TY - JOUR A1 - Çabuk, Uğur A1 - Ünlü, Ercan Selçuk T1 - A combined de novo assembly approach increases the quality of prokaryotic draft genomes JF - Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology N2 - Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes. KW - De novo assembly KW - Prokaryotes KW - Bacteria KW - NGS KW - Short reads KW - Draft genome Y1 - 2022 U6 - https://doi.org/10.1007/s12223-022-00980-7 SN - 0015-5632 SN - 1874-9356 VL - 67 SP - 801 EP - 810 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Tambunan, Van Basten T1 - Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil JF - Data in Brief N2 - Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) is an essential insect pollinator in oil palm plantations. Recently, researches have been undertaken to improve pollination efficiency using this species. A fundamental understanding of the genes related to this pollinator behavior is necessary to achieve this goal. Here, we present the draft genome sequence, annotation, and simple sequence repeat (SSR) marker data for this pollinator. In total, 34.97 Gb of sequence data from one male individual (monoisolate) were obtained using Illumina short-read platform NextSeq 500. The draft genome assembly was found to be 269.79 Mb and about 59.9% of completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment. Functional gene annotation predicted about 26.566 genes. Also, a total of 281.668 putative SSR markers were identified. This draft genome sequence is a valuable resource for understanding the population genetics, phylogenetics, dispersal patterns, and behavior of this species. KW - Whole-genome sequencing KW - NGS KW - Simple Sequence Repeat KW - Weevil KW - Curculionidae KW - Oil Palm KW - Pollinator KW - Genomics Y1 - 2021 U6 - https://doi.org/10.1016/j.dib.2021.106745 SN - 2352-3409 VL - 34 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Ajambang, Walter T1 - Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress JF - Data in Brief N2 - Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence. KW - Complete defoliation KW - Flower development KW - Leaf axil KW - NGS KW - RNA-seq KW - Sex KW - determination Y1 - 2022 U6 - https://doi.org/10.1016/j.dib.2022.107914 SN - 2352-3409 VL - 41 PB - Elsevier CY - Amsterdam ER -