Illumina sequencing data of the complete chloroplast genome of rare species Juniperus seravschanica (Cupressaceae) from Kazakhstan.

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The distribution area of J. seravschanica extends from Central Asia (Kazakhstan, Uzbekistan, Kyrgyzstan, Tajikistan, and Turkmenistan) to northern and eastern Afghanistan, northern Pakistan, Kashmir, southeastern Iran, and Oman. J. seravschanica occurred in the southern part of Kazakhstan along with the ranges Karatau, Talas Alatau, Kyrgyz Alatau, Chu-Ili, Karzhantau, and Ugam. The distribution area of J. seravschanica is constantly decreasing due to intensive logging, forest fires, and excessive cattle grazing. The species has ecological importance in the stabilization of mountain slopes against erosion, for hydrobiological regulation, and as a significant medicinal herb. The species J. excelsa M. Bieb., J. polycarpos K.Koch (var. polycarpos and var. turcomanica R.P.Adams), and J. seravschanica are morphologically very similar with some difficulties in species identification. For a better understanding of the evolutionary relationship of these species in the Juniperus genus, it is important to obtain genetic information on the highly conserved chloroplast (cp) genome. Due to the conserved genomic structure, the cp genome nucleotide sequences are widely used in species distinguishing and reconstructing phylogenetic relationships. Unfortunately, there are no publicly available nucleotide sequences of cp genomes data for J. polycarpos (var. polycarpos and var. turcomanica), J. excelsa and J. seravschanica. We report the de novo assembly of the J. seravschanica chloroplast genome by applying next-generation sequencing technology based on Illumina NovaSeq 6000. The assembled cp genome of J. seravschanica is 127,609 bp in length and contained 118 genes, including 82 protein-coding genes, 32 transfer RNA genes, and 4 ribosomal RNA genes. In total 152 simple sequence repeats were identified in the chloroplast genome sequence of J. seravschanica. The Bioproject (PRJNA883033), Sequence Read Archive (SRR21673293), and GenBank (OL684343) data were deposited at National Center for Biotechnology Information.", "claims": [{"id": "claim-method", "statement": "Maximum parsimony concatenated phylogenetic tree based on matK and rbcL nucleotide sequences with 1000 bootstraps.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36687154", "locator": "sections[5] \"Data Description\" paragraph 5", "quote": "Maximum parsimony concatenated phylogenetic tree based on matK and rbcL nucleotide sequences with 1000 bootstraps."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Sequence Read Archive (Original data) (National Center for Biotechnology Information).\nComplete chloroplast genome of Juniperus seravschanica (Original data) (National Center for Biotechnology Information).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36687154", "locator": "sections[17] \"Data Availability\" paragraphs 1-3", "quote": "Sequence Read Archive (Original data) (National Center for Biotechnology Information).\nComplete chloroplast genome of Juniperus seravschanica (Original data) (National Center for Biotechnology Information)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The assembled cp genome of J. seravschanica is 127,609 bp in length and contained 118 genes, including 82 protein-coding genes, 32 transfer RNA genes, and 4 ribosomal RNA genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36687154", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The assembled cp genome of J. seravschanica is 127,609 bp in length and contained 118 genes, including 82 protein-coding genes, 32 transfer RNA genes, and 4 ribosomal RNA genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The assembled cp genome of J. seravschanica is 127,609 bp in length and contained 118 genes, including 82 protein-coding genes, 32 transfer RNA genes, and 4 ribosomal RNA genes.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36687154"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. 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