Abstract
Introduction The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. Methods In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. Results The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions ( petN-psbM , rps16-trnQ , rpl32-trnL , rpl32 , and ycf1 ) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Discussion Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.
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Claims 16
Claim · model-written summary
Linderniaceae plastid genomes range from 152,386 to 154,402 bp.
- Taxon
- LinderniaceaeLinderniaceaee0
- Outcome
- plastid genome sizee0
- Value
- 152,386 bp to 154,402 bpe0
Verbatim
e0“The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure.”
Claim · model-written summary
Linderniaceae plastomes have a typical quartile structure.
- Taxon
- LinderniaceaeLinderniaceaee0
- Outcome
- typical quartile structuree0
Verbatim
e0“The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure.”
Claim · model-written summary
All plastomes encoded 114 unique genes.
- Taxon
- LinderniaceaeLinderniaceaet0
- Outcome
- unique genese0
- Value
- 114 unique genese0
Verbatim
e0“All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes.”
t0“Linderniaceae”
Claim · model-written summary
The 114 genes comprise 80 protein-coding, 30 tRNA and four rRNA genes.
- Taxon
- LinderniaceaeLinderniaceaet0
- Outcome
- protein-coding genes, 30 tRNA genes, and four rRNA genese0
Verbatim
e0“All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes.”
t0“Linderniaceae”
Claim · model-written summary
Inverted repeats were more conserved than single-copy regions.
- Taxon
- LinderniaceaeLinderniaceaet0
- Outcome
- inverted repeat regionse0
- Direction
- more conservede0
- Comparator
- single-copy regionse0
Verbatim
e0“The inverted repeat regions were more conserved compared with the single-copy regions.”
t0“Linderniaceae”
Claim · model-written summary
The plastomes contained 1803 microsatellites.
- Taxon
- LinderniaceaeLinderniaceaet0
- Outcome
- microsatellitese0
- Value
- 1803 microsatellitese0
Verbatim
e0“A total of 1803 microsatellites and 1909 long sequence repeats were identified”
t0“Linderniaceae”
Claim · model-written summary
The plastomes contained 1909 long sequence repeats.
- Taxon
- LinderniaceaeLinderniaceaet0
- Outcome
- long sequence repeatse0
- Value
- 1909 long sequence repeatse0
Verbatim
e0“A total of 1803 microsatellites and 1909 long sequence repeats were identified”
t0“Linderniaceae”
Claim · model-written summary
Five hypervariable regions were identified.
- Taxon
- LinderniaceaeLinderniaceaet0
- Outcome
- hypervariable regionse0
- Value
- five hypervariable regionse0
Verbatim
e0“five hypervariable regions ( petN-psbM , rps16-trnQ , rpl32-trnL , rpl32 , and ycf1 ) were screened out”
t0“Linderniaceae”
Claim · model-written summary
Most protein-coding genes were relatively conserved.
- Taxon
- LinderniaceaeLinderniaceaet0
- Outcome
- protein-coding genes were relatively conservede0
Verbatim
e0“Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species.”
t0“Linderniaceae”
Claim · model-written summary
The ycf2 gene was under positive selection in a few species.
- Taxon
- LinderniaceaeLinderniaceaet0
- Gene
- ycf2e0
- Outcome
- positive selectione0
- Qualifier
- in a few speciese0
Verbatim
e0“only the ycf2 gene found under positive selection in a few species”
t0“Linderniaceae”
Claim · model-written summary
Linderniaceae was a distinct phylogenetic lineage.
- Taxon
- LinderniaceaeLinderniaceaee0
- Outcome
- distinctive lineagee0
Verbatim
e0“Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage”
Claim · model-written summary
Currently circumscribed Vandellia was non-monophyletic.
- Outcome
- non-monophyletice0
Verbatim
e0“the presently circumscribed Vandellia and Torenia were non-monophyletic”
Claim · model-written summary
Currently circumscribed Torenia was non-monophyletic.
- Outcome
- non-monophyletice0
ToreniaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the presently circumscribed Vandellia and Torenia were non-monophyletic”
Claim · model-written summary
Linderniaceae plastomes were conserved in structure, gene order and content.
- Taxon
- LinderniaceaeLinderniaceaee0
- Outcome
- structure, gene order, and gene contente0
Verbatim
e0“the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content”
Claim · model-written summary
Evidence supported Yamazakia as separate from Vandellia.
- Outcome
- separating from Vandelliae0
YamazakiaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we supported the newly established Yamazakia separating from Vandellia”
Claim · model-written summary
Evidence supported Picria as a separate genus.
- Outcome
- a separate genuse0
Verbatim
e0“the monotypic Picria as a separate genus”