The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California.
G3 (Bethesda)
; 14(8)2024 Aug 07.
Article
em En
| MEDLINE
| ID: mdl-38845594
ABSTRACT
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 â¼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genoma de Planta
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Espécies em Perigo de Extinção
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Asteraceae
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Anotação de Sequência Molecular
País/Região como assunto:
America do norte
Idioma:
En
Revista:
G3 (Bethesda)
Ano de publicação:
2024
Tipo de documento:
Article