Abstract
The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.
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Claims 9
Claim · model-written summary
New plastomes showed increased simple sequence repeats during complex thalloid liverwort diversification.
- Taxon
- Conocephalum, Riccia and Sphaerocarpos species
Sphaerocarpos_1022.jpg?width=60)
Conocephalum
Ricciae0 - Outcome
- simple sequence repeatse0
- Direction
- increasee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_1022.jpg?width=500)
Verbatim
e0“The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage”
Claim · model-written summary
Long TA motifs required long-read nanopore sequencing for reliable plastome assembly.
Not reportedTaxon
Verbatim
e0“The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads”
Claim · model-written summary
SSR accumulation enabled inverted-repeat expansion incorporating rps12 and rps7.
Not reportedTaxon
Verbatim
e0“The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes”
Claim · model-written summary
Inverted-repeat expansion at genus level was first reported for non-flowering plants.
Verbatim
e0“The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants”
Claim · model-written summary
Plastome SSR presence was specific to simple thalloid species among liverwort lineages.
Verbatim
e0“the presence of SSR in plastomes is specific for simple thalloid species”
Claim · model-written summary
Phylogenomic trees confirmed Marchantiidae monophyly.
- Taxon
- MarchantiidaeMarchantiidaee0
- Outcome
- monophyly of Marchantiidaee0
Verbatim
e0“Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae”
Claim · model-written summary
Dumortiera-Reboulia relationships varied by dataset.
Verbatim
e0“dataset-dependent results of Dumortiera-Reboulia relationships”
Claim · model-written summary
A significant barcoding gap appeared even between recently divergent Conocephalum species.
- Taxon
- Conocephalum speciesConocephalume0
- Outcome
- barcoding gape0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species”
Claim · model-written summary
Sliding-window analysis identified 18 optimal 500 bp barcodes for all studied species.
- Outcome
- barcodes that enable the molecular identification of all studied speciese0
- Value
- 18e0
- Qualifier
- 500 bp longe0
Not reportedTaxon
Verbatim
e0“The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species”