* Correspondence:
Yingjuan Su, Xingang West Road, Guangzhou, Guangdong, IA 510275, China.
Email: suyj@mail.sysu.edu.cn
Ting Wang, Wushan Road, Guangzhou, Guangdong, IA 510640, China.
Email: tingwang@scau.edu.cn
Abstract Recent taxonomic and molecular phylogenetic studies
have shown that Gymnosphaera should be recognized as an
independent taxonomic unit at the genus level under the family
Cyatheaceae. In this study, the
complete chloroplast genomes of the eight species of Cyatheaceae were
sequenced, and their phylogenetic relationships were reconstructed using
the maximum likelihood, Bayesian inference, maximum parsimony, and
neighbor-joining methods, and the characteristics of their simple
sequence repeats (SSRs) were compared and analyzed for the first time.
The results showed that when Cyatheaceae was divided into three
genera,the number, relative abundance, relative density, and GC content
of all SSRs and of SSRs of certain unit lengths in the chloroplast
genomes of the eight species of Cyatheaceae were genus specific in the
whole chloroplast genomes and in their different regions (large
single-copy, small single-copy, inverted repeat, intergenic spacer,
intron, rRNA gene, and coding sequence regions). The SSRs overall and
the single-nucleotide SSRs had significant differences in number,
relative abundance, relative density, and GC content between the
chloroplast genomes, their intergenic regions, and large single-copy
regions. When Cyatheaceae was divided into two genera, only the
difference in GC content was significant. Therefore, our results support
the restoration of the hierarchical status of Gymnosphaera . This
study provides an important basis
for the identification of the phylogenetic relationship of Cyatheaceae
plants.
Keywords Cyatheaceae, Phylogeny, SSR, Gymnosphaera
Also known as microsatellites, simple sequence repeats (SSRs) are short
tandem repeat sequences with a motif length of 1-6 bp that are
characterized by high variability, high repeatability, codominant
inheritance, and interspecies generality. SSRs have been widely used in
species identification, genetic diversity, and phylogenetic
relationships(Chmielewski et al., 2015; Dashnow et al., 2015). SSRs are
caused by slipped strand mispairing and subsequent errors during DNA
replication, repair, and recombination (Levinson & Gutman, 1987). They
are widespread in the genomes of prokaryotes, eukaryotes, and some
viruses(Mrazek et al., 2007; Toth
et al., 2000; Zhao et al., 2011). SSRs are mainly found in intergenic
and noncoding regions, with a few in introns (Toth et al., 2000; Li et
al., 2004 ). Under selection, the number of genomic SSRs is
significantly higher than that under random accumulation(Ellegren,
2004). The characteristics of genomic SSRs in different taxa (such as
their distribution pattern) accurately reflect their phylogenetic
relationships (Srivastava et al., 2019). SSRs are highly mutagenic and
are an important source of genetic evolution, and they can play an
important role in genome evolution by generating and maintaining
quantitative genetic variation (Chaoui et al., 2012; Gemayel et al.,
2010; Kashi & King, 2006). Therefore, the identification and
characterization of SSRs can contribute to the study of population
variation, germline identification, and genetic diversity.
Cyatheaceae belong to the phylum Pteridophyta, the class Polypodiopsida,
and the order Cyatheales, with more than 600 species present today.
Cyatheaceae account for the vast majority of known tree ferns and are
mainly distributed in warm and humid tropical and subtropical regions
(Kramer, 1990; Korall et al., 2006; Smith et al., 2006; PPG I, 2016).
The classification of the genera in Cyatheaceae has always been a
difficult problem. In the early classification system, Christensen
(1906) classified Cyatheaceae into Cyathea Sm. (with a complete
cup-shaped indusium), Hemitelia R. Br. (with a partial indusium),
and Alsophila R. Br. (without an indusium) based on the
characteristics of indusium. Holttum (1963) treated Cyatheaceae plants
as a genus (Cyathea ) and divided it into two subgenera,Cyathea subg. Cyathea (marginate scales) andCyathea subg. Sphaeropteris (Bernh.) Holttum (conform
scales), based on the structural characteristics of the scales at the
base of the petiole. Based on the study of the American Cyatheaceae
plants, Tryon (1970) delineated three evolutionary paths and six genera,
namely, (1) Sphaeropteris Bernh (with conform scales); (2)Alsophila and Nephelea R. M. Tryon (with marginate scales
and apical setae); and (3) Trichipteris C. Presl, Cyatheaand Cnemidaria C. Presl (with marginate scales but without apical
setae). Ching (1978) classified the Cyatheaceae plants that grow in
China into three genera: Sphaeropteris , Gymnosphaera andAlsophila . On this basis, Xia (1989) reduced the generaAlsophila and Alsophila to subgenera, respectively, and
combined them into Alsophila .
Recent molecular phylogenetic studies have shown that Cyatheaceae
includes four monophyletic groups, namely, Alsophila ,Cyathea , Gymnosphaera , and Sphaeropteris (Dong &
Zuo, 2018; Janssen & Rakotondrainibe, 2008; Korall et al., 2007; Korall
& Pryer, 2014). The morphological characteristics ofGymnosphaera , such as marginate scales, a slightly black rachis,
and the lack of an indusium, and molecular evidence suggest that it is
different from other Cyatheaceae plants, and particularly obvious is its
different sporogenesis from Alsophila (Gymnosphaeraproduces 64 spores per sac, Alsophila produces 16 spores per sac)
(Dong & Zuo, 2018). Still, some scholars classify Gymnosphaerainto the genus Alsophila (Xia 1989; Zhang and Nishida, 2013; PPG
I, 2016).
In this study, the chloroplast genomes of eight species of Cyatheaceae
were sequenced, and the chloroplast genome, the SSRs of different unit
lengths in the chloroplast genome, and the number, relative abundance,
relative density, and GC content of all SSRs and SSRs of specific unit
lengths in the intergenic spacer regions (IGS), intron regions, and
protein-coding sequence regions (CDS) of the chloroplast genome were
compared and analyzed to reveal the phylogenetic significance of the SSR
characteristics of the chloroplast genome of Cyatheaceae plants.