Abstract
Abstract This study presented the first complete plastome of Elatostema lineolatum var. major, a wild edible plant from Kanglung, Bhutan. The 150 292 bp genome exhibited the typical quadripartite angiosperm structure, comprising a large single-copy (LSC) region (83 953 bp), a small single-copy (SSC) region (17 207 bp), and two inverted repeats (24 566 bp each). It encoded 131 genes, including 86 protein-coding, 37 tRNAs, and 8 rRNAs. Comparative analysis revealed high synteny and gene order conservation among Elatostema species, reinforcing its monophyly. Analysis of 242 Urticaceae plastomes showed conserved structures, with genome sizes ranging from 142 627 to 170 958 bp (mean: 154 906.10 ± 5432.30 bp). GC content varied slightly (35.32–37.22%, mean: 36.31 ± 0.47%), aligning with values for Procris crenata (36.5%) and Urtica fissa (36.60%). The quadripartite structure remained stable, with LSC (83 919.20 ± 4288.10 bp), SSC (18 611.88 ± 2407.50 bp), and IR (26 186.78 ± 3841.20 bp) regions consistent across Urticaceae. Eleven hypervariable regions were identified through nucleotide diversity analysis, with ycf1 emerging as a promising DNA barcode. Additionally, SSRs serve as valuable molecular markers for population genetics. Phylogenetic analysis placed E. lineolatum near E. dissectum, supporting recent divergence. Ortholog analysis suggested evolutionary stability, aiding taxonomic resolution. Ka/Ks analysis detected positive selection in ycf2, indicating adaptation to diverse habitats in Bhutan. This study provides insights into the genomic structure and evolutionary dynamics of E. lineolatum, a wild edible plant, contributing to our understanding of Urticaceae evolution and offering valuable resources for future research on biodiversity, conservation, and its ecological significance in Bhutan.
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Claims 19
Claim · model-written summary
The first complete plastome was presented for Elatostema lineolatum var. major.
- Taxon
- Elatostema lineolatum var. major
Elatostema lineolatum var. majore0 - Outcome
- complete plastomee0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the first complete plastome of Elatostema lineolatum var. major”
Claim · model-written summary
The plastome was 150 292 bp and had a quadripartite structure.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- genomee0
- Value
- 150 292 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The 150 292 bp genome exhibited the typical quadripartite angiosperm structure”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
The large single-copy region was 83 953 bp.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- large single-copy (LSC) regione0
- Value
- 83 953 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a large single-copy (LSC) region (83 953 bp)”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
The small single-copy region was 17 207 bp.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- small single-copy (SSC) regione0
- Value
- 17 207 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a small single-copy (SSC) region (17 207 bp)”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
Each inverted repeat was 24 566 bp.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- inverted repeatse0
- Value
- 24 566 bpe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“two inverted repeats (24 566 bp each)”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
The plastome encoded 131 genes.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- genese0
- Value
- 131 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“It encoded 131 genes, including 86 protein-coding, 37 tRNAs, and 8 rRNAs”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
The plastome encoded 86 protein-coding genes.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- protein-codinge0
- Value
- 86 protein-codinge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“86 protein-coding”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
The plastome encoded 37 tRNAs.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- tRNAse0
- Value
- 37 tRNAse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“37 tRNAs”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
The plastome encoded 8 rRNAs.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- rRNAse0
- Value
- 8 rRNAse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“8 rRNAs”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
Elatostema plastomes had high synteny and conserved gene order.
- Taxon
- Elatostema species
Elatostemae0 - Outcome
- high synteny and gene order conservatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“high synteny and gene order conservation among Elatostema species”
Claim · model-written summary
Urticaceae plastomes had conserved structures and sizes from 142 627 to 170 958 bp.
- Taxon
- UrticaceaeUrticaceaee0
- Outcome
- genome sizese0
- Value
- 142 627 to 170 958 bpe0
Verbatim
e0“Analysis of 242 Urticaceae plastomes showed conserved structures, with genome sizes ranging from 142 627 to 170 958 bp (mean: 154 906.10 ± 5432.30 bp)”
Claim · model-written summary
Urticaceae plastome GC content ranged 35.32–37.22%.
- Taxon
- UrticaceaeUrticaceaet0
- Outcome
- GC contente0
- Value
- 35.32–37.22%e0
Verbatim
e0“GC content varied slightly (35.32–37.22%, mean: 36.31 ± 0.47%)”
t0“Urticaceae”
Claim · model-written summary
The Urticaceae quadripartite structure was stable across species.
- Taxon
- UrticaceaeUrticaceaee0
- Outcome
- quadripartite structuree0
Verbatim
e0“The quadripartite structure remained stable, with LSC (83 919.20 ± 4288.10 bp), SSC (18 611.88 ± 2407.50 bp), and IR (26 186.78 ± 3841.20 bp) regions consistent across Urticaceae”
Claim · model-written summary
Eleven hypervariable regions were identified.
- Taxon
- UrticaceaeUrticaceaet0
- Outcome
- hypervariable regionse0
- Value
- Elevene0
Verbatim
e0“Eleven hypervariable regions were identified through nucleotide diversity analysis”
t0“Urticaceae”
Claim · model-written summary
The ycf1 region was identified as a promising DNA barcode.
- Taxon
- UrticaceaeUrticaceaet0
- Gene
- ycf1e0
- Outcome
- promising DNA barcodee0
Not reportedComparatorValue
Verbatim
e0“ycf1 emerging as a promising DNA barcode”
t0“Urticaceae”
Claim · model-written summary
SSRs were identified as useful population genetic markers.
- Taxon
- UrticaceaeUrticaceaet0
- Outcome
- molecular markers for population geneticse0
Not reportedComparatorValue
Verbatim
e0“SSRs serve as valuable molecular markers for population genetics”
t0“Urticaceae”
Claim · model-written summary
Phylogeny placed E. lineolatum near E. dissectum.
- Taxon
- E. lineolatumElatostema lineolatume0
- Outcome
- near E. dissectume0
- Comparator
- E. dissectume0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Phylogenetic analysis placed E. lineolatum near E. dissectum”
Claim · model-written summary
Ortholog analysis suggested evolutionary stability.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Outcome
- evolutionary stabilitye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Ortholog analysis suggested evolutionary stability”
t0“Elatostema lineolatum var. major”
Claim · model-written summary
Ka/Ks analysis detected positive selection in ycf2.
- Taxon
- Elatostema lineolatum var. majorElatostema lineolatum var. majort0
- Gene
- ycf2e0
- Outcome
- positive selectione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Ka/Ks analysis detected positive selection in ycf2”
t0“Elatostema lineolatum var. major”