Abstract
Background: In the Sesamum species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships. Results: In the present study, we generated complete chloroplast genomes of six wild relatives ( Sesamum alatum , Sesamum angolense , Sesamum pedaloides , Ceratotheca sesamoides (syn. Sesamum sesamoides ), Ceratotheca triloba (syn. Sesamum trilobum ), and Sesamum radiatum ) and a Korean cultivar, Sesamum indicum cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863–153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including ndhA , ndhE , ndhF , ycf1 , and psaC–ndhD . Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05 million years ago (Mya). In addition, S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others. Conclusion: Altogether, we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum , respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the Sesamum species complex.
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Claims 11
Claim · model-written summary
Complete chloroplast genomes were generated for six wild relatives and a Korean cultivar.
- Material
- Sesamum indicum cv. Goenbaeke0
- Outcome
- complete chloroplast genomese0
- Value
- six wild relativese0
SesamumOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we generated complete chloroplast genomes of six wild relatives ( Sesamum alatum , Sesamum angolense , Sesamum pedaloides , Ceratotheca sesamoides (syn. Sesamum sesamoides ), Ceratotheca triloba (syn. Sesamum trilobum ), and Sesamum radiatum ) and a Korean cultivar, Sesamum indicum cv. Goenbaek.”
Claim · model-written summary
The chloroplast genomes had a typical quadripartite structure.
- Outcome
- typical quadripartite chloroplast structuree0
Not reportedTaxon
Verbatim
e0“A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed.”
Claim · model-written summary
The chloroplast genomes contained 114 unique genes, including 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs.
- Outcome
- unique genese0
- Value
- 114 unique genese0
- Qualifier
- 80 coding genes, four ribosomal RNAs, and 30 transfer RNAse0
Not reportedTaxon
Verbatim
e0“A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted.”
Claim · model-written summary
The chloroplast genomes ranged from 152, 863 to 153, 338 bp and showed IR contraction and expansion.
- Outcome
- chloroplast genomese0
- Value
- 152, 863–153, 338 bpe0
- Qualifier
- IR contraction/expansion phenomenone0
Not reportedTaxon
Verbatim
e0“The chloroplast genomes (152, 863–153, 338 bp) exhibited the IR contraction/expansion phenomenon”
Claim · model-written summary
Coding and non-coding regions of the chloroplast genomes were conserved.
Not reportedTaxon
Verbatim
e0“were quite conserved in both coding and non-coding regions.”
Claim · model-written summary
Several genes had high nucleotide diversity.
- Gene
- ndhA , ndhE , ndhF , ycf1 , and psaC–ndhDe0
- Outcome
- nucleotide diversity indexe0
- Direction
- high valuese0
Not reportedTaxon
Verbatim
e0“high values of the nucleotide diversity index were found in several genes, including ndhA , ndhE , ndhF , ycf1 , and psaC–ndhD .”
Claim · model-written summary
Concordant tree topologies suggest ndhF can discriminate taxa.
Not reportedTaxon
Verbatim
e0“Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination.”
Claim · model-written summary
S. radiatum and its sister C. sesamoides diverged approximately 0.05 million years ago.
- Taxon
- S. radiatum
Sesamum radiatume0 - Outcome
- occurred concomitantlye0
- Value
- 0.05 million years agoe0
- Qualifier
- approximatelye0
- Comparator
- C. sesamoidese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05 million years ago (Mya).”
Claim · model-written summary
S. alatum formed a distinct clade with a long genetic distance and possible early speciation.
- Taxon
- S. alatum
Sesamum alatume0 - Outcome
- forming a single cladee0
- Qualifier
- long genetic distance and potential early speciation evente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others.”
Claim · model-written summary
The authors proposed renaming C. sesamoides as S. sesamoides.
- Taxon
- C. sesamoides
_(16347957338).jpg?width=60)
Ceratotheca sesamoidese0 - Outcome
- rename C. sesamoidese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_(16347957338).jpg?width=500)
Verbatim
e0“we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum , respectively”
Claim · model-written summary
The authors proposed renaming C. triloba as S. trilobum.
- Taxon
- C. triloba
Ceratotheca trilobae0 - Outcome
- S. trilobume0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum , respectively”