دورية أكاديمية
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The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California.

التفاصيل البيبلوغرافية
العنوان: The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California.
المؤلفون: McEvoy SL; Department of Conservation and Research, Santa Barbara Botanic Garden, Santa Barbara, CA 93105, USA., Meyer RS; Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Hasenstab-Lehman KE; Department of Conservation and Research, Santa Barbara Botanic Garden, Santa Barbara, CA 93105, USA., Guilliams CM; Department of Conservation and Research, Santa Barbara Botanic Garden, Santa Barbara, CA 93105, USA.
المصدر: G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Aug 07; Vol. 14 (8).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN: 2160-1836 (Electronic) Linking ISSN: 21601836 NLM ISO Abbreviation: G3 (Bethesda) Subsets: MEDLINE
أسماء مطبوعة: Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Bethesda, MD : Genetics Society of America, 2011-
مواضيع طبية MeSH: Endangered Species* , Asteraceae*/genetics , Genome, Plant* , Molecular Sequence Annotation*, California ; Phylogeny
مستخلص: We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a haploid consensus genome of 1.67 Gb as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTRs) covered 44.0% of the genome with Copia families predominant at 22.9% followed by Gypsy at 14.2%. Both Gypsy and Copia elements were common in ancestral peaks of LTRs, and the most abundant element was a Gypsy element containing nested Copia/Angela sequence similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 33,257 genes and 68,942 transcripts, of which 99% were functionally annotated. BUSCO scores for the annotated proteins were 96.0% complete of which 77.6% was single copy and 18.4% duplicates. Whole genome duplication synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.
Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
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معلومات مُعتمدة: S10 OD010786 United States OD NIH HHS; BayWa r.e
فهرسة مساهمة: Keywords: Deinandra increscens subsp. villosa; Asteraceae; Compositae; Madiinae; conservation; endangered; endemic; tandem genes; whole genome duplication
تواريخ الأحداث: Date Created: 20240607 Date Completed: 20240807 Latest Revision: 20240809
رمز التحديث: 20240809
مُعرف محوري في PubMed: PMC11304951
DOI: 10.1093/g3journal/jkae117
PMID: 38845594
قاعدة البيانات: MEDLINE
الوصف
تدمد:2160-1836
DOI:10.1093/g3journal/jkae117