The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis

Xia, Chen; Zuo, Youwei; Xue, Tiantian; Kang, Ming; Zhang, Huan; Zhang, Xiaoxia; Wang, Binru; Zhang, Jiabin; Hongping, Deng

doi:10.3389/fpls.2023.1224308

Cited by 2 publications

References 90 publications

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

McEvoy,

Meyer,

Hasenstab-Lehman

et al. 2024

G3: Genes, Genomes, Genetics

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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 Gbp 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 (LTR) 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 LTR, 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 (WGD) 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.

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

McEvoy,

Meyer,

Hasenstab-Lehman

et al. 2024

G3: Genes, Genomes, Genetics

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Genome Report: The reference genome of an endangered Asteraceae,Deinandra increscenssubsp.villosa, endemic to the Central Coast of California

McEvoy,

Meyer,

Hasenstab-Lehman

et al. 2024

Preprint

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We present a high-quality reference genome of the federally endangered Gaviota tarplant,Deinandra increscenssubsp.villosa(Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Stewards of remaining populations have planned to apply conservation strategies informed by whole genome approaches. Generating PacBio Hifi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a genome of 1.67 Gbp as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. BUSCO completeness for the final assembly was 98.1% with 15.7% duplicate copies. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTR) covered 44.0% of the genome withCopiafamilies predominant at 22.9% followed byGypsyat 14.2%. BothGypsyandCopiaelements were common in ancestral peaks of LTR, and the most abundant element was aGypsyelement containing nestedCopia/Angelasequenced similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 41,039 genes and 69,563 transcripts, of which >99% were functionally annotated. BUSCO duplication rates remained very high with proteins at 50.4% complete duplicates and 46.0% single copy. Whole genome duplication (WGD) 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. Tandem genes were twice as prevalent as WGD genes suggesting tandem genes could be an important strategy of environmental adaptation in this species.Article SummaryWe introduce a high-quality reference genome for the endangered Gaviota tarplant. The assembly is 1.67 Gbp with 98.1% BUSCO completeness and 41 K annotated genes. We find extensiveCopialong terminal repeat sequences and tandem genes that suggest environmental adaptation strategies. Comparisons with sunflower suggest a shared polyploidization event around 27 million years ago, close to the date of the common ancestor divergence. This work underlines the importance of genomic studies in accurately understanding adaptations and conservation needs.

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The genetic structure and demographic history revealed by whole-genome resequencing provide insights into conservation of critically endangered Artocarpus nanchuanensis

Cited by 2 publications

References 90 publications

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

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

Genome Report: The reference genome of an endangered Asteraceae,Deinandra increscenssubsp.villosa, endemic to the Central Coast of California

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