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Research article
Hong Liu
South-central University for Nationalities
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7227-2476
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated.
Results: To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection.
Conclusion: This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.
Keywords
Saxifragaceae, Chrysosplenium, Chloroplast genome, Opposite leaves, Alternate leaves, Phylogenomics
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This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.jpg
Additional File 1: The protein sequences (A) and expression values in leaf (B) of both chloroplast rpl32 (Cp_rpl32) and its nuclear homolog (Nu_rpl32) in C. sinicum.
- Additionalfile5.jpg
Additional File 5: Analyses of repeat sequences in the ten species of Saxifragaceae. (A) The analysis of simple sequence repeats (SSRs) in chloroplast genomes of Saxifragaceae. (B) The repeat types in Saxifragaceae.
- Additionalfile6.jpg
Additional File 6: The comparative analysis with Shuffle-LAGAN program of the whole chloroplast genome of seven different species from the family of Saxifragaceae.
- Additionalfile2.docx
- Additionalfile4.xlsx
- Additionalfile3.jpg
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Editorial decision: Minor revision
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Editor invited
On 19 Jul, 2020
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Editorial decision: Minor revision
On 28 Jun, 2020
Review #2 received
Received 24 Jun, 2020
Reviewer #2 agreed
On 05 Jun, 2020
Review #1 received
Received 05 Jun, 2020
Reviewers invited
Invitations sent on 03 Jun, 2020
Reviewer #1 agreed
On 03 Jun, 2020
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Epigenetics & Genomics
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See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Hong Liu
South-central University for Nationalities
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7227-2476
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
Version 5
Posted 03 Sep, 2020
No community comments so far
Submission checks complete
On 01 Sep, 2020
Editorial decision: Accept
On 01 Sep, 2020
No comments provided
Submission checks complete
On 26 Aug, 2020
Editorial decision: Minor revision
On 25 Aug, 2020
No comments provided
Editorial decision: Minor revision
On 19 Aug, 2020
Editor assigned
On 10 Aug, 2020
Submission checks complete
On 09 Aug, 2020
Editor invited
On 09 Aug, 2020
No comments provided
Reviewer #2 agreed
On 29 Jul, 2020
Review #2 received
Received 29 Jul, 2020
Editorial decision: Minor revision
On 29 Jul, 2020
Review #1 received
Received 25 Jul, 2020
Reviewers invited
Invitations sent on 24 Jul, 2020
Reviewer #1 agreed
On 24 Jul, 2020
Editor assigned
On 20 Jul, 2020
Submission checks complete
On 19 Jul, 2020
Editor invited
On 19 Jul, 2020
No comments provided
Editorial decision: Minor revision
On 28 Jun, 2020
Review #2 received
Received 24 Jun, 2020
Reviewer #2 agreed
On 05 Jun, 2020
Review #1 received
Received 05 Jun, 2020
Reviewers invited
Invitations sent on 03 Jun, 2020
Reviewer #1 agreed
On 03 Jun, 2020
Editor assigned
On 28 May, 2020
First submitted
On 27 May, 2020
Submission checks complete
On 27 May, 2020
Editor invited
On 27 May, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated.
Results: To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection.
Conclusion: This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.jpg
Additional File 1: The protein sequences (A) and expression values in leaf (B) of both chloroplast rpl32 (Cp_rpl32) and its nuclear homolog (Nu_rpl32) in C. sinicum.
- Additionalfile5.jpg
Additional File 5: Analyses of repeat sequences in the ten species of Saxifragaceae. (A) The analysis of simple sequence repeats (SSRs) in chloroplast genomes of Saxifragaceae. (B) The repeat types in Saxifragaceae.
- Additionalfile6.jpg
Additional File 6: The comparative analysis with Shuffle-LAGAN program of the whole chloroplast genome of seven different species from the family of Saxifragaceae.
- Additionalfile2.docx
- Additionalfile4.xlsx
- Additionalfile3.jpg
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