Seid Mohammed Ebu, Lopamudra Ray, Ananta N Panda, Sudhansu K Gouda
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BNPI-92 shared 2930 gene cluster (core gene) with B. cereus ATCC 14579<sup> T</sup> (AE016877), B. paranthracis Mn5T (MACE01000012), B. thuringiensis ATCC 10792 T (ACNF01000156), and B. antrics Amen T (AE016879) strains. For our strain, the maximum gene cluster (190) was shared with B. cereus ATCC 14579<sup> T</sup> (AE016877). For Ortho Venn pair wise analysis, the maximum overlapping gene clusters thresholds have been detected between Bacillus s p.BNPI-92 and Ba. cereus ATCC 14579<sup> T</sup> (5414). Average nucleotide identity (ANI) such as OriginalANI and OrthoANI, in silicon digital DND-DNA hybridization (isDDH), Type (Strain) Genome Server (TYGS), and Genome-Genome Distance Calculator (GGDC) were more essentially related Bacillus sp. BNPI-92 with B. cereus ATCC 14579<sup> T</sup> strain. Therefore, based on the combination of RAST annotation, OrthoVenn server, ANI and isDDH result Bacillus sp.BNPI-92 strain was strongly confirmed to be a B. cereus type strain. It was designated as B. cereus BNPI-92 strain. In B. cereus BNPI-92 strain whole genome sequence, PHA biosynthesis encoding genes such as phaP, phaQ, phaR (PHA synthesis repressor phaR gene sequence), phaB/phbB, and phaC were predicted on the same operon. These gene clusters were designated as phaPQRBC. However, phaA was located on other operons.</p><p><strong>Conclusions: </strong>This newly obtained isolate was found to be new a strain based on comparative genomic analysis and it was also observed as a potential candidate for PHA biosynthesis.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"132"},"PeriodicalIF":3.6000,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10665291/pdf/","citationCount":"0","resultStr":"{\"title\":\"De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. 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引用次数: 0
摘要
背景:某些芽孢杆菌在聚羟基烷酸酯(PHA)的生产中起着至关重要的作用。然而，这些分离物大多在科学报道的情况下没有得到物种水平的正确鉴定。结果:通过NGS分析，共预测到5719个基因。基于RAST服务器的基因组注释，预测了5,527,513 bp的序列，蛋白质编码序列数为5679 bp。其基因组序列的GC含量和contigs分别为35.1%和156。在RAST服务器分析中，生成了子系统(43%)和非子系统覆盖(57%)。Ortho Venn比较基因组分析表明，芽孢杆菌BNPI-92与蜡样芽孢杆菌ATCC 14579 T (AE016877)、副嗜血杆菌Mn5T (MACE01000012)、苏云金芽孢杆菌ATCC 10792 T (ACNF01000156)和猪源芽孢杆菌Amen T (AE016879)具有2930基因簇(核心基因)。该菌株与蜡样芽孢杆菌ATCC 14579 T (AE016877)共有最大基因簇(190)。通过Ortho Venn配对分析，发现芽孢杆菌p.BNPI-92与Ba之间存在最大重叠基因簇阈值。cereus ATCC 14579 T(5414)。在硅数字ddn - dna杂交(isDDH)、类型(菌株)基因组服务器(TYGS)和基因组-基因组距离计算器(GGDC)中，OriginalANI和OrthoANI等平均核苷酸同源性(ANI)更本质地将芽孢杆菌sp. BNPI-92与蜡样芽孢杆菌ATCC 14579 T菌株联系起来。因此，结合RAST注释、OrthoVenn server、ANI和isDDH结果，强烈确认Bacillus sp.BNPI-92菌株为蜡样芽孢杆菌型菌株。鉴定为蜡样芽孢杆菌BNPI-92菌株。在蜡样芽孢杆菌BNPI-92菌株全基因组序列中，在同一操纵子上预测了PHA生物合成编码基因phaP、phaQ、phaR (PHA合成抑制因子phaR基因序列)、phaB/phbB和phaC。这些基因簇被命名为phaPQRBC。然而，phaA位于其他操作子上。结论:通过比较基因组分析，发现该分离株为新菌株，是PHA生物合成的潜在候选菌株。
De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain.
Background: Certain Bacillus species play a vital role in polyhydroxyalkanoate (PHA) production. However, most of these isolates did not properly identify to species level when scientifically had been reported.
Results: From NGS analysis, 5719 genes were predicted in the de novo genome assembly. Based on genome annotation using RAST server, 5,527,513 bp sequences were predicted with 5679 bp number of protein-coding sequence. Its genome sequence contains 35.1% and 156 GC content and contigs, respectively. In RAST server analysis, subsystem (43%) and non-subsystem coverage (57%) were generated. Ortho Venn comparative genome analysis indicated that Bacillus sp. BNPI-92 shared 2930 gene cluster (core gene) with B. cereus ATCC 14579 T (AE016877), B. paranthracis Mn5T (MACE01000012), B. thuringiensis ATCC 10792 T (ACNF01000156), and B. antrics Amen T (AE016879) strains. For our strain, the maximum gene cluster (190) was shared with B. cereus ATCC 14579 T (AE016877). For Ortho Venn pair wise analysis, the maximum overlapping gene clusters thresholds have been detected between Bacillus s p.BNPI-92 and Ba. cereus ATCC 14579 T (5414). Average nucleotide identity (ANI) such as OriginalANI and OrthoANI, in silicon digital DND-DNA hybridization (isDDH), Type (Strain) Genome Server (TYGS), and Genome-Genome Distance Calculator (GGDC) were more essentially related Bacillus sp. BNPI-92 with B. cereus ATCC 14579 T strain. Therefore, based on the combination of RAST annotation, OrthoVenn server, ANI and isDDH result Bacillus sp.BNPI-92 strain was strongly confirmed to be a B. cereus type strain. It was designated as B. cereus BNPI-92 strain. In B. cereus BNPI-92 strain whole genome sequence, PHA biosynthesis encoding genes such as phaP, phaQ, phaR (PHA synthesis repressor phaR gene sequence), phaB/phbB, and phaC were predicted on the same operon. These gene clusters were designated as phaPQRBC. However, phaA was located on other operons.
Conclusions: This newly obtained isolate was found to be new a strain based on comparative genomic analysis and it was also observed as a potential candidate for PHA biosynthesis.
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