Abstract
BACKGROUND: The liverwort Apopellia endiviifolia, a dioicous, simple thalloid species, is notable for its cryptic diversity, habitat adaptability, and genomic innovation, and it represents a clade that is sister to all other Jungermanniopsida. These features make A. endiviifolia an essential model for exploring speciation mechanisms and the evolution of genome structures within liverworts. FINDINGS: We present the genome assembly of a haploid A. endiviifolia isolate with a total size of 2,914,960,273 bp and an N50 of 468,157,909 bp, demonstrating high completeness (99.2% BUSCO) and a high consensus quality (quality value 47.6). The assembly consisted of 9 chromosomes, which included 18 telomeres and 9 centromeres (ranging from 1.9 to 5 Mbp in length). RNA sequencing-based annotation identified 34,615 genes, predominantly protein coding. The transposable elements comprised 12.16% long terminal repeat elements and 57 Helitrons. Among the retroelements, the Copia and Gypsy superfamilies comprised 8.94% and 2.95% of the genome, respectively. The Ty3/Gypsy superfamily was significantly enriched in centromeric regions. The average GC content ranged from 38.8% to 39.6%, with gene density varying between 5.52 and 9.78 genes per 500 kbp. Synteny analysis of related liverwort species has revealed complex chromosomal relationships, indicating extensive genome rearrangements among species. CONCLUSIONS: This study provides the first high-quality reference genome assembly of the haploid liverwort A. endiviifolia. Assembly and annotation offer valuable resources for investigating liverwort evolution, centromere biology, and genome expansion in simple thalloid liverworts.
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Claims 12
Claim · model-written summary
A haploid A. endiviifolia genome assembly was produced at 2,914,960,273 bp with N50 468,157,909 bp.
- Taxon
- Apopellia endiviifolia
_5726.JPG?width=60)
Apopellia endiviifoliae0 - Outcome
- genome assemblye1
- Value
- 2,914,960,273 bpe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_5726.JPG?width=500)
Verbatim
e0“The liverwort Apopellia endiviifolia”
e1“We present the genome assembly of a haploid A. endiviifolia isolate with a total size of 2,914,960,273 bp and an N50 of 468,157,909 bp”
Claim · model-written summary
The assembly had 99.2% BUSCO completeness and quality value 47.6.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- completenesse1
- Value
- 99.2% BUSCOe1
- Qualifier
- quality value 47.6e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“demonstrating high completeness (99.2% BUSCO) and a high consensus quality (quality value 47.6)”
Claim · model-written summary
The assembly comprised nine chromosomes, 18 telomeres and nine centromeres.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- chromosomese1
- Value
- 9 chromosomese1
- Qualifier
- 18 telomeres and 9 centromerese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“The assembly consisted of 9 chromosomes, which included 18 telomeres and 9 centromeres (ranging from 1.9 to 5 Mbp in length)”
Claim · model-written summary
Annotation identified 34,615 predominantly protein-coding genes.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- genese1
- Value
- 34,615 genese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“RNA sequencing-based annotation identified 34,615 genes, predominantly protein coding”
Claim · model-written summary
Long terminal repeat elements comprised 12.16% of transposable elements.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- long terminal repeat elementse1
- Value
- 12.16%e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“The transposable elements comprised 12.16% long terminal repeat elements and 57 Helitrons”
Claim · model-written summary
The transposable elements included 57 Helitrons.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- Helitronse1
- Value
- 57 Helitronse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“57 Helitrons”
Claim · model-written summary
Copia elements comprised 8.94% of the genome.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- Copiae1
- Value
- 8.94%e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“the Copia and Gypsy superfamilies comprised 8.94% and 2.95% of the genome, respectively”
Claim · model-written summary
Gypsy elements comprised 2.95% of the genome.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- Gypsye1
- Value
- 2.95%e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“the Copia and Gypsy superfamilies comprised 8.94% and 2.95% of the genome, respectively”
Claim · model-written summary
Ty3/Gypsy was significantly enriched in centromeric regions.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Gene
- Ty3/Gypsye1
- Outcome
- enriched in centromeric regionse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“The Ty3/Gypsy superfamily was significantly enriched in centromeric regions”
Claim · model-written summary
Average GC content ranged from 38.8% to 39.6%.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- average GC contente1
- Value
- 38.8% to 39.6%e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“The average GC content ranged from 38.8% to 39.6%”
Claim · model-written summary
Gene density ranged from 5.52 to 9.78 genes per 500 kbp.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- gene densitye1
- Value
- 5.52 and 9.78 genes per 500 kbpe1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“gene density varying between 5.52 and 9.78 genes per 500 kbp”
Claim · model-written summary
Synteny analysis indicated extensive rearrangements among related liverworts.
- Taxon
- Apopellia endiviifoliaApopellia endiviifoliae0
- Outcome
- complex chromosomal relationshipse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Apopellia endiviifolia”
e1“Synteny analysis of related liverwort species has revealed complex chromosomal relationships, indicating extensive genome rearrangements among species”