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23 October 2017 Development and Characterization of EST-SSR Markers Via Transcriptome Sequencing in Brainea insignis (Aspleniaceae s.l.)
Haijun Liu, Zhihua Yan, Hualing Xu, Chunmei Li, Qiang Fan, Wenbo Liao, Boyong Liao
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Brainea insignis (Hook.) J. Sm. (Aspleniaceae) is a tree fern that thrived in the Tertiary period (De Gasper et al., 2016) and belongs to the monotypic genus Brainea J. Sm. Currently, it is widely distributed across tropical and subtropical areas of Asia and found on damp and exposed hillsides (300–1700 m a.s.l.) with high light availability and low soil water content (Wang et al., 2013). Brainea insignis has been listed as a protected species (Category II) in China (Order of the Forestry Bureau and Ministry of Agriculture of China, 1999), as well as a near-threatened (NT) species in India (Fraser-Jenkins, 2012). Furthermore, some wild populations near cities in the Pearl River Delta, such as the Huichen population near Huizhou and the Yinpinzui population near Dongguan, have been seriously affected by urbanization in southern China over the past 50 yr. Thus, microsatellite markers, which have been shown to be beneficial to the conservation of other fern species such as Blechnum orientale L. and Chieniopteris harlandii (Hook.) Ching, would be valuable as a first step in assessing the genetic structure and diversity of wild populations of B. insignis.

To date, simple sequence repeat (SSR) markers have only been developed in several fern species, such as Isoetes sinensis Palmer (Gichira et al., 2016), Athyrium distentifolium Tausch ex Opiz (Woodhead et al., 2005), Neottopteris nidus (L.) J. Sm. ex Hook. (Jia et al., 2016), and Huperzia serrata (Thunb.) Trevis. (Luo et al., 2010). No efficient molecular markers have been reported for B. insignis, and no genetic studies have been performed for this species. Brainea insignis, which first appeared during the Devonian period of the Paleozoic Era, is an important relict and endangered fern species that has played a significant role in the origin and evolution of palaeoflora and other ferns (Liao and Zhang, 1994; Liu et al., 2016). The development of reliable SSR markers would be beneficial to studies on genetic diversity, reproductive biology, and phylogeography of B. insignis and related species.

In this study, the transcriptome of B. insignis was sequenced using the Illumina platform and was de novo assembled into 85,415 transcripts (72,897 unigenes after removing redundant transcripts), which were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) and Transcriptome Shotgun Assembly (TSA) databases (SRR5883471 and GFUE00000000; BioProject: PRJNA396460). Based on these sequences, 27 novel polymorphic expressed sequence tag (EST)-SSR primer pairs were developed, their polymorphisms were characterized across three populations of B. insignis, and their transferability was also inspected with respect to three other ferns.

Table 1.

Characteristics of 27 EST-SSR markers developed for Brainea insignis.



One seedling of B. insignis was sampled from Tiantou Mountain in Shenzhen, Guangdong Province, China (Appendix 1), and planted in the greenhouse of Sun Yat-sen University (Guangzhou, Guangdong Province, China). Fresh leaves were collected from the seedling for RNA extraction via the modified cetyltrimethylammonium bromide (CTAB) method (Fu et al., 2004; Chen et al., 2011), and the subsequent protocols for transcriptome sequencing were as follows: mRNAs were extracted from the total RNA using Oligotex-dT30 (TaKaRa Biotechnology Co., Dalian, China) and ultrasonically fragmented and converted to double-stranded cDNAs. After adding an “A” nucleotide at the 3′-end of the cDNAs, adapters were ligated to both ends, and the QIAquick Gel Extraction Kit (QIAGEN, Hilden, Germany) was used to purify and collect cDNAs of approximately 215 bp in length. Finally, each amplified molecule was sequenced using Illumina sequencing technology (Illumina, San Diego, California, USA) to obtain short reads of 90 bp from both ends. A total of 23.9 million 125-bp paired-end reads were obtained and de novo assembled into 72,897 unigenes using Trinity version 2.3.2 (Grabherr et al., 2011), with a minimum length of 201 bp and an average length of 799 bp. The MISA tool (Thiel et al., 2003) was used with the default parameters except that settings for mononucleotide repeats were removed from analysis; 15,006 SSRs were detected from 12,058 unigenes. Among these SSR loci, dinucleotide repeats (74.66%) were the most common, followed by single nucleotide (13.8%), trinucleotide (10.82%), tetranucleotide (0.63%), hexanucleotide (0.07%), and pentanucleotide (0.03%) repeats. With the help of the online perl scripts p3-in and p3-out ( and Primer3 (Rozen and Skaletsky, 1999), a total of 4928 paired primers were successfully designed.

In addition, 72 individuals of B. insignis were collected from three populations in Guangdong Province, China. Voucher specimens for these populations were deposited at the Herbarium of Sun Yat-sen University (SYS; Appendix 1). The genomic DNA was extracted from silica-dried leaves using a modified CTAB method (Doyle and Doyle, 1987). The top 100 primer pairs with the highest SSR repeat motifs were synthesized, and PCR amplification was performed on six individuals that were randomly selected from the three populations of B. insignis (two individuals for each population). PCR amplifications were performed in 20-µL reaction volumes, containing 25 ng of genomic DNA, 2 µL 10× buffer (with Mg2+), 0.25 mM of dNTPs, 0.2 µM of each primer, and 1 unit of Easy-Taq DNA polymerase (TransGen Biotech Co. Ltd., Beijing, China). PCR reactions were conducted with the following conditions: initial denaturing at 94°C for 2 min; followed by 35 cycles of 94°C for 30 s, appropriate annealing temperature (Table 1) for 30 s, and 72°C for 40 s; and a final extension at 72°C for 5 min (Fan et al., 2013). The PCR products were electrophoresed and visualized in 2% agarose gel. The results showed that 52 primer pairs were successfully amplified in six individuals with the expected product sizes. After amplification, the PCR products were further inspected with capillary gel electrophoresis (Fragment Analyzer; Advanced Analytical Technologies, Ankeny, Iowa, USA) using the Quant-iT PicoGreen dsDNA reagent kit (35–500 bp; Invitrogen, Carlsbad, California, USA). PROSize 2.0 software (Advanced Analytical Technologies) was used to analyze the sample size, and 27 primer pairs showed polymorphisms among the six tested individuals (GenBank accession number: MF150401–MF150427 ; Table 1). To determine and annotate the putative function, 27 EST-SSRs were compared with the public sequence database, contrasting BLASTX with the nonredundant (Nr) protein database. The results showed that 22 primer pairs had significant BLASTX hits to the protein database and that one was annotated as a plastid gene.

Table 2.

Polymorphism of the 27 EST-SSRs in three populations of Brainea insignis.a


The 27 primer pairs were then amplified across all 72 individuals in the three populations to assess their polymorphism levels (Table 2). The number of alleles, observed heterozygosity, and expected heterozygosity were calculated using GenAlEx 6.501 software (Peakall and Smouse, 2012). Null alleles were checked using the program MICRO-CHECKER version 2.2.3 (van Oosterhout et al., 2004). Linkage disequilibrium testing and deviation from Hardy-Weinberg equilibrium (HWE) were carried out using GENEPOP 4.3 (Rousset, 2008). Signs of null alleles were detected on loci BS61 and BS69 in three populations and loci BS80 in one population. The results showed that the number of alleles ranged from three to 10 in all three populations of B. insignis. Observed and expected heterozygosity ranged, respectively, from 0.469 to 1.000 and from 0.539 to 0.840 in population DG, from 0.105 to 1.000 and from 0.566 to 0.842 in population HD, and from 0.286 to 1.000 and from 0.523 to 0.865 in population SZ. The linkage disequilibrium test showed no significantly linked pairs of primers after a Bonferroni correction. HWE tests showed that all three populations significantly deviated from HWE in most loci (Table 2).

Furthermore, individuals of B. orientale (Aspleniaceae) and C. harlandii (Aspleniaceae) were collected to test the transferability of these primers. The results showed that 14 primer sets could be amplified in B. orientale, while 13 could be amplified in C. harlandii (Table 3).


In our study, we obtained 72,897 unigenes of B. insignis via transcriptome sequencing and developed 27 novel EST-SSRs for the species. Some of these primers could be amplified in B. orientale and C. harlandii, showing good transferability to other fern species. These polymorphic markers are valuable for genetic conservation studies in the endangered B. insignis and other related fern species.

Table 3.

Cross-amplification of 27 Brainea insignis EST-SSR markers in other ferns.a



This work was supported by the Administration Bureau of Neilingding-Futian National Nature Reserve in Guangdong (4206874); the Urban Management Bureau of Shenzhen Municipality (71020106 and 71020140); the Basic Work Special Project of the National Ministry of Science and Technology of China (2013FY111500); the Natural Science Foundation of Guangdong Province, China (2016A030313326); and the Science and Technology Planning Project of Guangdong Province, China (2015A030302020).



Chen, S. F., R. C. Zhou, Y. L. Huang, M. Zhang, G. L. Yang, C. R. Zhong, and S. H. Shi. 2011. Transcriptome sequencing of a highly salt tolerant mangrove species Sonneratia alba using Illumina platform. Marine Genomics 4: 129–136. Google Scholar


De Gasper, A. L., V. A. D. O. Dittrich, A. R. Smith, and A. Salino. 2016. A classification for Blechnaceae (Polypodiales: Polypodiopsida): New genera, resurrected names, and combinations. Phytotaxa 275: 191–227. Google Scholar


Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochemical Bulletin 19: 11–15. Google Scholar


Fan, Q., S. F. Chen, M. W. Li, S. Y. He, R. C. Zhou, and W. B. Liao. 2013. Development and characterization of microsatellite markers from the transcriptome of Firmiana danxiaensis (Malvaceae s.l.). Applications in Plant Sciences 1: 1300047. Google Scholar


Fraser-Jenkins, C. R. 2012. Rare and threatened Pteridophytes of Asia 2. Endangered species of India—the higher IUCN categories. Bulletin of the National Museum of Nature and Science, Series B 38: 153–181. Google Scholar


Fu, X. H., S. L. Deng, G. H. Su, Q. L. Zeng, and S. H. Shi. 2004. Isolating high-quality RNA from mangroves without liquid nitrogen. Plant Molecular Biology Reporter 22: 197. Google Scholar


Gichira, A. W., Z. C. Long, Q. F. Wang, J. M. Chen, and K. Liao. 2016. Development of expressed sequence tag-based microsatellite markers for the critically endangered Isoëtes sinensis (Isoetaceae) based on transcriptome analysis. Genetics and Molecular Research 15: 15038497. Google Scholar


Grabherr, M. G., B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson, I. Amit, X. Adiconis, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29: 644–652. Google Scholar


Jia, X. P., Y. M. Deng, X. B. Sun, L. J. Liang, and J. L. Su. 2016. De novo assembly of the transcriptome of Neottopteris nidus using Illumina paired-end sequencing and development of EST-SSR markers. Molecular Breeding 36: 94. Google Scholar


Liao, W. B., and H. D. Zhang. 1994. The characteristics of pteridophyte flora from Guangdong Province. Redai Yaredai Zhiwu Xuebao 2: 1–11. Google Scholar


Liu, H. J., K. W. Xu, H. B. Sun, Q. H. He, Q. Fan, and W. B. Liao. 2016. Structure characteristics and succession analysis of Brainea insignis community in Jingxin Reservoir area. Xibei Zhiwu Xuebao 36: 2094–2102. Google Scholar


Luo, H. M., Y. Li, C. Sun, Q. O. Wu, J. Y. Song, Y. Z. Sun, A. Steinmetz, and S. L. Chen. 2010. Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatus reveals putative genes involved in lycopodium alkaloid biosynthesis and developmental regulation. BMC Plant Biology 10: 209. Google Scholar


Order of the Forestry Bureau and Ministry of Agriculture of China. 1999. The protected native plant list in China (1st list). Ministry of Agriculture, Beijing, China. Google Scholar


Peakall, R., and P. E. Smouse. 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-An update. Bioinformatics (Oxford, England) 28: 2537–2539. Google Scholar


Rousset, F. 2008. GENEPOP'007: A complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8: 103–106. Google Scholar


Rozen, S., and H. Skaletsky. 1999. Primer3 on the WWW for general users and for biologist programmers. In S. Misener and S. A. Krawetz [eds.], Methods in molecular biology, vol. 132: Bioinformatics: Methods and protocols, 365–386. Humana Press, Totowa, New Jersey, USA. Google Scholar


Thiel, T., W. Michalek, R. K. Varshney, and A. Graner. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106: 411–422. Google Scholar


van Oosterhout, C., W. F. Hutchinson, D. P. M. Wills, and P. Shipley. 2004. MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535–538. Google Scholar


Wang, F. G., F. W. Xing, S. Y. Dong, and M. Kato. 2013. Blechnaceae. In Z. Y. Wu, P. H. Raven, and D. Y. Hong [eds.], Flora of China, Vol. 2–3, 411–417. Science Press, Beijing, China, and Missouri Botanical Garden Press, St. Louis, Missouri, USA. Google Scholar


Woodhead, M., J. Russell, J. Squirrell, P. M. Hollingsworth, K. Mackenzie, M. Gibby, and W. Powell. 2005. Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions. Molecular Ecology 14: 1681–1695. Google Scholar


Appendix 1.

Location and voucher information of Brainea insignis and other related species used in this study.

Haijun Liu, Zhihua Yan, Hualing Xu, Chunmei Li, Qiang Fan, Wenbo Liao, and Boyong Liao "Development and Characterization of EST-SSR Markers Via Transcriptome Sequencing in Brainea insignis (Aspleniaceae s.l.)," Applications in Plant Sciences 5(10), (23 October 2017).
Received: 28 June 2017; Accepted: 1 August 2017; Published: 23 October 2017

Aspleniaceae s.l.
Brainea insignis
transcriptome sequencing
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