Journal of Applied Ichthyology最新文献

{"title":"How (not) to read fish genomics data – The importance of cytogenomics knowledge in the current flood of sequenced genomes","authors":"Radka Symonová","doi":"10.1111/jai.14365","DOIUrl":"10.1111/jai.14365","url":null,"abstract":"<p>Biologists have been facing a tremendous data explosion during the last years. This is particularly apparent in the still increasing amount of sequenced genomes. However, it is not always straightforward to understand and properly utilize these data that may be publicly available in an incomplete form. This is the case of the current flood of fish genomes among others. In reaction to this situation a recent study by Randhawa and Pawar (<span>2021</span>) tried to exploit these data, however, in an improper way. This study is not the only one suffering from serious problems with handling genomic data and contextualizing them in organismal evolution. On the other hand (Randhawa & Pawar, <span>2021</span>) accumulated several serious issues in a single paper and further analysed their incorrect findings. This short communication aims to elucidate unclarities in that study and to provide some simple hints how to avoid similar issues. This is particularly relevant for fish genomics, where an immense biodiversity results in a so far unexplored diversity of genome traits.</p><p>The study by Randhawa and Pawar (<span>2021</span>) is based on the NCBI repository of genomic data (Genome, <span>2022</span>). Even such excellent and indispensable tools like NCBI/Genome are not absolutely flawless as they rely on data submitted by other scientists. Hence, it is crucial to always manually check all downloaded data. The best way is to sort the dataset according to e.g. genome size (GS) and according to GC content (GC%). Then, the incorrect values are immediately apparent on both of ends of the dataset upon these procedures. Namely, the incomplete genome assemblies result in too small genome sizes (e.g. <i>Squalius pyrenaicus</i> with a fully non-sense genome size of 48 Mb reported by Randhawa & Pawar, <span>2021</span>). As a result, such incomplete assemblies can yield fully aberrant values of GC%, both extremely low (e.g. <i>Chionodraco hamatus</i> with GC = 25.4%) or extremely high (e.g. <i>S. pyrenaicus</i> with GC = 51.1%). Such values have to be, of course, discarded. A similar mistake was identified in the paper by Lu & Luo, <span>2020</span>, who presented the channel catfish to have GC = 31.5% and claimed this value as the lowest one within their dataset. In this particular case, it is apparent that this value is incorrect in their dataset and too low for a vertebrate genome. The value of GC% is crucial for several reasons and particularly regarding the genome completeness, since GC-rich regions were underrepresented from technical reasons in the earlier versions of genome assemblies (Rhie et al., <span>2021</span>).</p><p>A fully different however equally important issue is where to place the borderline between the incomplete and still usable but low(er) quality genome assemblies. This is crucial to be able to decide, which values are to be discarded and which retained. This issue cannot be easily solved because there is usually no gap ","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":"2025 1","pages":""},"PeriodicalIF":0.7,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jai.14365","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45253653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Length‐weight relationships of 14 fish species from Narmada River, India","authors":"A. Dwivedi","doi":"10.1111/jai.14364","DOIUrl":"https://doi.org/10.1111/jai.14364","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43104258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First record of a barb,\u0000 Pethia stoliczkana\u0000 (Day) from Brahmaputra drainage, Assam, India","authors":"Dipanka Nath, R. Dutta, Raktim Sarmah, A. M. Ahmed, H. Pokhrel, L. Mudoi, S. K. Bhagabati","doi":"10.1111/jai.14363","DOIUrl":"https://doi.org/10.1111/jai.14363","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41508615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial diversity and phylogenetic structure of Yellowcheek (\u0000 Elopichthys bambusa\u0000 ) in the Yangtze River","authors":"K. Abbas, Xiaoyun Zhou, Wen Wang","doi":"10.1111/jai.14362","DOIUrl":"https://doi.org/10.1111/jai.14362","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41682739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anesthetic efficacy of clove oil and\u0000 2‐phenoxyethanol\u0000 as hematological, histopathological and echocardiographic on broodstock Danube sturgeon (\u0000 Acipenser gueldenstaedtii\u0000 )","authors":"K. Ak","doi":"10.1111/jai.14361","DOIUrl":"https://doi.org/10.1111/jai.14361","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46143991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parental care and early development of the labrisomid blenny\u0000 Labrisomus philippii\u0000 (Labrisomidae) from northern Chile","authors":"Cristian Azócar, F. Zavala-Muñoz, M. Landaeta, Milton Aviles, M. Araya","doi":"10.1111/jai.14355","DOIUrl":"https://doi.org/10.1111/jai.14355","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45135380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Replacement of fishmeal by fermented silkworm pupae meal in diets of largemouth bass (\u0000 Micropterus salmoides\u0000 ): Effects on growth performance and feed utilization","authors":"Qihuan Zhang, Yurong Bian, Yuhan Zhao, Yang Xu, Jiankai Wu, Dezhong Wang, Jun Wang, Aimin Wang, Z. Qi","doi":"10.1111/jai.14358","DOIUrl":"https://doi.org/10.1111/jai.14358","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42460151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Length–weight relationships for nine fish species from the Ulungur River basin, Northwest China","authors":"Le Wang, Xuefeng Yu, D. Song, Chen Zhao, Xue Du, Huibo Wang, T. Huo","doi":"10.1111/jai.14356","DOIUrl":"https://doi.org/10.1111/jai.14356","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41898887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Length‐weight relations for finfish species landed as trawl by‐catch from north‐western Bay of Bengal","authors":"Ghosh Shubhadeep, Edward Loveson, Menon Muktha, Divipala Indira, P. Behera, Felix Jasmin, H. M. Manas, Pattnaik Phalguni, Das Madhumita, Rao Gourisankar, M. Satishkumar, A. P. Dineshbabu, A. Gopalakrishnan","doi":"10.1111/jai.14357","DOIUrl":"https://doi.org/10.1111/jai.14357","url":null,"abstract":"","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43676587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Length-weight relationships of four indigenous fish species from the Nujiang River, China","authors":"Songhao Ji,&nbsp;Liuyong Ding,&nbsp;Juan Tao","doi":"10.1111/jai.14354","DOIUrl":"10.1111/jai.14354","url":null,"abstract":"<p>Specimens of four fish species (<i>Garra nujiangensis</i> Chen, Zhao &amp; Yang, 2009, <i>Poropuntius opisthopterus</i> (Wu, 1977), <i>Creteuchiloglanis macropterus</i> (Ng, 2004), and <i>Glyptothorax lanceatus</i> Ng, Jiang &amp; Chen, 2012) were caught in the Nujiang River, China. Fish were sampled between May 2017 to July 2021 in irregular intervals, using gill nets (mesh sizes 6, 10, and 16 cm) and cage nets (mesh size 1 cm). Total length (to nearest 0.1 cm, L) and total weight (to nearest 0.001 g, W) were determined. Length-weight relationships (LWRs) were estimated through the linear regression of W = <i>a</i>L^<i>b</i>. The <i>r</i>² values for all LWRs estimates were all above .96, indicating that no serious outlier values were included in the samples.</p>","PeriodicalId":14894,"journal":{"name":"Journal of Applied Ichthyology","volume":"38 6","pages":"567-569"},"PeriodicalIF":0.9,"publicationDate":"2022-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45255542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}