See the published version of this article at BMC Plant Biology.
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
Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea
Jie Yu
Southwest University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Plant Biology.
Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.
Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.
Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.
Keywords
Pilea, plastid genome, interspecific diversity, hypervariable region, phylogenetic relationship
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
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
Version 4
Posted 21 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 22 Nov, 2020
Editor assigned
On 11 Nov, 2020
Submission checks complete
On 11 Nov, 2020
Editor invited
On 11 Nov, 2020
No comments provided
Editorial decision: Minor revision
On 08 Nov, 2020
Review #1 received
Received 01 Nov, 2020
Reviewer #1 agreed
On 29 Oct, 2020
Reviewers invited
Invitations sent on 25 Oct, 2020
Editor assigned
On 19 Oct, 2020
Submission checks complete
On 18 Oct, 2020
Editor invited
On 18 Oct, 2020
No comments provided
Review #2 received
Received 22 Sep, 2020
Editorial decision: Major revision
On 22 Sep, 2020
Review #1 received
Received 21 Sep, 2020
Reviewer #2 agreed
On 31 Aug, 2020
Reviewers invited
Invitations sent on 26 Aug, 2020
Reviewer #1 agreed
On 26 Aug, 2020
Editor assigned
On 28 Jul, 2020
Submission checks complete
On 27 Jul, 2020
Editor invited
On 27 Jul, 2020
First submitted
On 25 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Learn more about our company.
This preprint is under consideration at BMC Plant Biology. A preprint is 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
Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea
Jie Yu
Southwest University
Corresponding Author
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
Version 4
Posted 21 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 22 Nov, 2020
Editor assigned
On 11 Nov, 2020
Submission checks complete
On 11 Nov, 2020
Editor invited
On 11 Nov, 2020
No comments provided
Editorial decision: Minor revision
On 08 Nov, 2020
Review #1 received
Received 01 Nov, 2020
Reviewer #1 agreed
On 29 Oct, 2020
Reviewers invited
Invitations sent on 25 Oct, 2020
Editor assigned
On 19 Oct, 2020
Submission checks complete
On 18 Oct, 2020
Editor invited
On 18 Oct, 2020
No comments provided
Review #2 received
Received 22 Sep, 2020
Editorial decision: Major revision
On 22 Sep, 2020
Review #1 received
Received 21 Sep, 2020
Reviewer #2 agreed
On 31 Aug, 2020
Reviewers invited
Invitations sent on 26 Aug, 2020
Reviewer #1 agreed
On 26 Aug, 2020
Editor assigned
On 28 Jul, 2020
Submission checks complete
On 27 Jul, 2020
Editor invited
On 27 Jul, 2020
First submitted
On 25 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Plant Biology.
Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.
Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.
Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7