Visitors   Views   Downloads

Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect

View preprint
674 days ago
Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect https://t.co/XYsbbuGsKR
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

Supplemental Information

Cycas panzhihuaensis psbA-trnH haplotype and outgroup intergenic spacer region, partial sequence, chloroplast

DOI: 10.7287/peerj.preprints.27265v1/supp-1

Cycas panzhihuaensis psbM-trnD haplotype and outgroup intergenic spacer region, partial sequence, chloroplast

DOI: 10.7287/peerj.preprints.27265v1/supp-2

Cycas panzhihuaensis trnS-trnG haplotype and outgroup intergenic spacer region, partial sequence, chloroplast

DOI: 10.7287/peerj.preprints.27265v1/supp-3

Cycas panzhihuaensis haplotype and outgroup phytochrome P gene (PHYP), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-4

Cycas panzhihuaensis haplotype and outgroup actin 5 gene (AC5), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-5

Cycas panzhihuaensis haplotype and outgroup heat shock protein 70 kDa gene (HSP70), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-6

Cycas panzhihuaensis haplotype and outgroup aspartate aminotransferase gene (AAT), partial sequence, single-copy nuclear genes

DOI: 10.7287/peerj.preprints.27265v1/supp-7

Microsatellite raw data (11 SSR markers) of Cycas panzhihuaensis from 102 individuals from 7 populations

DOI: 10.7287/peerj.preprints.27265v1/supp-8

Information of cpDNA and nDNA fragments and primers sequences used in this study

DOI: 10.7287/peerj.preprints.27265v1/supp-9

Information of SSR marker primers used in this study

DOI: 10.7287/peerj.preprints.27265v1/supp-10

Sample locations, sample sizes (n), the composition of haplotypes, haplotype diversity (Hd) and nucleotide diversity (π) surveyed for cpDNA and nDNA of C. panzhihuaensis investigated in this study

Hd: Haplotype (gene) diversity; π: Nucleotide diversity

DOI: 10.7287/peerj.preprints.27265v1/supp-11

Figure plot of geographical distance (X axial) against genetic distance (FST, Y axial) for seven populations C. panzhihuaensis based on different DNA datasets

(a) cpDNA; (b) PHYP; (c) N3.

DOI: 10.7287/peerj.preprints.27265v1/supp-12

Principal coordinate analysis and STRUCTURE analyses of 102 individuals from seven populations of C. panzhihuaensis based on phenotypes of 11 microsatellite markers

(a) Principal coordinate analysis (PCoA). (b) Estimated genetic clustering obtained by STRUCTURE analyses using Bayesian approach (K= 5).

DOI: 10.7287/peerj.preprints.27265v1/supp-13

Mismatch distribution plot of C. panzhihuaensis based on different datasets

(a) cpDNA; (b) PHYP; (c) N3.

DOI: 10.7287/peerj.preprints.27265v1/supp-14

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Siyue Xiao performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Yunheng Ji contributed reagents/materials/analysis tools.

Jian Liu approved the final draft.

Xun Gong conceived and designed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Field sampling were approved by Natural Reserve of Jiaozishan, Yunnan province and Natural Reserve of Panzhihua, Sichuan province.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The DNA sequences matrices and the raw microsatellite data have uploaded as the Supplemental Files.

Data Deposition

The following information was supplied regarding data availability:

The raw DNA sequence matrices ( three chloroplastic DNA regions psbA-trnH, psbM-trnD, and trnS-trnG, four single-copy nuclear genes PHYP, AC5, HSP70, and AAT from 61 individuals) are provided in the supplementary files 1, 2, 3, 4, 5, 6, 7 respectively. The raw microsatellite data from eleven microsatellite loci and 102 individualsis provided in the supplementary files 8. These data revealed the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from seven known locations so far.

The raw sequences and data are included in the supplement files.

Funding

This work was supported by the National Key R & D Program of China (2017YF0505200). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies