Environmental bioremediation relies heavily on the realized potential of efficient bioremediation agents or microbial strains of interest. Identifying suitable microbial agents for plant biomass waste valorization requires (i) high-quality genome assemblies to predict the full metabolic and functional potential, (ii) accurate mapping of lignocellulose metabolizing enzymes. However, fragmented nature of the sequenced genomes often limits the prediction ability due to breaks occurring in coding sequences. To address these challenges and as part of our ongoing agri-culturomics efforts, we have performed a hybrid genome assembly using Illumina and Nanopore reads with modified assembly protocol, for a novel Streptomyces strain isolated from the rhizosphere niche of green leafy vegetables grown in a commercial urban farm. High-quality genome was assembled with the size of 8.6 Mb in just two contigs with N50 of 8,542,030 and coverage of 383X. This facilitated identification and complete arrangement of approximately 248 CAZymes and 38 biosynthetic gene clusters in the genome. Multiple gene clusters consisting of cellulases and hemicellulases associated with substrate recognition domain were identified in the genome. Genes for lignin, chitin, and even some aromatic compounds degradation were found in the Streptomyces sp. genome which makes it a promising candidate for lignocellulosic waste valorization.

环境生物修复在很大程度上依赖于有效的生物修复剂或感兴趣的微生物菌株的实现潜力。为植物生物质废物增值确定合适的微生物试剂需要 (i) 高质量的基因组组装来预测全部代谢和功能潜力，(ii) 准确定位木质纤维素代谢酶。然而，测序基因组的片段化性质通常会由于编码序列中发生的中断而限制预测能力。为了应对这些挑战，并且作为我们正在进行的农业文化组学工作的一部分，我们使用 Illumina 和 Nanopore 读取以及修改后的组装协议进行了混合基因组组装，用于新型链霉菌从商业城市农场种植的绿叶蔬菜的根际生态位中分离出的菌株。仅在两个重叠群中组装了大小为 8.6 Mb 的高质量基因组，N50 为 8,542,030，覆盖率为 383X。这促进了基因组中大约 248 个 CAZymes 和 38 个生物合成基因簇的鉴定和完整排列。在基因组中鉴定了由与底物识别结构域相关的纤维素酶和半纤维素酶组成的多个基因簇。在链霉菌中发现了木质素、几丁质甚至一些芳香族化合物降解的基因。基因组，使其成为木质纤维素废物增值的有希望的候选者。