2026-10-07T20:45:39Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33979093 2026-09-24T04:48:51Z category_24271 category_24310 category_24394 item_type_3 month_year_09_2026

Plastid genomes and 45S nuclear rDNA cistrons of six Polyscias species assembled from publicly available SRA data Trinh Hoai Vu (25100938) Lado Jickerson Pitogo (25101602) Faizal Maulana (23095885) Nguyen Thi My Duyen (25101604) Do Tan Khang (23753049) Xina V. Vinalay (25101606) Annalee S. Hadsall (25101608) Young Sang Park (24659565) Jong-Soo Kang (3797866) Jee Young Park (4585180) Tae-Jin Yang (50211) Phylogeny and comparative analysis Genomics Plant biology not elsewhere classified Polyscias Araliaceae chloroplast genome plastome 45S nuclear rDNA internal transcribed spacer phylogenomics Third Party Assembly TPA Rfam <pre><pre>Twelve annotated nucleotide assemblies for six Polyscias (Araliaceae) species: six complete plastid (chloroplast) genomes (~156 kb each) and six complete 45S nuclear ribosomal DNA cistrons (18S-ITS1-5.8S-ITS2-26S; ~5.8 kb each). Every sequence was assembled by the authors from third-party, publicly available SRA reads that were generated by other groups; the source SRA run for each sequence is given in the FASTA header and in sample_metadata.tsv. Because the underlying reads were not generated by the authors, these derived assemblies are eligible for INSDC deposition only as Third Party Assembly (TPA:assembly) records and INSDC accessions may not be available for them; they are archived here so the results remain openly available, citable and reproducible. Files: FASTA sequences; NCBI 5-column feature tables (.tbl) and GenBank flatfiles (.gbf) with full annotation; per-sequence metadata (sample_metadata.tsv); README. Assembly programs: plastid genomes - dnaLCW v4.21 (Illumina) and GetOrganelle v1.7.7.1 (PacBio HiFi); 45S nrDNA - dnaLCW v4.21 (Illumina) and hifiasm v0.25.0 (PacBio HiFi). The 18S, 5.8S and 26S boundaries of the 45S cistrons were located with Infernal cmscan against the Rfam covariance models SSU_rRNA_eukarya, 5_8S_rRNA and LSU_rRNA_eukarya. Primary read data (INSDC Sequence Read Archive): SRR19607894, SRR19607893, SRR19607909, SRR28058088, SRR28058077, SRR28058093.</pre></pre> 2026-09-24T04:48:51Z Dataset Dataset 10.6084/m9.figshare.33979093.v1 https://figshare.com/articles/dataset/Plastid_genomes_and_45S_nuclear_rDNA_cistrons_of_six_i_Polyscias_i_species_assembled_from_publicly_available_SRA_data/33979093 CC BY 4.0