Ecological Genetics and Genomics最新文献

{"title":"Genetic diversity of Tn916 transposon and its association with tetracycline resistance in Staphylococcus aureus isolates","authors":"Hengameh Feyzbakhsh Markhali ,&nbsp;Hadi Habibollahi ,&nbsp;Mohammad Reza Safari Motlagh ,&nbsp;Behzad Kaviani ,&nbsp;Cesar Augusto Roque-Borda","doi":"10.1016/j.egg.2024.100306","DOIUrl":"10.1016/j.egg.2024.100306","url":null,"abstract":"<div><div><em>Staphylococcus aureus,</em> a major pathogen responsible for hospital-acquired infections, poses a severe global health threat due to its virulence and increasing antimicrobial resistance. This study confirmed the presence of the <em>tet(M)</em> gene and the Tn<em>916</em> transposon in tetracycline-resistant <em>S. aureus</em> isolates<em>.</em> We explored genetic polymorphism by analyzing the positions of Tn<em>916</em> and Shine-Dalgarno sequences in 30 pathogenic <em>S. aureus</em> isolates. Antibiotic resistance profiles against five antibiotics, including tetracycline, were assessed using disc diffusion methods. PCR was utilized to detect the presence of the <em>tet(M) gene</em> and Tn<em>916</em> transposon, and sequence sizes between these genetic elements were determined using specific primers. The resulting band patterns were converted into a binary matrix, and a phylogenetic tree was constructed using the Past3 software. All <em>S. aureus</em> isolates examined showed tetracycline resistance and contained the <em>tet(M)</em> gene and Tn<em>916</em> transposon. Analysis of the distances between Tn<em>916</em> and Shine-Dalgarno sequences revealed diverse band patterns among the strains. Phylogenetic clustering based on PCR band patterns classified the strains into seven distinct clusters, indicating significant genetic diversity and polymorphism. Molecular docking studies supported our findings, suggesting potential applications in developing effective treatments against <em>S. aureus</em> infections.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100306"},"PeriodicalIF":0.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142705027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variability of bread wheat (Triticum aestivum L.) genotypes under drought conditions targeting the CWANA region","authors":"Zakaria El Gataa ,&nbsp;khalil El Messoadi ,&nbsp;Fatima Ezzahra Rachdad ,&nbsp;Imane Imseg ,&nbsp;Lamyae Ed-Daoudy ,&nbsp;Khaoula Lahrichi ,&nbsp;Wuletaw Tadesse","doi":"10.1016/j.egg.2024.100307","DOIUrl":"10.1016/j.egg.2024.100307","url":null,"abstract":"<div><div>Drought stress limits grain yield in bread wheat, challenging agricultural productivity in regions like Morocco, where yields are below global standards. A gap in stable drought-tolerant varieties remains, requiring further research. This study evaluates 200 bread wheat genotypes under rain-fed and irrigated conditions (2020–2021) to identify candidates with improved drought tolerance. The research measured eight traits and used PCA, HCA, ANOVA, and Pearson correlation to identify key traits for drought tolerance, group similar genotypes, assess significant differences, and evaluate trait relationships. The results showed significant variation, with genotypes G150 and G57 yielding 4.03 t/ha and 4.0 t/ha, respectively, outperforming the average yield of 2.5 t/ha under drought stress. Notably, the days to heading at the Merchouch station (rainfed) exhibited the lowest coefficient of variation (CV) at 3.2 %, while the days to maturity at the Sidi Al-Aidi station (irrigated) showed the lowest CV at 2.5 %. The analysis revealed significant genotype-by-environment (G x E) interactions, underscoring the importance of selecting genotypes suitable for specific environmental conditions. Genotypes such as G150 and G57 demonstrated superior performance under drought stress, while others excelled in non-stress conditions. PCA identified key traits contributing to drought tolerance, including grain yield, biomass, and days to heading (r = 0.48), which were positively correlated with yield potential. Grain yield, a critical agronomic trait, showed moderate heritability, indicating both genetic and environmental influences. Identifying drought-tolerant genotypes offers valuable material for breeding programs to improve drought resilience and yield stability in the CWANA region, supporting food security amid changing climates.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100307"},"PeriodicalIF":0.0,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142656018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review on omics approaches, towards understanding environmental resilience of indigenous Nguni sheep: Implications for their conservation and breeding programs in South Africa","authors":"Nkosinathi Nxumalo ,&nbsp;Clint Rhode ,&nbsp;Nokuthula Kunene ,&nbsp;Annelin Molotsi","doi":"10.1016/j.egg.2024.100305","DOIUrl":"10.1016/j.egg.2024.100305","url":null,"abstract":"<div><div>Genetic heterogeneity, as the driver of evolutionary potential and counterbalance to inbreeding depression, is an important consideration for ensuring livestock adaptability, robustness and resilience to erratic and challenging environments. Accordingly, the low genetic diversity within exotic livestock breeds may suggest survival uncertainty and extinction risk, as agroecological environments are consistently changing due to global climate change. Indigenous livestock breeds, such as the southern African Nguni sheep, have been reported to be genetically and phenotypically diverse and adapted to their local environmental adversities, including high temperatures, drought, and diseases. Characterising and understanding the molecular determinants underpinning their robustness may assist in selecting and breeding for highly productive livestock progeny that are resilient to a broader spectrum of environmental challenges. Also, understanding indigenous livestock breeds genetic uniqueness will further emphasize their significance as a valuable genetic resource and strengthen the impetus for their conservation. This review first reiterates the concept of southern African indigenous sheep ecotype (Nguni sheep) as a valuable genetic resource for future breeding programmes against local environmental adversities, and further discuss the importance of understanding the genetic mechanisms underpinning their adaptative traits to southern Africa which have not been adequately explored. Some of the previously reported genes, associated with indigenous sheep breeds adaptation to southern African environments includes: <em>MYH9</em> (energy metabolism), <em>PITIX</em>1(high altitude adaptation), <em>CREB3L2, CREB3, GNAQ, DCTN4</em> (thermoregulation), <em>EGLN1, EPAS1</em> (hypoxia associated genes). Finally, we highlighted contemporary omics techniques, commonly used in livestock genomic studies, that may assist in revealing the genomic basis of Nguni sheep unique genotypes of environmental resilience.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100305"},"PeriodicalIF":0.0,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142705026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of combining ability and heterosis in sorghum [Sorghum bicolor (L) Moench] genotypes under moisture stress areas","authors":"Temesgen Begna ,&nbsp;Techale Birhan ,&nbsp;Taye Tadesse","doi":"10.1016/j.egg.2024.100304","DOIUrl":"10.1016/j.egg.2024.100304","url":null,"abstract":"<div><div>The most important prerequisite in sorghum crop improvement is the identification of suitable parents that can combine well and produce superior hybrids. However, a narrow genetic base, lack of potential hybrids and lack of information on the genetic components are the most important limiting factors for sorghum yield improvement. Therefore, the experiment was conducted to estimate the combining abilities and heterosis for yield and agronomic traits. A total of 42 sorghum genotypes were evaluated using an alpha lattice experimental design with two replications at Mieso and Kobo during the cropping season of 2019. Combined analysis of variance revealed highly significant differences due to genotypes for days to flowering, plant height, days to maturity, effective productive tillers, panicle exersion, panicle length, panicle width, panicle yield, grain yield and thousand seed weight traits. Based on general combining ability analysis, inbred lines P-9505 and P-9534 were identified as the best general combiners for both days to flowering and plant height traits; whereas inbred lines P-9501 and B5 were identified as the best general combiners for stay green traits. The hybrid crosses P-9534 x Melkam, B6 x ICRS-14 and MARC3 x Melkam were identified as the best specific combiners for grain yield, while the hybrid TX-623 x ICRS-14 was the best specific combiner for days to flowering, days to maturity, panicle length, panicle width and thousand-seed weight. The estimates of general and specific combining ability revealed the preponderance of non-additive gene action since the ratio of general combining ability to specific combining ability was less than unity for all the traits under study except for plant height. The maximum grain yield was obtained from the hybrids P-9534 x Melkam (6.32 tha^-1), followed by the hybrids B6 x ICRS-14 (5.92 tha^-1), TX-623 x ICRS-14 (5.88 tha^-1), P9511 x Melkam (5.78 tha^-1) and P-850341 x ICRS-14 (5.57 tha^-1). Among the hybrids, B6 x ICRS-14 exhibited (112.41 %) yield advantage over the mid parents, hybrid TX-623 x ICRS-14 exhibited (68.71 %) yield advantage over the better parent, whereas P-9534 x Melkam exhibited (30.71 %) yield advantage over the standard check for grain yield. Finally, based on the mean yield performance, heterosis response and combining ability estimates for grain yield and its components, the hybrid crosses P-9534 x Melkam, B6 x ICRS-14, TX-623 x ICRS-14, MARC3 x Melkam, MARC3 x ICRS-14, P9511 x Melkam and P-850341xICRS-14 were found to be the most promising and potential hybrids that could be exploited commercially after critical evaluation for their superiority and yield stability across locations over the years.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100304"},"PeriodicalIF":0.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142656019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the drought-tolerance and growth-promoting potential of strawberry (Fragaria × ananassa Duch.) rhizobacteria for consortium bioformulation","authors":"Vinay Kumar Dhiman ,&nbsp;Neerja Rana ,&nbsp;Sudarshna ,&nbsp;Vivek Kumar Dhiman ,&nbsp;Prashant Sharma ,&nbsp;Devendra Singh","doi":"10.1016/j.egg.2024.100303","DOIUrl":"10.1016/j.egg.2024.100303","url":null,"abstract":"<div><div>Plant growth-promoting rhizobacteria (PGPR) are known to influence plant root cells to regulate and induce specific traits related to growth promotion and survival. In the present study, rhizobacteria from strawberry plants were screened for stress tolerance under osmotic stress in TSB-mediated PEG 6000 (−0.73 MPa) and tested their ability to produce proline, exopolysaccharide, and free amino acids, all of which induce and regulate stress tolerance. The rhizobacteria were also distinguished for the production of 1-aminocyclopropane-1-carboxylate deaminase (ACCd) for the mitigation of drought stress. Among the 111 rhizobacterial isolates, 41 isolates grow above threshold limit in osmotic stress tolerance, 33 of which exhibited stress tolerance. Further characterization screened 27 isolates as capable growth promoters. Among the experimentally screened rhizobacteria, the isolates SBU4 and SDK8 [<em>Pseudomonas fluorescens</em> (OP627557) (PGPR1) and <em>Pseudomonas glycinae</em> (OP627558) (PGPR2)] exhibited the most promising phyto-beneficial potential. Both the isolates grew exponentially well during the log phase, with increased growth in Log CFU ml⁻¹ under experimentally produced osmotic stress. The drought stress tolerance test results of the SBU4 and SDK8 isolates revealed the presence of proline (1.93 μg mL⁻¹, 2.05 μg mL⁻¹), exopolysaccharide (2.19 mg mg⁻¹ protein, 2.58 mg mg⁻¹ protein), and free amino acid (11.47 μmol g⁻¹, 13.32 μmol g⁻¹) and positive growth in ACCd-enriched DF media, an ACCd assay (α-ketobutyrate (0.56 μmol/ml, 0.64 μmol/ml) and ammonia (0.37 μg mL⁻¹, 0.53 μg mL⁻¹)). The isolates SBU4 and SDK8 performed well in qualitative tests for P solubilization, N fixing ability, siderophore chelation, HCN, and ammonia production, as well as in assays involving P producers (94.57 μg mL⁻¹ and 92.86 μg mL⁻¹), siderophore units (52.14 % SU and 63.12 % SU), and IAA producers (74.63 μg mL⁻¹ and 72.64 μg mL⁻¹). These rhizobacterial isolates were optimized under various growth factors (pH, temperature, incubation) to achieve a relatively high log CFU ml⁻¹. The isolates achieved maximum Log CFU mL⁻¹ when cultured in either a specific range of pH or temperature or growth period (incubation) under standard test conditions. The growth of cultures on cross-streaked nutrient agar plates was tested for an efficient, effective consortium bioformulation that enhances growth and specific traits (drought stress mitigation) in strawberry plants.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100303"},"PeriodicalIF":0.0,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142578056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype × environment interaction and stability analysis of advanced field pea (Pisum sativum L.) genotypes in Southeastern Ethiopia","authors":"Gizachew Yilma Kebede,&nbsp;Temesgen Abo Eritro,&nbsp;Deressa Tesfaye Gutu","doi":"10.1016/j.egg.2024.100302","DOIUrl":"10.1016/j.egg.2024.100302","url":null,"abstract":"<div><div>Field pea is a leguminous crops that have a significant economic contributions to sustainable Ethiopian agriculture. The experiment was conducted at four location in 2015/16 to 2016/17 main cropping seasons with the objectives of to determine the magnitude of genotype by environment interactions and its stability of thirteen field pea genotypes using randomized complete block design with four replications. The AMMI analysis revealed that significant (p&lt;0.01) differences between genotypes, environments and genotype by environment interactions for grain yield. This indicates the genotypes responded differently across environments. The highest mean grain yield was recorded from genotype G₁₂ which records (2992 kg ha⁻¹) followed by genotype G₄ 2974 kg ha⁻¹ across environments. The AMMI analysis showed that genotypes, environments and there interaction accounted about 72.9 %, 1.2 % and 5.7 % of the total sum of squares respectively. The GGE biplot first two principal components explained about 57.42 % of the total sum square of GEI. The GGE biplot revealed that G₄ and G₁₂ were the most stable and high yielding genotypes, while G₁₀ and G₉ were the lowest yielder and stable genotypes. The results indicated that genotypes responded differently to environmental conditions and the environments influenced genotype performances.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100302"},"PeriodicalIF":0.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142538829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of varying levels of Gibberellic Acid (GA3) on plant growth, flowering, flower quality, seed yield, and quality of Petunia(Petunia × hybrida Vilm.)","authors":"K. Sravya ,&nbsp;B.S. Dilta ,&nbsp;Rohit Verma ,&nbsp;Suman Bhatia ,&nbsp;A.C. Jnanesha ,&nbsp;S. Ranjith Kumar ,&nbsp;S. Bharath Kumar ,&nbsp;R.K. Lal","doi":"10.1016/j.egg.2024.100301","DOIUrl":"10.1016/j.egg.2024.100301","url":null,"abstract":"<div><div>Petunia, a popular ornamental plant, is known for its vivid flowers and wide color range. Petunia has long been valued for its aesthetic appeal, but recent research has begun to shed light on its possible medicinal properties. <em>Petunia × hybrida</em> is widely recognized for its medicinal characteristics, phytochemical content, and potential health benefits. A research study was undertaken between the years 2021 and 2022. The field experiment was laid out in a randomized complete block design (RCBD), with 11 treatments replicated three times. The treatments included 10 GA3 concentrations from 25 to 250 ppm applied 45 days post-transplantation, along with control—Petunia cv. 'White' seedlings were transplanted in main plots with 30 × 30 cm spacing. Based on the results, it was noted that foliar feeding the leaves with 200 ppm GA3 produced notable outcomes in various characteristics. This treatment recorded a higher plant height (53.45 cm), spread (50.32 cm), and branches per plant (26.77 cm). It also minimized time to first flowering (78.81 days), 50 % flowering (96.67 days), and peak flowering (107.33 days). Furthermore, 200 ppm GA3 optimized flowering duration (123.47 days), flower diameter (6.76 cm), flowers per plant (405.60), seeded capsules per plant (367.13), and seeds per capsule (535.67). Seed yield was maximized at all levels: per plant (12.51 g), per plot (54.33 g), and per hectare (380.33 kg). Seed quality parameters also peaked, including 1000-seed weight (93.65 mg), germination (93.75 %), germination speed (10.59), seedling length (3.63 cm), and dry weight (0.331 mg). Vigor indices I (340.54) and II (30.99) were significantly higher, while seed electrical conductivity was significantly low (77.13 μSm-1) with this treatment.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100301"},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic basis of coat colour variation in members of genus Panthera","authors":"Sanyam Jain,&nbsp;Smita Rastogi Verma","doi":"10.1016/j.egg.2024.100300","DOIUrl":"10.1016/j.egg.2024.100300","url":null,"abstract":"<div><div>Coat colouration in mammals depends upon the quantity, quality and distribution of melanin in the body, which is produced through a complicated and tightly regulated metabolic pathway operating in the melanosomes of mammalian melanocytes. The branches of this pathway produce two pigments, namely eumelanin and pheomelanin, the ratio of which determines the colour appearance. Loss-of-function and/or gain-of-function mutations in the genes encoding enzymes, receptors, and signals involved in this pathway alter the amount of pigment(s) produced, contributing to the diversity of hair colours/patterns observed. Furthermore, the variety is enhanced by changes in the genetic control of melanocyte differentiation, melanoblast migration and melanin transportation. This phenomenon of variability in colour coat pattern is well characterized in domestic and wild cats, therefore this literature review aims to concatenate the fragmented information available on the genetic analysis of coat colour polymorphism in big cats of the genus <em>Panthera</em>, namely the tiger, lion, jaguar, leopard, and snow leopard, simultaneously underscoring the adaptive significance of such polymorphic colour coats.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100300"},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and structure of Tunisian and Indian date palm (Phoenix dactylifera and sylvestris) cultivars and genotypes revealed by AFLP markers","authors":"Karim Kadri ,&nbsp;Anoop Anand Malik ,&nbsp;Hammadi Hamza ,&nbsp;Salem Marzougui ,&nbsp;Mohamed Aziz Elhoumaizi ,&nbsp;Shyam Sundar Sharma ,&nbsp;Mohammed Elsafy","doi":"10.1016/j.egg.2024.100299","DOIUrl":"10.1016/j.egg.2024.100299","url":null,"abstract":"<div><div>The date palm breeding programs need to discover valid genetic fingerprints to characterize cultivars and assess their genetic diversity. This study assessed the genetic diversity among thirty-nine date palm cultivars from Tunisia (<em>Phoenix dactylifera</em>) and India (<em>Phoenix sylvestris</em>) by using six AFLP (Amplified Fragment Length Polymorphism) markers. 360 loci were amplified, with 127 loci polymorphic (34.35 %). The Jaccard's similarity coefficient ranged from 0.161 to 0.931, with the mean genetic distances of 0.568. AFLP's average marker index value was 7.28, with a resolving power of 10.91. The analysis of population structure showed two main clusters with a clear separation between Tunisian and Indian cultivars.</div><div>Furthermore, the heatmap analysis allowed the identification of 10 bands specific to the Indian accessions, which were not detected in Tunisian genotypes. These loci could be linked to genes involved in adapting the species in Indian lands, which allowed the study of the genetic diversity of date palm resources of different origins, confirming the existence of at least two origins of domestication. Additionally, identifying AFLP loci specific to <em>P. dactylifera</em> and <em>P. sylvestris</em> will significantly contribute to breeding programs by exploiting species-specific polymorphisms.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100299"},"PeriodicalIF":0.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142433520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering genome sequence of Paenibacillus illinoisensis strain YWY-3.1: A chitinase, cellulase, and amylase producer","authors":"Dinh Minh Tran ,&nbsp;Thi Huyen Nguyen ,&nbsp;To Uyen Huynh ,&nbsp;Iuliia Pentekhina","doi":"10.1016/j.egg.2024.100298","DOIUrl":"10.1016/j.egg.2024.100298","url":null,"abstract":"<div><div>The chitin-degrading <em>Paenibacillus illinoisensis</em> YWY-3.1 was isolated from the lake water at Yok Don National Park, Vietnam. Previous evaluations reported that strain YWY-3.1 had high activities of chitinases, cellulases, and amylases; it also produced remarkable levels of numerous promoting traits for plant growth. This study aimed to sequence and analyze the genome sequence of strain YWY-3.1 for further explorations and applications in agriculture and related fields. The whole genome sequencing revealed the <em>P. illinoisensis</em> YWY-3.1 genome contained 6,451,623 bp, 47.3 % GC, 5786 coding sequences, 88 tRNA, and 1 rRNA. It shared 95.49 % ANI and 87.1 % dDDH to those of <em>P. illinoisensis</em> NBRC 15959 (GCA 004000925). Among the coding sequences, COG deduced 4,991, and KEGG predicted 2819. The genome harbored 338 carbohydrate-active enzymes, including 195 GHs, 44 GTs, 13 PLs, 37 CEs, 3 AAs, and 46 CBMs; among them, 6 GH18 chitinases, 5 GH5 cellulases, 2 GH10 xylanases, 1 GH11 xylanase, and 2 GH13 α-amylases were identified. It contained 49 genes involved in environmental adaptation and plant growth. Moreover, 7 BGCs, with 3 being novel clusters, were identified from the genome. This work provided insight into the genomic information of <em>P. illinoisensis</em> YWY-3.1 and potential gene resources, especially chitinases, cellulases, xylanases, α-amylases, and novel BGCs for further explorations and applications.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"33 ","pages":"Article 100298"},"PeriodicalIF":0.0,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142422196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}