Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-028
A. Car, D. Hafner, S. Ljubimir, I. D. Radić, Svjetlana Bobanović-Ćolić, N. Jasprica
The initial colonization of bacteria and diatoms on a immersed artificial substrate and the development of diatom assemblages in relation to physico-chemical parameters were investigated on a weekly basis at one station in the marine Lake Mrtvo More, South Croatia, from April to October 2016. According to TRIX trophic index, lake showed different trophic character: (i) oligotrophic (at the beginning and the end of the study), (ii) mesotrophic (the end of June to mid-July), (iii) eutrophic (the end of July to mid-September). Heterotrophic bacteria increased to peak abundances (69,268 cells cm–2) at the beginning of June when the diatoms abundances start to increase. The lake has high diatom species richness (285 diatom taxa within 72 genera), with the highest species diversity index in August. Among diatoms, adnate were the primary colonizers, particularly Cocconeis dirupta W.Gregory var. flexella (Janisch and Rabenhorst) Grunow and Cocconeis scutellum Ehrenberg var. scutellum, while motile taxa joined the fouling communities from July to September. This study showed close relationship between diatom species composition and changes of physico-chemical parameters, particularly the nutrient concentrations.
2016年4月至10月，在克罗地亚南部Mrtvo More海洋湖的一个站点，每周调查一次浸入式人工基质上细菌和硅藻的初始定植以及硅藻组合的发展与理化参数的关系。根据TRIX营养指数，湖泊呈现出不同的营养特征:(i)贫营养(研究开始和结束时)，(ii)中营养(6月底至7月中旬)，(iii)富营养(7月底至9月中旬)。6月初，硅藻丰度开始增加，异养细菌丰度达到峰值(69268个细胞cm-2)。该湖硅藻物种丰富度较高，共有72属285个硅藻类群，物种多样性指数在8月份最高。在硅藻中，adate是主要的侵染者，特别是Cocconeis dirupta W.Gregory var. flexella (Janisch and Rabenhorst) Grunow和Cocconeis scutellum Ehrenberg var. scutellum，而活动类则在7 - 9月加入污染群落。研究表明，硅藻的种类组成与理化参数的变化，特别是营养物浓度的变化密切相关。
{"title":"Colonization of bacteria and diatoms on an artificial substrate in a marine lake (eastern Adriatic Sea, NE Mediterranean)","authors":"A. Car, D. Hafner, S. Ljubimir, I. D. Radić, Svjetlana Bobanović-Ćolić, N. Jasprica","doi":"10.37427/botcro-2020-028","DOIUrl":"https://doi.org/10.37427/botcro-2020-028","url":null,"abstract":"The initial colonization of bacteria and diatoms on a immersed artificial substrate and the development of diatom assemblages in relation to physico-chemical parameters were investigated on a weekly basis at one station in the marine Lake Mrtvo More, South Croatia, from April to October 2016. According to TRIX trophic index, lake showed different trophic character: (i) oligotrophic (at the beginning and the end of the study), (ii) mesotrophic (the end of June to mid-July), (iii) eutrophic (the end of July to mid-September). Heterotrophic bacteria increased to peak abundances (69,268 cells cm–2) at the beginning of June when the diatoms abundances start to increase. The lake has high diatom species richness (285 diatom taxa within 72 genera), with the highest species diversity index in August. Among diatoms, adnate were the primary colonizers, particularly Cocconeis dirupta W.Gregory var. flexella (Janisch and Rabenhorst) Grunow and Cocconeis scutellum Ehrenberg var. scutellum, while motile taxa joined the fouling communities from July to September. This study showed close relationship between diatom species composition and changes of physico-chemical parameters, particularly the nutrient concentrations.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"212-227"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46418252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-030
Xhavit Mala, Qenan Maxhuni
This paper reports Sternbergia colchiciflora Waldst. et Kit. as a new genus and species for the flora of Kosovo. Almost 30 adult individuals of this species were recorded for the first time in southwestern Kosovo during 2015, within the Canyon of the White Drin at Fshajt Bridge. Considering the low number of individuals and very limited distribution, this species should be treated as a critically endangered taxon in Kosovo.
{"title":"Sternbergia colchiciflora Waldst. et Kit. (Amaryllidaceae), a new genus and species in the flora of Kosovo","authors":"Xhavit Mala, Qenan Maxhuni","doi":"10.37427/botcro-2020-030","DOIUrl":"https://doi.org/10.37427/botcro-2020-030","url":null,"abstract":"This paper reports Sternbergia colchiciflora Waldst. et Kit. as a new genus and species for the flora of Kosovo. Almost 30 adult individuals of this species were recorded for the first time in southwestern Kosovo during 2015, within the Canyon of the White Drin at Fshajt Bridge. Considering the low number of individuals and very limited distribution, this species should be treated as a critically endangered taxon in Kosovo.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"236-238"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-030","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46599478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-025
Vahideh Kardavan Ghabel, R. Karamian
Licorice (Glycyrrhiza glabra L.) is known as an important medicinal plant throughout the world. Glycyrrhizin is one of the most important specialized metabolites produced by licorice. In order to study the effect of TiO2 nanoparticles (TiO2 NPs) and spermine on physiological and biochemical traits of licorice under cold stress conditions, a factorial experiment was conducted in a completely randomized design with three replications. Plants were exposed to optimum temperature (26 oC) as control and low temperature (4 oC) as cold stress conditions and also treated with TiO2 NPs (2 and 5 ppm) and spermine (1 mM), separately. Results from physiological and biochemical analyses of the aerial parts of licorice seedlings showed that the growth parameters and the content of photosynthetic pigments decreased in response to low temperature. TiO2 NPs and spermine treatments increased plant resistance to cold stress and decreased the level of oxidative damage by reduction of malondialdehyde (MDA) and hydrogen peroxide (H2O2) contents. In other hand, TiO2 NPs and spermine caused increase of phenolics, total protein and osmolytes contents under cold stress conditions. An increase in glycyrrhizin content was significantly induced by low temperature, TiO2 NPs and spermine.
{"title":"Effects of TiO2 nanoparticles and spermine on antioxidant responses of Glycyrrhiza glabra L. to cold stress","authors":"Vahideh Kardavan Ghabel, R. Karamian","doi":"10.37427/botcro-2020-025","DOIUrl":"https://doi.org/10.37427/botcro-2020-025","url":null,"abstract":"Licorice (Glycyrrhiza glabra L.) is known as an important medicinal plant throughout the world. Glycyrrhizin is one of the most important specialized metabolites produced by licorice. In order to study the effect of TiO2 nanoparticles (TiO2 NPs) and spermine on physiological and biochemical traits of licorice under cold stress conditions, a factorial experiment was conducted in a completely randomized design with three replications. Plants were exposed to optimum temperature (26 oC) as control and low temperature (4 oC) as cold stress conditions and also treated with TiO2 NPs (2 and 5 ppm) and spermine (1 mM), separately. Results from physiological and biochemical analyses of the aerial parts of licorice seedlings showed that the growth parameters and the content of photosynthetic pigments decreased in response to low temperature. TiO2 NPs and spermine treatments increased plant resistance to cold stress and decreased the level of oxidative damage by reduction of malondialdehyde (MDA) and hydrogen peroxide (H2O2) contents. In other hand, TiO2 NPs and spermine caused increase of phenolics, total protein and osmolytes contents under cold stress conditions. An increase in glycyrrhizin content was significantly induced by low temperature, TiO2 NPs and spermine.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"137-147"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49361795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-024
E. Kaya, F. V. Souza, J. Santos-Serejo, S. Galatali
Cryopreservation is an important technique for the long-term storage of economically important plant germplasm. In this study, an efficient protocol was developed for the long-term conservation of seven economically important Musa taxa: M. acuminata Colla ssp. burmannica N.W. Simmonds, M. acuminata Colla ssp. zebrina (Van Houtte) R.E. Nasution, M. balbisiana Colla, M. basjoo Sieb., M. ornata W. Roxburgh (St. Lavender), M. velutina H. Wendl. et Drude (Velvet Pink Banana), and M. acuminata × balbisiana. The seeds were dehydrated in a sterile laminar flow cabinet for different exposure times and then they were directly immersed in liquid nitrogen. The critical point was to support the initial germination of cryopreserved seeds and this was achieved by the excision of zygotic embryos after liquid nitrogen treatment that allowed the seed germination. The best moisture content for tolerance to cryopreservation ranged from 15.8% (M. acuminata ssp. zebrina) to 17.1% (M. ornata) and the maximum post-cryopreservation germination rates varied from 86.4% (M. velutina) to 55.0% (M. ornata). All seedlings derived from seeds germinated after cryopreservation were easily rooted and acclimated to greenhouse conditions.
{"title":"Influence of dehydration on cryopreservation of Musa spp. germplasm","authors":"E. Kaya, F. V. Souza, J. Santos-Serejo, S. Galatali","doi":"10.37427/botcro-2020-024","DOIUrl":"https://doi.org/10.37427/botcro-2020-024","url":null,"abstract":"Cryopreservation is an important technique for the long-term storage of economically important plant germplasm. In this study, an efficient protocol was developed for the long-term conservation of seven economically important Musa taxa: M. acuminata Colla ssp. burmannica N.W. Simmonds, M. acuminata Colla ssp. zebrina (Van Houtte) R.E. Nasution, M. balbisiana Colla, M. basjoo Sieb., M. ornata W. Roxburgh (St. Lavender), M. velutina H. Wendl. et Drude (Velvet Pink Banana), and M. acuminata × balbisiana. The seeds were dehydrated in a sterile laminar flow cabinet for different exposure times and then they were directly immersed in liquid nitrogen. The critical point was to support the initial germination of cryopreserved seeds and this was achieved by the excision of zygotic embryos after liquid nitrogen treatment that allowed the seed germination. The best moisture content for tolerance to cryopreservation ranged from 15.8% (M. acuminata ssp. zebrina) to 17.1% (M. ornata) and the maximum post-cryopreservation germination rates varied from 86.4% (M. velutina) to 55.0% (M. ornata). All seedlings derived from seeds germinated after cryopreservation were easily rooted and acclimated to greenhouse conditions.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"99-104"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44537674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-032
R. Yehia, Ali M. Ali
Research in the area of nanoparticles has grown considerably in recent years. Plant leaf extracts provide a platform for nanoparticle synthesis from metal and metal oxides, which is more economical and environmentally friendly than other methods, such as chemical reduction and physical methods. The present study conducted the biosynthesis of iron nanoparticles (FeNPs) using Thymus vulgaris L. (Thyme) leaf aqueous extract. The characterization of FeNPs was carried out by transmission electron microscopy (TEM), UV-visible spectrophotometry (UV-VIS), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and X-Ray diffraction (XRD) techniques. UV-VIS spectroscopy analysis demonstrated a visible peak around 440 nm. FTIR demonstrated the presence of iron metallic ions. Structural analysis of the nanoparticles by TEM showed agglomerations of spherical shapes. The average size of the synthesized FeNPs was around 40 nm. Regarding application, the ability of the FeNPs to degrade methyl orange was recorded as 95%. They were also examined for potential antimicrobial activity against pathogenic Gram-positive and Gram-negative bacteria and fungi. FeNPs demonstrated high antifungal activity against Candida albicans, C. parapsilosis and Aspergillus flavus, while their antibacterial activity was much weaker compared to commercial antibacterial agent. Thus, FeNPs synthesized using T. vulgaris could play an important role in controlling C. albicans, C. parasilosis and A. flavus and bioremediation of dyes.
{"title":"Biosynthesis and characterization of iron nanoparticles produced by Thymus vulgaris L. and their antimicrobial activity","authors":"R. Yehia, Ali M. Ali","doi":"10.37427/botcro-2020-032","DOIUrl":"https://doi.org/10.37427/botcro-2020-032","url":null,"abstract":"Research in the area of nanoparticles has grown considerably in recent years. Plant leaf extracts provide a platform for nanoparticle synthesis from metal and metal oxides, which is more economical and environmentally friendly than other methods, such as chemical reduction and physical methods. The present study conducted the biosynthesis of iron nanoparticles (FeNPs) using Thymus vulgaris L. (Thyme) leaf aqueous extract. The characterization of FeNPs was carried out by transmission electron microscopy (TEM), UV-visible spectrophotometry (UV-VIS), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and X-Ray diffraction (XRD) techniques. UV-VIS spectroscopy analysis demonstrated a visible peak around 440 nm. FTIR demonstrated the presence of iron metallic ions. Structural analysis of the nanoparticles by TEM showed agglomerations of spherical shapes. The average size of the synthesized FeNPs was around 40 nm. Regarding application, the ability of the FeNPs to degrade methyl orange was recorded as 95%. They were also examined for potential antimicrobial activity against pathogenic Gram-positive and Gram-negative bacteria and fungi. FeNPs demonstrated high antifungal activity against Candida albicans, C. parapsilosis and Aspergillus flavus, while their antibacterial activity was much weaker compared to commercial antibacterial agent. Thus, FeNPs synthesized using T. vulgaris could play an important role in controlling C. albicans, C. parasilosis and A. flavus and bioremediation of dyes.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"114-120"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-032","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48420316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-023
B. Tunçkol, Ahter Fişne, N. Aksoy, Z. Aytaç
Astragalus bartinense is described as a new species from Bartın Province in Northern Anatolia, Turkey. The new species is close to A. depressus L. and A. froedinii Murb., but distinctly differs from A. froedinii in having hairy fruit, long stipules (10–12 mm) and peduncle (10–25 mm). It also differs from A. depressus in having long stipules and a stipitate and glabrous ovary. Taxonomic descriptions, micromorphology of pollen and seed and geographical distribution are presented.
{"title":"Astragalus bartinense (Fabaceae), a new species from Turkey","authors":"B. Tunçkol, Ahter Fişne, N. Aksoy, Z. Aytaç","doi":"10.37427/botcro-2020-023","DOIUrl":"https://doi.org/10.37427/botcro-2020-023","url":null,"abstract":"Astragalus bartinense is described as a new species from Bartın Province in Northern Anatolia, Turkey. The new species is close to A. depressus L. and A. froedinii Murb., but distinctly differs from A. froedinii in having hairy fruit, long stipules (10–12 mm) and peduncle (10–25 mm). It also differs from A. depressus in having long stipules and a stipitate and glabrous ovary. Taxonomic descriptions, micromorphology of pollen and seed and geographical distribution are presented.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"131-136"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42736427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-026
SeoHwa Park, Jong-il Choi
Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi (Bangiales, Rhodophyta) has potentially high economic value. P. yezoensis has been used as food in East Asian countries for a long time, and, in addition to that its consumption is increasing worldwide owing to the growing interest in healthy seaweed food. A mutant (Py2K) with a high growth rate was developed using gamma rays to increase the production of P. yezoensis. De novo transcriptome analysis was performed to determine the mechanism underlying the high growth rate of this mutant. The transcriptomes from wild-type (PyWT) and mutant (Py2K) strains were assembled, and 167,165 genes were analyzed. A total of 15,979 genes were differentially expressed. Transcriptome analysis of nitrogen pathway revealed the increase in nitrogen availability through the upregulation of nitrate transporter gene (nrt) expression. Activation of nitrogen assimilation and re-assimilation and upregulation in alternative oxidase (aox) gene contributed to the increase in cellular nitrogen availability, thereby affecting the synthesis of phycobiliprotein. As a consequence, the efficiency of photosynthesis and the subsequent growth rate increased, which contributed to the color differences in thalli between PyWT and Py2K.
yezoensis (Ueda) M.S.Hwang et H.G.Choi (Bangiales, Rhodophyta)具有潜在的高经济价值。紫菜在东亚国家作为食品已经有很长一段时间了，此外，由于人们对健康海藻食品的兴趣日益浓厚，紫菜在世界范围内的消费量正在增加。利用伽马射线培养了一个生长速率高的突变体Py2K，提高了叶藻的产量。进行从头转录组分析以确定该突变体高生长速率的机制。对野生型(PyWT)和突变型(Py2K)菌株的转录组进行组装，分析了167,165个基因。共有15979个基因存在差异表达。氮途径转录组分析显示，氮可利用性的增加是通过上调硝酸盐转运基因(nrt)的表达。氮同化和再同化的激活以及替代氧化酶(aox)基因的上调导致细胞氮有效性的增加，从而影响藻胆蛋白的合成。因此，光合效率和随后的生长速度增加，这是PyWT和Py2K之间菌体颜色差异的原因。
{"title":"De novo transcriptome analysis of high growth rate Pyropia yezoensis (Bangiales, Rhodophyta) mutant with high utilization of nitrogen","authors":"SeoHwa Park, Jong-il Choi","doi":"10.37427/botcro-2020-026","DOIUrl":"https://doi.org/10.37427/botcro-2020-026","url":null,"abstract":"Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi (Bangiales, Rhodophyta) has potentially high economic value. P. yezoensis has been used as food in East Asian countries for a long time, and, in addition to that its consumption is increasing worldwide owing to the growing interest in healthy seaweed food. A mutant (Py2K) with a high growth rate was developed using gamma rays to increase the production of P. yezoensis. De novo transcriptome analysis was performed to determine the mechanism underlying the high growth rate of this mutant. The transcriptomes from wild-type (PyWT) and mutant (Py2K) strains were assembled, and 167,165 genes were analyzed. A total of 15,979 genes were differentially expressed. Transcriptome analysis of nitrogen pathway revealed the increase in nitrogen availability through the upregulation of nitrate transporter gene (nrt) expression. Activation of nitrogen assimilation and re-assimilation and upregulation in alternative oxidase (aox) gene contributed to the increase in cellular nitrogen availability, thereby affecting the synthesis of phycobiliprotein. As a consequence, the efficiency of photosynthesis and the subsequent growth rate increased, which contributed to the color differences in thalli between PyWT and Py2K.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"201-211"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41690910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-020
Kim Ngan Tran, Jong-il Choi
Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi is a popular edible macro-alga that is found mostly in intertidal zones. It is one of the most economically important seaweed species and has been cultivated extensively in the cold waters of East Asia. Various reports have been published on the isolation and characterization of improved strains of Pyropia. However, there are few studies focusing on the molecular basis underlying these mutant strains. In this study, we performed a comparative analysis of whole transcriptomes of wild-type (PyWT) and high-growth (Py500G) strains of P. yezoensis using next generation RNA sequencing (RNA-seq). After sequencing, a total of 167,110,896 paired-end reads with a length of 151 nucleotides, were obtained. De novo transcriptome assembly and redundancy removal generated 19,441 transcripts. The assembly was annotated in NCBI nr, Swiss-Prot, Pfam, KEGG, GO and KOG databases. To unravel the differences in Py500G and PyWT, we mapped Py500G and PyWT reads to the assembly and calculated the expression levels. In total, there were 454 transcripts that were differentially expressed. Among the differentially expressed transcripts, candidate genes were identified with well-known growth and development functions. This study not only identifies candidate genes responsible for the high-growth phenotype of Py500G, but it also provides more comprehensive genomic data for future research on P. yezoensis.
yezoensis (Ueda) M.S.Hwang et H.G.Choi是一种流行的食用大藻类，主要分布在潮间带。它是经济上最重要的海藻品种之一，在东亚的冷水中被广泛种植。关于焦皮菌改良菌株的分离和鉴定已经发表了许多报告。然而，很少有研究集中在这些突变株的分子基础上。在这项研究中，我们使用下一代RNA测序(RNA-seq)对野生型(PyWT)和高生长(Py500G)菌株的全转录组进行了比较分析。测序后，共获得167,110,896对末端reads，长度为151个核苷酸。从头转录组组装和冗余去除产生19,441个转录本。该装配在NCBI nr、Swiss-Prot、Pfam、KEGG、GO和KOG数据库中进行了注释。为了揭示Py500G和PyWT的差异，我们将Py500G和PyWT的读取映射到程序集并计算表达水平。总共有454个转录本存在差异表达。在差异表达的转录本中，候选基因被鉴定出具有众所周知的生长和发育功能。本研究不仅确定了Py500G高生长表型的候选基因，而且为今后对叶斑杉的研究提供了更全面的基因组数据。
{"title":"Comparative transcriptome analysis of high-growth and wild-type strains of Pyropia yezoensis","authors":"Kim Ngan Tran, Jong-il Choi","doi":"10.37427/botcro-2020-020","DOIUrl":"https://doi.org/10.37427/botcro-2020-020","url":null,"abstract":"Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi is a popular edible macro-alga that is found mostly in intertidal zones. It is one of the most economically important seaweed species and has been cultivated extensively in the cold waters of East Asia. Various reports have been published on the isolation and characterization of improved strains of Pyropia. However, there are few studies focusing on the molecular basis underlying these mutant strains. In this study, we performed a comparative analysis of whole transcriptomes of wild-type (PyWT) and high-growth (Py500G) strains of P. yezoensis using next generation RNA sequencing (RNA-seq). After sequencing, a total of 167,110,896 paired-end reads with a length of 151 nucleotides, were obtained. De novo transcriptome assembly and redundancy removal generated 19,441 transcripts. The assembly was annotated in NCBI nr, Swiss-Prot, Pfam, KEGG, GO and KOG databases. To unravel the differences in Py500G and PyWT, we mapped Py500G and PyWT reads to the assembly and calculated the expression levels. In total, there were 454 transcripts that were differentially expressed. Among the differentially expressed transcripts, candidate genes were identified with well-known growth and development functions. This study not only identifies candidate genes responsible for the high-growth phenotype of Py500G, but it also provides more comprehensive genomic data for future research on P. yezoensis.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"148-156"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46184797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-021
Anamarija Kolda, Z. Ljubešić, A. Gavrilovic, Jurica Jug-Dujakovic, K. Pikelj, D. Kapetanović
Seasonal sampling of the seawater column and sediment in Adriatic coastal areas affected by various anthropogenic activities, primarily aquaculture, was conducted during 2017. In total, 32 samples from two sites (central and southern Adriatic) were analysed by 16S rRNA amplicon sequencing. This approach was selected to test the possibilities of using metabarcoding in studying marine cyanobacteria, exploring their ecology and potential as an indicator group in anthropologically stressed coastal environments. Additionally, physicochemical water column parameters, sediment granulometry and composition were assessed. Water column revealed a seasonal variation of amplicon sequencing variants (ASVs) closely related to Cyanobium PCC-6307, Prochlorococcus MIT9313 and Synechococcus CC9902, as well as seasonal grouping of physico-chemical parameters in PCA analysis. Sediment analysis uncovered greater community richness of 13 cyanobacterial genera and two uncultured groups. The most abundant in sandy gravels and gravelly sand type of sediments were ASVs closely related to Pleurocapsa PCC-7319 and Xenococcus PCC-7305. Furthermore, identified cyanobacterial ASVs predominantly displayed similarity to isolates from tropical areas (e.g. Neolyngbya, Chroococcidiopsis, Trichodesmium, etc.), which could indicate the tropicalization process already ongoing in the fish fauna of the Adriatic Sea.
{"title":"Metabarcoding Cyanobacteria in coastal waters and sediment in central and southern Adriatic Sea","authors":"Anamarija Kolda, Z. Ljubešić, A. Gavrilovic, Jurica Jug-Dujakovic, K. Pikelj, D. Kapetanović","doi":"10.37427/botcro-2020-021","DOIUrl":"https://doi.org/10.37427/botcro-2020-021","url":null,"abstract":"Seasonal sampling of the seawater column and sediment in Adriatic coastal areas affected by various anthropogenic activities, primarily aquaculture, was conducted during 2017. In total, 32 samples from two sites (central and southern Adriatic) were analysed by 16S rRNA amplicon sequencing. This approach was selected to test the possibilities of using metabarcoding in studying marine cyanobacteria, exploring their ecology and potential as an indicator group in anthropologically stressed coastal environments. Additionally, physicochemical water column parameters, sediment granulometry and composition were assessed. Water column revealed a seasonal variation of amplicon sequencing variants (ASVs) closely related to Cyanobium PCC-6307, Prochlorococcus MIT9313 and Synechococcus CC9902, as well as seasonal grouping of physico-chemical parameters in PCA analysis. Sediment analysis uncovered greater community richness of 13 cyanobacterial genera and two uncultured groups. The most abundant in sandy gravels and gravelly sand type of sediments were ASVs closely related to Pleurocapsa PCC-7319 and Xenococcus PCC-7305. Furthermore, identified cyanobacterial ASVs predominantly displayed similarity to isolates from tropical areas (e.g. Neolyngbya, Chroococcidiopsis, Trichodesmium, etc.), which could indicate the tropicalization process already ongoing in the fish fauna of the Adriatic Sea.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":" ","pages":""},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46274090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-10-01DOI: 10.37427/botcro-2020-027
S. Černi, K. Hančević, D. Škorić
Although Croatia is not often perceived as a citrus growing country, citrus species have been planted in the Croatian southern coastal part for centuries. Citrus had always been important as a source of vitamins and micronutrients for local consumption, but with the introduction of Satsuma mandarins (Citrus unshiu Marc.) citrus production started its commercial development. The Croatian coast is probably the northernmost commercial citrus growing area globally with several agroecological constraints influencing citrus production. However, Satsuma mandarins, the most cold-tolerant citrus of economic interest, are successfully cultivated resulting in an excellent quality of fruits that easily finds a market niche. Unfortunately, with the import of plant material in the last century, the simultaneous introduction of viral and subviral pathogens occurred. The most important are Citrus tristeza virus and Citrus exocortis viroid. As certain rootstock-scion combinations are tolerant to virus or viroid infections and display no obvious symptoms, these pathogens have been continuously spreading by plant propagation. Molecular and biological analyses revealed the existence of pathotypes not believed to be endemically present in the Mediterranean region. Their high intra-isolate genetic variability and frequent coinfections suggest that this geographical region presents a sort of a biological enclave of potentially threatening pathogens. Their transmission from this agroecological niche to areas where sensitive rootstock-scion combinations are common presents a serious risk to citrus production, especially when global warming and the resulting migration of efficient vector species are considered. Comprehensive pathogen monitoring is important for improving citrus production and the prevention of pathogen transmission.
{"title":"Citruses in Croatia – cultivation, major virus and viroid threats and challenges","authors":"S. Černi, K. Hančević, D. Škorić","doi":"10.37427/botcro-2020-027","DOIUrl":"https://doi.org/10.37427/botcro-2020-027","url":null,"abstract":"Although Croatia is not often perceived as a citrus growing country, citrus species have been planted in the Croatian southern coastal part for centuries. Citrus had always been important as a source of vitamins and micronutrients for local consumption, but with the introduction of Satsuma mandarins (Citrus unshiu Marc.) citrus production started its commercial development. The Croatian coast is probably the northernmost commercial citrus growing area globally with several agroecological constraints influencing citrus production. However, Satsuma mandarins, the most cold-tolerant citrus of economic interest, are successfully cultivated resulting in an excellent quality of fruits that easily finds a market niche. Unfortunately, with the import of plant material in the last century, the simultaneous introduction of viral and subviral pathogens occurred. The most important are Citrus tristeza virus and Citrus exocortis viroid. As certain rootstock-scion combinations are tolerant to virus or viroid infections and display no obvious symptoms, these pathogens have been continuously spreading by plant propagation. Molecular and biological analyses revealed the existence of pathotypes not believed to be endemically present in the Mediterranean region. Their high intra-isolate genetic variability and frequent coinfections suggest that this geographical region presents a sort of a biological enclave of potentially threatening pathogens. Their transmission from this agroecological niche to areas where sensitive rootstock-scion combinations are common presents a serious risk to citrus production, especially when global warming and the resulting migration of efficient vector species are considered. Comprehensive pathogen monitoring is important for improving citrus production and the prevention of pathogen transmission.","PeriodicalId":6967,"journal":{"name":"Acta Botanica Croatica","volume":"79 1","pages":"228-235"},"PeriodicalIF":1.3,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.37427/botcro-2020-027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49388461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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