea and Plagiopylea. These findings suggest that adaptation of ciliates to anaerobic conditions is group-specific and has occurred multiple times. Our results also show the potential and the limitations of detecting ciliate MRO proteins using single-cell transcriptomes and improve the understanding of the multiple transitions from mitochondria to MROs within ciliates.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00147-w.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 4","pages":"609-623"},"PeriodicalIF":5.8,"publicationDate":"2022-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9378199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ontogenesis and systematic position of a new hypotrichous ciliate, Chaetospira sinica sp. nov., with an improved diagnosis of the poorly defined family Chaetospiridae Jankowski, 1985 (Protozoa, Ciliophora, Hypotrichia). 一种新的次毛纤毛虫,中国毛螺旋体的个体发生和系统位置,以及对定义不明确的毛螺旋体科Jankowski的改进诊断,1985(原生动物,纤毛虫,次毛虫)。
IF 5.8 2区 生物学
Marine Life Science & Technology Pub Date : 2022-11-18 eCollection Date: 2022-11-01 DOI: 10.1007/s42995-022-00146-x
Wenya Song, Xiaotian Luo, Yong Chi, Saleh A Al-Farraj, Chen Shao
{"title":"Ontogenesis and systematic position of a new hypotrichous ciliate, <i>Chaetospira sinica</i> sp. nov., with an improved diagnosis of the poorly defined family Chaetospiridae Jankowski, 1985 (Protozoa, Ciliophora, Hypotrichia).","authors":"Wenya Song, Xiaotian Luo, Yong Chi, Saleh A Al-Farraj, Chen Shao","doi":"10.1007/s42995-022-00146-x","DOIUrl":"10.1007/s42995-022-00146-x","url":null,"abstract":"<p><p>Ciliates are unique single-celled organisms that play important roles in ecological, environmental, evolutionary, and ontogenetic research. In the present study, phylogenetic analyses based on 18S rRNA gene sequence data reveal that <i>Chaetospira sinica</i> sp. nov. clusters with <i>Stichotricha aculeata</i> with strong to full support (97% ML, 1.00 BI), but is not closely related to members of Spirofilidae Gelei, 1929 to which <i>Chaetospira</i> and <i>Stichotricha</i> have previously been assigned. Phylogenetic analyses, together with morphological and morphogenetic data from <i>Chaetospira sinica</i> sp. nov., support the validity of family Chaetospiridae Jankowski, 1985. <i>Chaetospira</i> and <i>Stichotricha</i> are here assigned to the family Chaetospiridae, the improved diagnosis of which is as follows: non-dorsomarginalian Hypotrichia with flask-shaped body; oral region extending along narrow anterior neck region; lorica usually present; two ventral and two marginal cirral rows, all distinctly spiraled or obliquely curved; pretransverse and transverse cirri absent. The basic morphogenetic features in <i>C. sinica</i> sp. nov. can be summarized as: (1) the oral primordium for the opisthe develops de novo and the parental adoral zone is completely retained by the proter; (2) all ventral cirral anlagen and marginal anlagen developed intrakinetally; (3) three dorsal kineties anlagen formed intrakinetally in each daughter cell; and (4) macronuclear nodules fuse into a single mass. Exconjugant cells were also isolated and their morphologic and molecular data are provided.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 4","pages":"513-526"},"PeriodicalIF":5.8,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mapping the potential for offshore aquaculture of salmonids in the Yellow Sea. 绘制黄海鲑鱼近海养殖潜力图。
IF 5.8 2区 生物学
Marine Life Science & Technology Pub Date : 2022-08-18 eCollection Date: 2022-08-01 DOI: 10.1007/s42995-022-00141-2
Shuang-En Yu, Shuang-Lin Dong, Zhi-Xin Zhang, Yu-Yang Zhang, Gianluca Sarà, Jie Wang, Yun-Wei Dong
{"title":"Mapping the potential for offshore aquaculture of salmonids in the Yellow Sea.","authors":"Shuang-En Yu, Shuang-Lin Dong, Zhi-Xin Zhang, Yu-Yang Zhang, Gianluca Sarà, Jie Wang, Yun-Wei Dong","doi":"10.1007/s42995-022-00141-2","DOIUrl":"10.1007/s42995-022-00141-2","url":null,"abstract":"<p><p>Mariculture has been one of the fastest-growing global food production sectors over the past three decades. With the congestion of space and deterioration of the environment in coastal regions, offshore aquaculture has gained increasing attention. Atlantic salmon (<i>Salmo salar</i>) and rainbow trout (<i>Oncorhynchus mykiss</i>) are two important aquaculture species and contribute to 6.1% of world aquaculture production of finfish. In the present study, we established species distribution models (SDMs) to identify the potential areas for offshore aquaculture of these two cold-water fish species considering the mesoscale spatio-temporal thermal heterogeneity of the Yellow Sea. The values of the area under the curve (AUC) and the true skill statistic (TSS) showed good model performance. The suitability index (SI), which was used in this study to quantitatively assess potential offshore aquaculture sites, was highly dynamic at the surface water layer. However, high SI values occurred throughout the year at deeper water layers. The potential aquaculture areas for <i>S. salar</i> and <i>O. mykiss</i> in the Yellow Sea were estimated as 52,270 ± 3275 (95% confidence interval, CI) and 146,831 ± 15,023 km<sup>2</sup>, respectively. Our results highlighted the use of SDMs in identifying potential aquaculture areas based on environmental variables. Considering the thermal heterogeneity of the environment, this study suggested that offshore aquaculture for Atlantic salmon and rainbow trout was feasible in the Yellow Sea by adopting new technologies (e.g., sinking cages into deep water) to avoid damage from high temperatures in summer.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00141-2.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 3","pages":"329-342"},"PeriodicalIF":5.8,"publicationDate":"2022-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metabolic strategy of macrophages under homeostasis or immune stress in Drosophila. 果蝇在平衡或免疫压力下的巨噬细胞代谢策略
IF 5.8 2区 生物学
Marine Life Science & Technology Pub Date : 2022-08-16 eCollection Date: 2022-08-01 DOI: 10.1007/s42995-022-00134-1
Wang Luo, Sumin Liu, Fang Zhang, Long Zhao, Ying Su
{"title":"Metabolic strategy of macrophages under homeostasis or immune stress in <i>Drosophila</i>.","authors":"Wang Luo, Sumin Liu, Fang Zhang, Long Zhao, Ying Su","doi":"10.1007/s42995-022-00134-1","DOIUrl":"10.1007/s42995-022-00134-1","url":null,"abstract":"<p><p>Macrophages are well known for their phagocytic functions in innate immunity across species. In mammals, they rapidly consume a large amount of energy by shifting their metabolism from mitochondrial oxidative phosphorylation toward aerobic glycolysis, to perform the effective bactericidal function upon infection. Meanwhile, they strive for sufficient energy resources by restricting systemic metabolism. In contrast, under nutrient deprivation, the macrophage population is down-regulated to save energy for survival. <i>Drosophila melanogaster</i> possesses a highly conserved and comparatively simple innate immune system. Intriguingly, recent studies have shown that <i>Drosophila</i> plasmatocytes, the macrophage-like blood cells, adopt comparable metabolic remodeling and signaling pathways to achieve energy reassignment when challenged by pathogens, indicating the conservation of such metabolic strategies between insects and mammals. Here, focusing on <i>Drosophila</i> macrophages (plasmatocytes), we review recent advances regarding their comprehensive roles in local or systemic metabolism under homeostasis or stress, emphasizing macrophages as critical players in the crosstalk between the immune system and organic metabolism from a <i>Drosophila</i> perspective.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 3","pages":"291-302"},"PeriodicalIF":5.8,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10298670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Making comparable measurements of bacterial respiration and production in the subtropical coastal waters. 在亚热带沿海水域进行细菌呼吸和生产的可比测量。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2022-08-01 DOI: 10.1007/s42995-022-00133-2
Cui Guo, Ying Ke, Bingzhang Chen, Shuwen Zhang, Hongbin Liu
{"title":"Making comparable measurements of bacterial respiration and production in the subtropical coastal waters.","authors":"Cui Guo,&nbsp;Ying Ke,&nbsp;Bingzhang Chen,&nbsp;Shuwen Zhang,&nbsp;Hongbin Liu","doi":"10.1007/s42995-022-00133-2","DOIUrl":"https://doi.org/10.1007/s42995-022-00133-2","url":null,"abstract":"<p><p>Accurate estimates of bacterial carbon metabolic rates are indispensable for understanding the regulation of carbon fluxes in aquatic environments. Here, changes in bacterial growth, production, and cell volume in both pre-filtered and unfiltered seawater during 24 h incubation were monitored. The methodological artifacts during Winkler bacterial respiration (BR) measurements in subtropical Hong Kong coastal waters were assessed. Bacterial abundance increased by 3- and 1.8-fold in the pre-filtered and unfiltered seawater after incubation, respectively. Bacterial production (BP) and cell volume also showed significant enhancement. Compared with the BR measurements obtained by the Winkler method, the instantaneous free-living BR measurements, after correction, decreased by ~ 70%. The time-integrated free-living BR and BP during 24 h incubation in the pre-filtered sample provided an improved estimate of bacterial growth efficiency, which increased by ~ 52% compared to the common estimations using the noncomparable measurements of integrated free-living BR and instantaneous total BP. The overestimation of BR also exaggerated the contribution of bacteria to community respiration, affecting the understanding on the metabolic state of the marine ecosystems. Furthermore, the BR estimates by the Winkler method may be more biased in environments with a higher bacterial growth rate and tightly coupled grazing mortality, as well as in those with higher nutrient concentrations. These results reveal obvious problems associated with the BR methodology and raise a warning for caution when comparing BP and BR, as well as when making estimations of carbon flow through the complex microbial networks in aquatic ecosystems.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00133-2.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 3","pages":"414-427"},"PeriodicalIF":5.7,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, Apostichopus japonicus. Apostichopus japonicus海参乳头数量候选基因精细定位及关联分析。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2022-08-01 DOI: 10.1007/s42995-022-00139-w
Xinghai Zhu, Ping Ni, Marc Sturrock, Yangfan Wang, Jun Ding, Yaqing Chang, Jingjie Hu, Zhenmin Bao
{"title":"Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, <i>Apostichopus japonicus</i>.","authors":"Xinghai Zhu,&nbsp;Ping Ni,&nbsp;Marc Sturrock,&nbsp;Yangfan Wang,&nbsp;Jun Ding,&nbsp;Yaqing Chang,&nbsp;Jingjie Hu,&nbsp;Zhenmin Bao","doi":"10.1007/s42995-022-00139-w","DOIUrl":"https://doi.org/10.1007/s42995-022-00139-w","url":null,"abstract":"<p><p>The papilla number is one of the most economically important traits of sea cucumber in the China marketing trade. However, the genetic basis for papilla number diversity in holothurians is still scarce. In the present study, we conducted genome-wide association studies (GWAS) for the trait papilla number of sea cucumbers utilizing a set of 400,186 high-quality SNPs derived from 200 sea cucumbers. Two significant trait-associated SNPs that passed Bonferroni correction (<i>P</i> < 1.25E-7) were located in the intergenic region near <i>PATS1</i> and the genic region of <i>EIF4G</i>, which were reported to play a pivotal role in cell growth and proliferation. The fine-mapping regions around the top two lead SNPs provided precise causative loci/genes related to papilla formation and cellular activity, including <i>PPP2R3C</i>, <i>GBP1</i>, and <i>BCAS3</i>. Potential SNPs with <i>P</i> < 1E-4 were acquired for the following GO and KEGG enrichment analysis. Moreover, the two lead SNPs were verified in another population of sea cucumber, and the expressive detection of three potential candidate genes <i>PATS1</i>, <i>PPP2R3C</i>, and <i>EIF4G</i> that near or cover the two lead SNPs was conducted in papilla tissue of TG (Top papilla number group) and BG (Bottom papilla number group) by qRT-PCR. We found the significantly higher expression profile of <i>PATS1</i> (3.34-fold), <i>PPP2R3C</i> (4.90-fold), and <i>EIF4G</i> (4.23-fold) in TG, implying their potential function in papilla polymorphism. The present results provide valuable information to decipher the phenotype differences of the papilla trait and will provide a scientific basis for selective breeding in sea cucumbers.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-022-00139-w.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"4 3","pages":"343-355"},"PeriodicalIF":5.7,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10077181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9440208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Timing and characteristics of nuclear events during conjugation and genomic exclusion in Paramecium multimicronucleatum. 多微核草履虫偶联和基因组排除过程中核事件的时间和特征。
IF 5.7 2区 生物学
Marine Life Science & Technology Pub Date : 2022-08-01 DOI: 10.1007/s42995-022-00137-y
Xue Zhang, Xiaoteng Lu, Yong Chi, Yaohan Jiang, Chundi Wang, Saleh A Al-Farraj, Adriana Vallesi, Feng Gao
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引用次数: 11
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