Reference
Allen P, Bennett K, Heritage B (2014). SPSS version 22: A practical
guide. Melbourne, VIC: Cengage Learning.
Anderson, T. J. C., Su, X. h., Roddam, A., & Day, K. P. J. M. E.
(2010). Complex mutations in a high proportion of microsatellite loci
from the protozoan parasite Plasmodium falciparum. 9 (10),
1599-1608. doi: 10.1046/j.1365-294x.2000.01057.x
Beier, S., Thiel, T., Muench, T., Scholz, U., & Mascher, M. (2017).
MISA-web: a web server for microsatellite prediction.Bioinformatics, 33 (16), 2583-2585.
doi:10.1093/bioinformatics/btx198
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible
trimmer for Illumina sequence data. Bioinformatics, 30 (15),
2114-2120. doi:10.1093/bioinformatics/btu170
Chakraborty, R., Kimmel, M., Stivers, D. N., Davison, L. J., & Deka, R.
(1997). Relative mutation rates at di, tri-, and tetranucleotide
microsatellite loci. Proceedings of the National Academy of
Sciences of the United States of America, 94 (3), 1041-1046.
doi:10.1073/pnas.94.3.1041
Chaoui, L., Gagnaire, P.-A., Guinand, B., Quignard, J.-P.,
Tsigenopoulos, C., Kara, M. H., & Bonhomme, F. (2012). Microsatellite
length variation in candidate genes correlates with habitat in the
gilthead sea bream Sparus aurata. Molecular Ecology, 21 (22),
5497-5511. doi:10.1111/mec.12062
Chmielewski, M., Meyza, K., Chybicki, I. J., Dzialuk, A., Litkowiec, M.,
& Burczyk, J. (2015). Chloroplast microsatellites as a tool for
phylogeographic studies: the case of white oaks in Poland.Iforest-Biogeosciences and Forestry, 8 , 765-771.
doi:10.3832/ifor1597-008
Ching, R. C. . (1978). The chinese fern families and genera: systematic
arrangement and historical origin. Acta Phytotaxonomica
Sinica, 16 (4), 16-37.
Christensen C (1906). Index Filicum. H. Hagerup, Copenhagen.
Dashnow, H., Tan, S., Das, D., Easteal, S., & Oshlack, A. (2015).
Genotyping microsatellites in next-generation sequencing data. Bmc
Bioinformatics, 16 . doi:10.1186/1471-2105-16-s2-a5
Dong, S.Y., & Zuo, Z.Y. (2018). ON THE RECOGNITION OF GYMNOSPHAERA AS A
DISTINCT GENUS IN CYATHEACEAE. Annals of the Missouri Botanical
Garden, 103 (1), 1-23. doi:10.3417/2017049
Ellegren, H. (2004). Microsatellites: Simple sequences with complex
evolution. Nature Reviews Genetics, 5 (6), 435-445.
doi:10.1038/nrg1348
Frazer, K. A., Pachter, L., Poliakov, A., Rubin, E. M., & Dubchak, I.
(2004). VISTA: computational tools for comparative genomics.Nucleic Acids Research, 32 , W273-W279. doi:10.1093/nar/gkh458
Gao, L., Yi, X., Yang, Y.X., Su, Y.J., & Wang, T. (2009). Complete
chloroplast genome sequence of a tree fern Alsophila spinulosa: insights
into evolutionary changes in fern chloroplast genomes. Bmc
Evolutionary Biology, 9 . doi:10.1186/1471-2148-9-130
Gemayel, R., Vinces, M. D., Legendre, M., & Verstrepen, K. J. (2010).
Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory
Sequences. In A. Campbell, M. Lichten, & G. Schupbach (Eds.),Annual Review of Genetics, Vol 44 (Vol. 44, pp. 445-477).
Guo, Y. L., & Ge, S. (2005). Molecular phylogeny of Oryzeae (Poaceaf)
based on DNA sequences from chloroplast, mitochondrial, and nuclear
genomes. American Journal of Botany, 92 (9), 1548-1558.
doi:10.3732/ajb.92.9.1548
Hancock JM (1999). Microsatellites
and other simple sequences: genomic contextand mutational mechanisms.
In:Goldstein D, Schlötterer C, eds. Microsatellites: Evolution and
applications. New York: Oxford University Press. pp. 1-9.
Holttum RE(1963). Cyatheaceae in Steenis VC , Holttum RE, eds. Flora
Malesiana, Ser.2, Vol. 1. Groningen: Wolters-Noordhoff Publishing. pp.
65–176.
Janssen, T., & Rakotondrainibe, F. (2008). A revision of the indusiate
scaly tree ferns (Cyatheaceae, Cyathea subgen. Alsophila sect.
Alsophila) in Madagascar, the Comoros and the Seychelles.Adansonia, 30 (2), 221-374.
Kashi, Y., & King, D. G. (2006). Simple sequence repeats as
advantageous mutators in evolution. Trends in Genetics, 22 (5),
253-259. doi:10.1016/j.tig.2006.03.005
Katoh, K., & Standley, D. M. (2013). MAFFT Multiple Sequence Alignment
Software Version 7: Improvements in Performance and Usability.Molecular biology and evolution, 30 (4), 772-780.
doi:10.1093/molbev/mst010
Katti, M. V., Ranjekar, P. K., & Gupta, V. S. (2001). Differential
distribution of simple sequence repeats in eukaryotic genome sequences.Molecular biology and evolution, 18 (7), 1161-1167.
doi:10.1093/oxfordjournals.molbev.a003903
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M.,
Sturrock, S., . . . Drummond, A. (2012). Geneious Basic: An integrated
and extendable desktop software platform for the organization and
analysis of sequence data. Bioinformatics, 28 (12), 1647-1649.
doi:10.1093/bioinformatics/bts199
Korall, P., Conant, D. S., Metzgar, J. S., Schneider, H., & Pryer, K.
M. (2007). A molecular phylogeny of scaly tree ferns (Cyatheaceae).American Journal of Botany, 94 (5), 873-886.
doi:10.3732/ajb.94.5.873
Korall, P., Pryer, K. A., Metzgar, J. S., Schneider, H., & Conant, D.
S. (2006). Tree ferns: Monophyletic groups and their relationships as
revealed by four protein-coding plastid loci. Molecular
Phylogenetics and Evolution, 39 (3), 830-845.
doi:10.1016/j.ympev.2006.01.001
Korall, P., & Pryer, K. M. (2014). Global biogeography of scaly tree
ferns (Cyatheaceae): evidence for Gondwanan vicariance and limited
transoceanic dispersal. Journal of Biogeography, 41 (2), 402-413.
doi:10.1111/jbi.12222
Kramer KU (1990).Cyatheaceae. In Kubitzki K, Green PS, eds. The Families
and Genera of Vascular Plants, Vol. 1: Pteridophytes and Gymnosperms.
Berlin: SpringerVerlag.pp.69–74.
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular
Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.Molecular biology and evolution, 33 (7), 1870-1874.
doi:10.1093/molbev/msw054
Levinson, G., & Gutman, G. A. (1987). Slipped-strand mispairing: a
major mechanism for DNA sequence evolution. Molecular biology and
evolution, 4 (3), 203-221. doi: 10.1093/oxfordjournals.molbev.a040442
Li, F.W., Kuo, L.Y., Pryer, K. M., & Rothfels, C. J. (2016). Genes
Translocated into the Plastid Inverted Repeat Show Decelerated
Substitution Rates and Elevated GC Content. Genome Biology and
Evolution, 8 (8), 2452-2458. doi:10.1093/gbe/evw167
Li, Y. C., Korol, A. B., Fahima, T., Beiles, A., & Nevo, E. (2002).
Microsatellites: genomic distribution, putative functions and mutational
mechanisms: a review. Molecular Ecology, 11 (12), 2453-2465.
doi:10.1046/j.1365-294X.2002.01643.x
Li, Y. C., Korol, A. B., Fahima, T., & Nevo, E. (2004). Microsatellites
within genes: Structure, function, and evolution. Molecular
biology and evolution, 21 (6), 991-1007. doi:10.1093/molbev/msh073
Li, Y.L., Yang, X.X., Zhang, J.Y., Huang, S.W., Xiong, X.Y. (2014).
Studies on SSR molecular markers based on transcriptome of Taxus
chinensis var. mairei. Acta Horticulturae Sinica 4, 735-745.
Lim, K. G., Kwoh, C. K., Hsu, L. Y., & Wirawan, A. (2013). Review of
tandem repeat search tools: a systematic approach to evaluating
algorithmic performance. Briefings in Bioinformatics, 14 (1),
67-81. doi:10.1093/bib/bbs023
Liu, S.S., Ping, J.Y., Wang, Z., Wang, T., & Su, Y.J. (2018). Complete
chloroplast genome of the tree fern Alsophila podophylla (Cyatheaceae).Mitochondrial DNA Part B-Resources, 3 (1), 48-49.
doi:10.1080/23802359.2017.1419095
Liu, S.S., Wang, Z., Wang, H., Su, Y.J., & Wang, T. (2020). Patterns
and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic
Context using Plastomic Data of Ferns. Scientific Reports, 10 (1).
doi:10.1038/s41598-020-66219-y
Liu, S.X., Hou, W., Sun, T.L., Xu, Y.T., Li, P., Yue, B.S., . . . Li, J.
(2017). Genome-wide mining and comparative analysis of microsatellites
in three macaque species. Molecular Genetics and Genomics,
292 (3), 537-550. doi:10.1007/s00438-017-1289-1
Lohse, M., Drechsel, O., & Bock, R. (2007). OrganellarGenomeDRAW
(OGDRAW): a tool for the easy generation of high-quality custom
graphical maps of plastid and mitochondrial genomes. Current
Genetics, 52 (5-6), 267-274. doi:10.1007/s00294-007-0161-y
Manee, M. M., Algarni, A. T., Alharbi, S. N., Al-Shomrani, B. M.,
Ibrahim, M. A., Binghadir, S. A., & Al-Fageeh, M. B. (2020).
Genome-wide characterization and analysis of microsatellite sequences in
camelid species. Mammal Research, 65 (2), 359-373.
doi:10.1007/s13364-019-00458-x
Melotto-Passarin, D. M., Tambarussi, E. V., Dressano, K., De Martin, V.
F., & Carrer, H. (2011). Characterization of chloroplast DNA
microsatellites from Saccharum spp and related species. Genetics
and Molecular Research, 10 (3), 2024-2033. doi:10.4238/vol10-3gmr1019
Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F., &
Marshall, D. (2010). Tablet-next generation sequence assembly
visualization. Bioinformatics, 26 (3), 401-402.
doi:10.1093/bioinformatics/btp666
Mrazek, J., Guo, X., & Shah, A. (2007). Simple sequence repeats in
prokaryotic genomes. Proceedings of the National Academy of
Sciences of the United States of America, 104 (20), 8472-8477.
doi:10.1073/pnas.0702412104
Nie, X., Lv, S., Zhang, Y., Du, X., Wang, L., Biradar, S. S., . . .
Song, W. (2012). Complete Chloroplast Genome Sequence of a Major
Invasive Species, Crofton Weed (Ageratina adenophora). PLoS ONE,
7 (5). doi:10.1371/journal.pone.0036869
PPG I(2016). A community-derived classification for extant lycophytes
and ferns. Journal of Systematics and Evolution 54, 563-603.
Qi, W.H., Jiang, X.M., Du, L.M., Xiao, G.S., Hu, T.Z., Yue, B.S., &
Quan, Q.M. (2015). Genome-Wide Survey and Analysis of Microsatellite
Sequences in Bovid Species. PLoS ONE, 10 (7).
doi:10.1371/journal.pone.0133667
R Core Team (2013) R: A Language and Environment for Statistical
Computing. R Foundation for Statistical Computing, Vienna, Austria, pp.
2013.
Ren, L., Gao, G., Zhao, D., Ding, M., Luo, J., & Deng, H. (2007).
Developmental stage related patterns of codon usage and genomic GC
content: searching for evolutionary fingerprints with models of stem
cell differentiation. Genome Biology, 8 (3).
doi:10.1186/gb-2007-8-3-r35
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A.,
Hohna, S., . . . Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient
Bayesian Phylogenetic Inference and Model Choice Across a Large Model
Space. Systematic Biology, 61 (3), 539-542.
doi:10.1093/sysbio/sys029
Schlotterer, C., & Tautz, D. (1992). Slippage synthesis of simple
sequence DNA. Nucleic Acids Research, 20 (2), 211-215.
doi:10.1093/nar/20.2.211
Sharma, P. C., Grover, A., & Kahl, G. (2007). Mining microsatellites in
eukaryotic genomes. Trends in Biotechnology, 25 (11), 490-498.
doi:10.1016/j.tibtech.2007.07.013
Smith, A. R., Pryer, K. M., Schuettpelz, E., Korall, P., Schneider, H.,
& Wolf, P. G. (2006). A classification for extant ferns. Taxon,
55 (3), 705-731. doi:10.2307/25065646
Srivastava, S., Avvaru, A. K., Sowpati, D. T., & Mishra, R. K. (2019).
Patterns of microsatellite distribution across eukaryotic genomes.BMC Genomics, 20 . doi:10.1186/s12864-019-5516-5
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis
and post-analysis of large phylogenies. Bioinformatics, 30 (9),
1312-1313. doi:10.1093/bioinformatics/btu033
Swofford, D. (2002). PAUP4: Phylogenetic analysis using parsimony (and
other methods), version 4.0.Sunderland, MA: Sinauer.
Tonti‐Filippini, J., Nevill, P. G., Dixon, K., & Small, I. (2017). What
can we do with 1000 plastid genomes? In: Wiley Online Library.
Tortereau, F., Servin, B., Frantz, L., Megens, H.-J., Milan, D., Rohrer,
G., . . . Groenen, M. A. M. (2012). A high density recombination map of
the pig reveals a correlation between sex-specific recombination and GC
content. BMC Genomics, 13 . doi:10.1186/1471-2164-13-586
Toth, G., Gaspari, Z., & Jurka, J. (2000). Microsatellites in different
eukaryotic genomes: Survey and analysis. Genome Research, 10 (7),
967-981. doi:10.1101/gr.10.7.967
Tryon, R.M.(1970). The classification of Cyatheaceae.Contributions from the Gray Herbarium. 200, 1–53.
Wang, Q., Fang, L., Chen, J., Hu, Y., Si, Z., Wang, S., . . . Zhang, T.
(2015). Genome-Wide Mining, Characterization, and Development of
Microsatellite Markers in Gossypium Species. Scientific Reports,
5 . doi:10.1038/srep10638
Wang, T., He, Z., Wang, Z., Sun, X., & Su, Y. (2019). The first
complete chloroplast genome of Alsophila costularis (Cyatheaceae), a
least concerned relict tree fern. Mitochondrial DNA Part
B-Resources, 4 (1), 1897-1898. doi:10.1080/23802359.2019.1614888
Wang, T., Hong, Y., Wang, Z., & Su, Y. (2019). Characterization of the
complete chloroplast genome of Alsophila gigantea (Cyatheaceae), an
ornamental and CITES giant tree fern. Mitochondrial DNA Part
B-Resources, 4 (1), 967-968. doi:10.1080/23802359.2019.1580162
Wang, T., Su, Y.J., Zheng, B., Li, X.Y., Chen, G.P., & Zeng, Q.l.
(2003). Phylogenetic analysis of the chloroplast trnL intron and
trnL-trnF intergenic spacer sequences of the Cyatheaceae plants from
China. Journal of Tropical and Subtropical Botany, 11 (2),
137-142.
Whittaker, J. C., Harbord, R. M., Boxall, N., Mackay, I., Dawson, G., &
Sibly, R. M. (2003). Likelihood-based estimation of microsatellite
mutation rates. Genetics, 164 (2), 781-787.
Wu, F.H., Chan, M.T., Liao, D.C., Hsu, C.T., Lee, Y.W., Daniell, H., . .
. Lin, C.S. (2010). Complete chloroplast genome of Oncidium Gower Ramsey
and evaluation of molecular markers for identification and breeding in
Oncidiinae. BMC Plant Biology, 10 . doi:10.1186/1471-2229-10-68
Xia, Q.(1989). The classification of the cyatheaceae in
china. Acta Phytotaxonomica Sinica 27, 1-16.
Zerbino, D. R., & Birney, E. (2008). Velvet: Algorithms for de novo
short read assembly using de Bruijn graphs. Genome Research,
18 (5), 821-829. doi:10.1101/gr.074492.107
Zhang, X.C., Nishida, H. (2013). Cyatheaceae, Flora of China,
Vol.2–3. Beijing: Science Press; St. Louis: Missouri Botanical Garden
Press. pp. 134–138
Zhao, X., Tan, Z., Feng, H., Yang, R., Li, M., Jiang, J., . . . Yu, R.
(2011). Microsatellites in different Potyvirus genomes: Survey and
analysis. Gene, 488 (1-2), 52-56. doi:10.1016/j.gene.2011.08.016
Zhu, M., Zhao, G., Ping, J., Liang, Y., Feng, P., Su, Y., & Wang, T.
(2020). Complete chloroplast genome of Sphaeropteris brunoniana
(Cyatheaceae). Mitochondrial DNA. Part B, Resources, 5 (3),
2938-2939. doi:10.1080/23802359.2020.1787893
Appendix table 1-8 List of simple sequence repeats(SSRs) in the
chloroplast genomes of 8 species in Cyatheaceae.
Appendixtable 9 The number, relativeabundance, and relative density of
SSR motifs in the chloroplast genomes of 8 species in Cyatheaceae.
Appendix table 10 The number, relative abundance, relative density and
GC content of different types of motif SSRs in different regions in the
chloroplast genomes of 8 species in Cyatheaceae.
Appendix table 11 Significant differences in the number, relative
abundance, relative density, and GC content of the chloroplast genomes,
Mono- to Pentanucleotide SSRs, IGS, LSC, intron and CDS regions SSRs of
chloroplast genomes, and the mono- to pentanucleotide SSRs in the
chloroplast genomes of 8 Cyatheaceae species
Appendix table 1 List of simple sequence repeats (SSRs) in the
chloroplast genomes of Alsophila denticulata