{"title":"Complete genome sequence of Halomonas boliviensis strain kknpp38, a chlorine-resistant bacterium isolated from the early-stage marine biofilm","authors":"T.J. Sushmitha , Meora Rajeev , Subba Rao Toleti , Shunmugiah Karutha Pandian","doi":"10.1016/j.margen.2021.100890","DOIUrl":"10.1016/j.margen.2021.100890","url":null,"abstract":"<div><p><em>H. boliviensis</em> strain kknpp38 is a dense exopolysaccharide (EPS) producing bacterium, isolated from the early-stage (72-h-old) of marine biofilm. Laboratory experiments demonstrated that this isolate forms a potent biofilm on various artificial substrata <em>viz.</em> polystyrene, stainless steel as well as titanium and possesses high tolerance to chlorine disinfection. To determine the genes and biosynthetic pathways involved in the EPS production, whole-genome sequencing was performed using high-throughput Illumina tag sequencing. The high-quality reads were first <em>de novo</em> assembled using Unicycler genome assembler (version 0.4.9b) and then annotated using Prokka (version 1.13). The complete genome comes from one circular chromosome containing 4.96 Mbp DNA with G + C content of 55%, and encompasses genes encoding 4476 proteins, 2 rRNAs, and 57 tRNAs. Intriguingly, genomic analysis revealed the existence of genes involved in ATP-binding cassette (ABC) transporter-dependent EPS biosynthesis pathways (<em>ugd, ugd2, galU</em>). In addition, we identified genes involved in ectoine (<em>ectA, ectB, ectC, ectD</em>) and polyhydroxyalkanoates (PHAs; <em>fabA, fabB, fabD, fabF, fabH, fabV, fabZ, phaC, phaD, phaG, phaR, phaZ1</em>) production, which are known to involve in bacterial adaptation in saline environment. The outcomes of this study expand scientific understanding on the genes and pathways involved in EPS biosynthesis by marine bacteria.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.margen.2021.100890","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48975395","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}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2021.100891
Yung Mi Lee , Yerin Park , Heesoo Kim , Seung Chul Shin
{"title":"Complete genome sequence of Rhodoferax sp. PAMC 29310 from a marine sediment of the East Siberian Sea","authors":"Yung Mi Lee , Yerin Park , Heesoo Kim , Seung Chul Shin","doi":"10.1016/j.margen.2021.100891","DOIUrl":"10.1016/j.margen.2021.100891","url":null,"abstract":"<div><p><em>Rhodoferax</em> sp. PAMC 29310 was isolated from a surface marine sediment of the East Siberian Sea, Arctic. Whole-genome sequencing of the strain <em>Rhodoferax</em> sp. PAMC 29310 was achieved using PacBio RS II and Illumina platform. The resulting complete genome comprised of 4,593,249 base pairs (G + C content of 58.0%) with a single chromosome, 4546 protein-coding genes, 57 tRNAs and 6 rRNA operons. A complete set of genes encoding the enzymes of glycolysis and citric acid cycle were identified. No genes encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and nitrogenase reductase (<em>nif</em>) were present indicating that strain PAMC 29310 is not capable of fixing of carbon and nitrogen. PAMC 29310 genome contains genes for dissimilatory and assimilatory nitrate reduction. Gene encoding choline dehydrogenase enzyme which functions at the first step in the synthesis of betaine, one of the most effective osmoprotectants, was detected. In particular, among the genomes of the genus <em>Rhodoferax</em> strains, gene encoding nitrite reductase (<em>nir</em>K), which reduces nitrite to nitric oxide and <em>tetA</em> gene encoding tetracycline resistance protein involved in the resistance to tetracycline were identified only in the genome of <em>Rhodoferax</em> sp. PAMC 29310. As the first genome from the strain which was isolated from marine sediment in the genus <em>Rhodoferax</em>, investigation of physiological characteristics based on the complete genome sequences will help understand the adaptation of <em>Rhodoferax</em> sp. PAMC 29310 in the marine sediment.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.margen.2021.100891","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43974557","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}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2022.100930
Nan Geng , Di Yang , Jia Hua , Long-Jia Huang , Han Dong , Cong Sun , Lin Xu
{"title":"Complete genome sequence of Kordiimonas pumila N18T sheds light on biogeochemical roles of the genus Kordiimonas","authors":"Nan Geng , Di Yang , Jia Hua , Long-Jia Huang , Han Dong , Cong Sun , Lin Xu","doi":"10.1016/j.margen.2022.100930","DOIUrl":"10.1016/j.margen.2022.100930","url":null,"abstract":"<div><p><em>Kordiimonas pumila</em> N18<sup>T</sup> (=KCTC 62164<sup>T</sup> = MCCC 1K03436<sup>T</sup>) was isolated from coastal sediments collected in Zhoushan, P. R. China. Ensuing genome sequencing revealed that it consists of a single chromosome with a size of 4,041,658 bp and a DNA G+C content of 47.4%. The genomic annotations further identified 3724 open reading frames (ORFs), 4 rRNA genes, and 43 tRNA genes in the <em>Kordiimonas pumila</em> N18<sup>T</sup> genome. The percentages of ORFs assigned to the CAZy, COG, GO, and KEGG databases were 1.0, 84.8, 19.9, and 59.3%, respectively. Comparative genomic analysis with four other <em>Kordiimonas</em> genomes indicated that the pan- and core-genomes of the genus <em>Kordiimonas</em> consists of 8985 and 1470 orthologous clusters, respectively. Functional annotations of the genus <em>Kordiimonas</em> core genome further revealed that they utilize monosaccharides, peptides, and esters as energy substrates because of the absence of several glycoside hydrolases, glycosyl transferases, aminopeptidases, carbohydrate esterase coding genes, and polysaccharide lyases coding genes in their genomes. Moreover, the genus <em>Kordiimonas</em> possesses survival advantages in ammonium-, phosphorus-, and iron- deficient environments, which are vital for inhabiting marine environments. Overall, this study reports the complete genome of the order <em>Kordiimonadales</em> and broadens the understanding of its ecological roles.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46694861","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}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2021.100899
Xue-Gong Li , Ze-Xi Jiao , Huan-Huan Zhang , Jun Xu , Wei-Jia Zhang , Xiao-Qing Qi , Long-Fei Wu
{"title":"Complete genome sequence of Crassaminicella sp. 143-21,isolated from a deep-sea hydrothermal vent","authors":"Xue-Gong Li , Ze-Xi Jiao , Huan-Huan Zhang , Jun Xu , Wei-Jia Zhang , Xiao-Qing Qi , Long-Fei Wu","doi":"10.1016/j.margen.2021.100899","DOIUrl":"10.1016/j.margen.2021.100899","url":null,"abstract":"<div><p><em>Crassaminicella</em> sp. 143-21, a putative new species isolated from deep-sea hydrothermal vent chimney on the Central Indian Ridge (CIR), is an anaerobic, thermophilic and rod-shaped bacterium belonging to the family <em>Clostridiaceae</em>. In this study, we present the complete genome sequence of strain 143-21, comprising 2,756,133 bp with a G + C content of 31.1%. In total, 2427 protein coding genes, 121 tRNA genes and 33 rRNA genes were obtained. Genomic analysis of strain 143-21 revealed that numerous genes related to organic matter transport and catabolism, including peptide transport, amino acid transport, saccharide transport, ethanolamine transport and corresponding metabolic pathways. Further, the genome contains a large proportion of genes involved in translation, ribosomal structure, and signal transduction. These genes might facilitate microbial survival in deep-sea hydrothermal vent environment. The genome of strain 143-21 will be helpful for further understanding its adaptive strategies in the deep-sea hydrothermal vent environment.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.margen.2021.100899","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41577488","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}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2022.100931
Jiangqi Wang , Linxi Jin , Jianxin Wang , Zhuhua Chan , Runying Zeng , Jie Wu , Wu Qu
{"title":"The first complete genome sequence of Microbulbifer celer KCTC12973T, a type strain with multiple polysaccharide degradation genes","authors":"Jiangqi Wang , Linxi Jin , Jianxin Wang , Zhuhua Chan , Runying Zeng , Jie Wu , Wu Qu","doi":"10.1016/j.margen.2022.100931","DOIUrl":"10.1016/j.margen.2022.100931","url":null,"abstract":"<div><p>Genus <em>Microbulbifer</em> plays important roles in element cycling process in marine environments, and the first type strain KCTC 12973<sup>T</sup> (=ISL-39<sup>T</sup> = CCUG 54356<sup>T</sup>) of <em>M. celer</em> was isolated and identified in 2007. However, the genome sequence of <em>M. celer</em> KCTC 12973<sup>T</sup> is still unclear, which complicates the functional exploration and new species identification of other species belonged to this genus. This study reported the complete genome sequence of <em>M. celer</em> KCTC 12973<sup>T</sup> with a genome size of 4,346,001 bp. A total of 3601 protein-coding genes were annotated in the genome. The potential genes involved in the polysaccharide degradation, including cellulose, chitin, xylan, and pectate, were found in the protein-coding genes. Besides, the reductase genes of nitrate and nitrite were also annotated in the genome. These findings indicated the potential crucial ecological functions of <em>M. celer</em> KCTC 12973<sup>T</sup> for carbon and nitrogen cycles in marine ecosystems.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42595270","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}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2022.100933
Jose Martin Pujolar , Magnus Wulff Jacobsen , Francesca Bertolini
{"title":"Comparative genomics and signatures of selection in North Atlantic eels","authors":"Jose Martin Pujolar , Magnus Wulff Jacobsen , Francesca Bertolini","doi":"10.1016/j.margen.2022.100933","DOIUrl":"10.1016/j.margen.2022.100933","url":null,"abstract":"<div><p>Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (<em>Anguilla Anguilla</em>) and American eel (<em>A. rostrata</em>). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non-overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the F<sub>ST</sub> and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874778722000113/pdfft?md5=e3325ec928b2b342d7540740a1df1523&pid=1-s2.0-S1874778722000113-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39633921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2022.100935
Yi Li , Xiao-Meng Sun , Yan-Ru Dang , Ning-Hua Liu , Qi-Long Qin , Yu-Qiang Zhang , Xi-Ying Zhang
{"title":"Genomic analysis of Marinomonas profundi M1K-6T reveals its adaptation to deep-sea environment of the Mariana Trench","authors":"Yi Li , Xiao-Meng Sun , Yan-Ru Dang , Ning-Hua Liu , Qi-Long Qin , Yu-Qiang Zhang , Xi-Ying Zhang","doi":"10.1016/j.margen.2022.100935","DOIUrl":"10.1016/j.margen.2022.100935","url":null,"abstract":"<div><p>The Mariana Trench is the deepest site on earth with diverse extreme conditions such as high hydrostatic pressure, low temperature and lack of light. Organisms surviving in this extreme environment and their life strategies have been largely uninvestigated. Here, we report the complete genome of <em>Marinomonas profundi</em> M1K-6<sup>T</sup>, isolated from the Mariana Trench deep seawater. The assembled genome comprised 3,648,059 bp without any plasmid. Gene annotation showed that strain M1K-6<sup>T</sup> possesses a series of genes encoding cold-shock proteins, DEAD box RNA helicase and enzymes for biosynthesis of unsaturated fatty acids, implying its high cold tolerance. Abundant genes responsible for transports of ion, branched-chain amino acids and organic compatible solutes were detected, which could maintain cellular osmotic balance disturbed by high hydrostatic pressure. In addition, detected genes (related to storage carbon, transport systems and two-component regulatory systems) could help strain M1K-6<sup>T</sup> to improve its ecological fitness in the deep-sea microaerobic and nutrient-limiting environments. Genomic information on <em>M. profundi</em> M1K-6<sup>T</sup>, provides insights into the adaptation strategies of <em>Marinomonas</em> spp. in the extreme deep-sea environment of the Mariana Trench.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43391743","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}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2022.100932
Jingjing Duan , Wenbin Guo
{"title":"The complete genome sequence of Shewanella inventionis D1489 reveals its potential for the production of eicosapentaenoic acid","authors":"Jingjing Duan , Wenbin Guo","doi":"10.1016/j.margen.2022.100932","DOIUrl":"10.1016/j.margen.2022.100932","url":null,"abstract":"<div><p><em>Shewanella inventionis</em> D1489, isolated from a marine sediment sample from the Yap trench, is a psychrophile bacterium with optimal and maximum growth temperatures of 17 °C and 37 °C, respectively. Here, we present the complete genome of <em>Shewanella inventionis</em> D1489, which will facilitate the genome mining of eicosapentaenoic acid (EPA) biosynthesis coding gene cluster. The sequenced genome consists of 4,831,636 bases, with mean G + C content of 42.404%. A total of 4295 coding genes including 97 tRNAs and 25 rRNA were predicted in the genome. The genome provides basic genetic information for the understanding of its adaptation to cold environment.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43433180","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}
Marine genomicsPub Date : 2022-04-01DOI: 10.1016/j.margen.2021.100889
Kyuin Hwang , Hanna Choe , Kyung Mo Kim
{"title":"Complete genome of Nocardioides aquaticus KCTC 9944T isolated from meromictic and hypersaline Ekho Lake, Antarctica","authors":"Kyuin Hwang , Hanna Choe , Kyung Mo Kim","doi":"10.1016/j.margen.2021.100889","DOIUrl":"10.1016/j.margen.2021.100889","url":null,"abstract":"<div><p><em>Nocardioides aquaticus</em> KCTC 9944<sup>T</sup> is an aerobic, non-motile, Gram-positive, psychrotolerant, non-spore-forming bacterium isolated from the surface water of Ekho Lake in the Vestfold Hills, East Antarctica. This meromictic lake separated from Antarctic seawater thousands of years ago exhibits steep gradients of salinity and temperature in the upper layer of the water column. The cells of <em>N. aquaticus</em> thriving in Ekho Lake are able to grow in wide ranges of temperature (3 to 43.5 °C) and salinity (0 to 15% NaCl). Here, we sequenced the complete genome of <em>N. aquaticus</em> KCTC 9944<sup>T</sup>, aiming to better understand the adaptation of this bacterium to the strong environmental gradients at the molecular level. The genome consists of 4,580,814 bp (G + C content of 73.2%) with a single chromosome, 4432 protein-coding genes, 51 tRNAs and 2 rRNA operons. The genome possesses genes for the Entner-Doudoroff pathway, photoheterotrophy, the conversion of acetate to acetyl-CoA, gluconeogenesis, and energy storage that are all advantageous to oligotrophic bacteria. The presence of genes involved in osmotic balance, fatty acid desaturation, cold and heat shock responses, and the oxygen affinities of respiratory oxidases are likely associated with high tolerance to strong gradients of salinity, temperature and oxygen concentration.</p></div>","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.margen.2021.100889","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43734068","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}
Marine genomicsPub Date : 2022-02-01DOI: 10.1016/j.margen.2021.100914
Midhuna Immaculate Joseph Maran, Dicky John Davis G.
{"title":"Benefits of merging paired-end reads before pre-processing environmental metagenomics data","authors":"Midhuna Immaculate Joseph Maran, Dicky John Davis G.","doi":"10.1016/j.margen.2021.100914","DOIUrl":"10.1016/j.margen.2021.100914","url":null,"abstract":"<div><h3>Background</h3><p>High throughput sequencing<span><span> of environmental DNA<span> has applications in biodiversity monitoring, taxa abundance estimation, understanding the dynamics of </span></span>community ecology, and marine species studies and conservation. Environmental DNA, especially, marine eDNA, has a fast degradation rate. Aside from the good quality reads, the data could have a significant number of reads that fall slightly below the default PHRED quality threshold of 30 on sequencing. For quality control, trimming methods are employed, which generally precede the merging of the read pairs. However, in the case of eDNA, a significant percentage of reads within the acceptable quality score range are also dropped.</span></p></div><div><h3>Methods</h3><p>To infer the ideal merge tool that is sensitive to eDNA, two Hiseq paired-end eDNA datasets were utilized to study the merging by the tools – FLASH (Fast Length Adjustment of SHort reads), PANDAseq, COPE, BBMerge, and VSEARCH without preprocessing. We assessed these tools on the following parameters: Time taken to process, the quality, and the number of merged reads.</p><p>Trimmomatic, a widely-used preprocessing tool, was also assessed by preprocessing the datasets at different parameters for the two approaches of preprocessing: Sliding Window and Maximum Information. The preprocessed read pairs were then merged using the ideal merge tool identified earlier.</p></div><div><h3>Results</h3><p>FLASH is the most efficient merge tool balancing data conservation, quality of reads, and processing time. We compared Trimmomatic's two quality trimming options with increasing strictness with FLASH's direct merge. The raw reads processed with Trimmomatic then merged, yielded a significant drop in reads compared to the direct merge. An average of 29% of reads was dropped when directly merged with FLASH. Maximum Information option resulted in 30.7% to 68.05% read loss with lowest and highest stringency parameters, respectively. The Sliding Window approach conserves approximately 10% more reads at a PHRED score of 25 set as the threshold for a window of size 4. The lowered PHRED cut off conserves about 50% of the reads that could potentially be informative. We noted no significant reduction of data while optimizing the number of reads read in a window with the ideal quality (Q) score.</p></div><div><h3>Conclusions</h3><p><span>Losing reads can negatively impact the downstream processing of the environmental data, especially for </span>sequence alignment studies. The quality trim-first-merge-later approach can significantly decrease the number of reads conserved. However, direct merging of pair-end reads using FLASH conserved more than 60% of the reads. Therefore, direct merging of the paired-end reads can prevent potential removal of informative reads that do not comply by the trimming tool's strict checks. FLASH to be an efficient tool in conserving reads while carrying out quality trimming","PeriodicalId":18321,"journal":{"name":"Marine genomics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39959561","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}