Item request has been placed!
×
Item request cannot be made.
×
![loading](/sites/all/modules/hf_eds/images/loading.gif)
Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis.
Item request has been placed!
×
Item request cannot be made.
×
![loading](/sites/all/modules/hf_eds/images/loading.gif)
- المؤلفون: Wu Q;Wu Q; Zang F; Zang F; Xie X; Xie X; Ma Y; Ma Y; Zheng Y; Zheng Y; Zang D; Zang D
- المصدر:
Scientific reports [Sci Rep] 2020 Oct 01; Vol. 10 (1), pp. 16249. Date of Electronic Publication: 2020 Oct 01.- نوع النشر :
Journal Article; Research Support, Non-U.S. Gov't- اللغة:
English - المصدر:
- معلومة اضافية
- المصدر: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE
- بيانات النشر: Original Publication: London : Nature Publishing Group, copyright 2011-
- الموضوع:
- نبذة مختصرة : Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.
- References: Wu, Z. Y., Raven, P. H. & Hong, D. Y. Flora of China Vol. 4 (Science Press & Missouri Botanical Garden Press, Beijing & St. Louis, 1999).
Zang, D. K. Rare and Endangered Plants in Shandong (China Forestry Press, Beijing, 2017).
Wade, E. M. et al. Plant species with extremely small populations (PSESP) in China: A seed and spore biology perspective. Plant Diversity 38, 209–220. https://doi.org/10.1016/j.pld.2016.09.002 (2016). (PMID: 10.1016/j.pld.2016.09.002301594686112217)
Liang, S. B. & Li, X. W. A new species of Populus from Shandong. Bull. Bot. Res. 6, 135–137 (1986).
Zhang, L., Wang, M., Ma, T. & Liu, J. Taxonomic status of Populus wulianensis and P. ningshanica (Salicaceae). PhytoKeys 108, 117–129. https://doi.org/10.3897/phytokeys.108.25600 (2018). (PMID: 10.3897/phytokeys.108.25600)
Qin, H. et al. China Checklist of Higher Plants, In the Biodiversity Committee of Chinese Academy of Sciences ed., Catalogue of Life China: 2020 Annual Checklist(Beijing, China, 2020).
Li, F., Li, W. & Fan, S. Arboraceous Flora of Shandong Vol. 1 (Science Press, Beijing, 2016).
Wang, Y. et al. Establishment of generation system for Populus wulianensis and control of vitrification of its test-tube seedlings. Mol. Plant Breeding 17, 6434–6446 (2019).
Li, S. et al. Development and comparative genomic mapping of Dasypyrum villosum 6V#4S-specific PCR markers using transcriptome data. Theor. Appl. Genet. 130, 2057–2068. https://doi.org/10.1007/s00122-017-2942-0 (2017). (PMID: 10.1007/s00122-017-2942-028653149)
de Oliveira, E. J. et al. Polymorphic microsatellite marker set for Carica papaya L. and its use in molecular-assisted selection. Euphytica 173, 279–287. https://doi.org/10.1007/s10681-010-0150-y (2010). (PMID: 10.1007/s10681-010-0150-y)
Zarini, H. N., Jafari, H., Ramandi, H. D., Bolandi, A. R. & Karimishahri, M. R. A comparative assessment of DNA fingerprinting assays of ISSR and RAPD markers for molecular diversity of Saffron and other Crocus spp. in Iran. Nucleus 62(1), 39–50. https://doi.org/10.1007/s13237-018-0261-8 (2019). (PMID: 10.1007/s13237-018-0261-8)
Tamaki, I., Setsuko, S. & Tomaru, N. Genetic diversity and structure of remnant Magnolia stellata populations affected by anthropogenic pressures and a conservation strategy for maintaining their current genetic diversity. Conserv. Genet. 17, 715–725. https://doi.org/10.1007/s10592-016-0817-6 (2016). (PMID: 10.1007/s10592-016-0817-6)
Powell, W., Machray, G. C. & Provan, J. Polymorphism revealed by simple sequence repeat. Trends Plant Sci. 1, 215–222. https://doi.org/10.1016/1360-1385(96)86898-1 (1996). (PMID: 10.1016/1360-1385(96)86898-1)
Li, W. et al. De Novo transcriptomic analysis and development of EST–SSRs for Styrax japonicus. Forests. 9, 1–14. https://doi.org/10.3390/f9120748 (2018). (PMID: 10.3390/f9120748)
Bouck, A. & Vision, T. The molecular ecologist’s guide to expressed sequence tags. Mol. Ecol. 16, 907–924. https://doi.org/10.1111/j.1365-294X.2006.03195.x (2010). (PMID: 10.1111/j.1365-294X.2006.03195.x)
Ling, P. et al. EST-SSR marker characterization based on RNA-sequencing of Lolium multiflorum and cross transferability to related species. Mol. Breeding 38, 80. https://doi.org/10.1007/s11032-018-0775-4 (2018). (PMID: 10.1007/s11032-018-0775-4)
Xing, W. et al. De novo assembly of transcriptome from Rhododendron latoucheae Franch. using Illumina sequencing and development of new EST-SSR markers for genetic diversity analysis in Rhododendron. Tree Genet. Genomes 13, 53. https://doi.org/10.1007/s11295-017-1135-y (2017). (PMID: 10.1007/s11295-017-1135-y)
Bazzo, B. R. et al. Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species. BMC Plant Biol. 18, 276. https://doi.org/10.1186/s12870-018-1509-9 (2018). (PMID: 10.1186/s12870-018-1509-9304198316233587)
Jeong, S. W. et al. Development of EST-SSR markers through de novo RNA sequencing and application for biomass productivity in kenaf (Hibiscus cannabinus L.). Genes Genomics 39, 1139–1156. https://doi.org/10.1007/s13258-017-0582-z (2017). (PMID: 10.1007/s13258-017-0582-z)
Tang, D. Q. et al. De novo sequencing of the Freesia hybrida petal transcriptome to discover putative anthocyanin biosynthetic genes and develop EST-SSR markers. Acta Physiol. Plant. 40, 168 (2018). (PMID: 10.1007/s11738-018-2739-z)
Xu, Q. S. et al. Transcriptome profiling using single-molecule direct RNA sequencing approach for in-depth understanding of genes in secondary metabolism pathways of Camellia sinensis. Front. Plant Sci. 8, 1205. https://doi.org/10.3389/fpls.2017.01205 (2017). (PMID: 10.3389/fpls.2017.01205287442945504172)
Jo, I. H. et al. Isoform sequencing provides a more comprehensive view of the panax ginseng transcriptome. Genes 8, 228 (2017). (PMID: 10.3390/genes8090228)
Bhati, M., Kadri, N. K., Crysnanto, D. & Hubert, P. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics. 21, 27 (2020). (PMID: 10.1186/s12864-020-6446-y)
Shi, J. S., Wang, Z. H. & Chen, J. H. Progress on whole genome sequencing in woody plants. Hereditas 34, 145–156 (2012). (PMID: 22382056)
Xiang, X., Zhang, Z., Wang, Z., Zhang, X. & Wu, G. Transcriptome sequencing and development of EST-SSRmarkers in Pinus dabeshanensis, an endangered conifer endemic to China. Mol. Breeding 35, 158. https://doi.org/10.1007/s11032-015-0351-0 (2015). (PMID: 10.1007/s11032-015-0351-0)
Zulkapli, M. M. et al. Iso-Seq analysis of Nepenthes ampullaria, Nepenthes rafflesiana andNepenthes × hookeriana for hybridisation study in pitcher plants. Genomics Data 12, 130–131. https://doi.org/10.1016/j.gdata.2017.05.003 (2017). (PMID: 10.1016/j.gdata.2017.05.003285298815429222)
Thomas, S., Underwood, J. G., Tseng, E. & Holloway, A. K. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS ONE 9, e94650 (2014). (PMID: 10.1371/journal.pone.0094650)
Zhang, D. Y., Zhang, T. X. & Wang, G. X. Development and application of second-generation sequencing technology. Environ. Sci. Technol. 39, 96–102 (2016).
Abdel-Ghany, S. E. et al. A survey of the sorghum transcriptome using single-molecule long reads. Nat. Commun. 7, 11706. https://doi.org/10.1038/ncomms11706 (2016). (PMID: 10.1038/ncomms11706273392904931028)
Hoang, N. V. et al. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics 18, 395. https://doi.org/10.1186/s12864-017-3757-8 (2017). (PMID: 10.1186/s12864-017-3757-8285324195440902)
Kuang, X., Sun, S., Wei, J., Li, Y. & Sun, C. Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis. BMC Plant Biol. 19, 210. https://doi.org/10.1186/s12870-019-1809-8 (2019). (PMID: 10.1186/s12870-019-1809-8311133676530051)
He, L. et al. Hybrid sequencing of full-length cDNA transcripts of stems and leaves in Dendrobium officinale. Genes 8, 257 (2017). (PMID: 10.3390/genes8100257)
Hovde, B. T. et al. Detection of abrin-like and prepropulchellin-like toxin genes and transcripts using whole genome sequencing and full-length transcript sequencing of Abrus precatorius. Toxins 11, 691. https://doi.org/10.3390/toxins11120691 (2019). (PMID: 10.3390/toxins111206916950105)
Chen, X. et al. Full-length transcriptome sequencing and methyl jasmonate-induced expression profile analysis of genes related to patchoulol biosynthesis and regulation in Pogostemon cablin. BMC Plant Biol. 19, 266 (2019). (PMID: 10.1186/s12870-019-1884-x)
Tian, X. et al. Transcriptome sequencing and EST-SSR marker development in Salix babylonica and S. suchowensis. Tree Genet. Genomes 15, 9. https://doi.org/10.1007/s11295-018-1315-4 (2019). (PMID: 10.1007/s11295-018-1315-4)
Xia, H. et al. Distinguishing upland and lowland rice ecotypes by selective SSRs and their applications in molecular-assisted selection of rice drought resistance. Euphytica 206, 11–20. https://doi.org/10.1007/s10681-015-1446-8 (2015). (PMID: 10.1007/s10681-015-1446-8)
Wang, P. et al. Characterization and development of EST-SSR markers from a cold-stressed transcriptome of centipedegrass by illumina paired-end sequencing. Plant Mol. Biol. Rep. 35, 215–223. https://doi.org/10.1007/s11105-016-1017-8 (2017). (PMID: 10.1007/s11105-016-1017-8)
Gordon, S. P. et al. Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing. PLoS ONE 10, e0132628. https://doi.org/10.1371/journal.pone.0132628 (2015). (PMID: 10.1371/journal.pone.0132628261771944503453)
Iori, V. et al. Physiology and genetic architecture of traits associated with cadmium tolerance and accumulation in Populus nigra L. Trees 30, 125–139. https://doi.org/10.1007/s00468-015-1281-5 (2016). (PMID: 10.1007/s00468-015-1281-5)
Ariani, A., Romeo, S., Groover, A. T. & Sebastiani, L. Comparative epigenomic and transcriptomic analysis of Populus roots under excess Zn. Environ. Exp. Bot. 132, 16–27. https://doi.org/10.1016/j.envexpbot.2016.08.005 (2016). (PMID: 10.1016/j.envexpbot.2016.08.005)
Yang, X. et al. Transcriptome profiling of Populus tomentosa under cold stress. Ind. Crops Products 135, 283–293. https://doi.org/10.1016/j.indcrop.2019.04.056 (2019). (PMID: 10.1016/j.indcrop.2019.04.056)
Chen, J., Chen, B. & Zhang, D. Q. Transcript profiling of Populus tomentosagenes in normal, tension, and opposite wood by RNA-seq. BMC Genomics 16, 164. https://doi.org/10.1186/s12864-015-1390-y (2015). (PMID: 10.1186/s12864-015-1390-y258869504372042)
An, D., Cao, H. X., Li, C., Humbeck, K. & Wang, P. Isoform sequencing and state-of-art applications for unravelling complexity of plant transcriptomes. Genes 9, 43. https://doi.org/10.3390/genes9010043 (2018). (PMID: 10.3390/genes90100435793194)
Zhang, Y. et al. Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers. Hereditas 153, 4. https://doi.org/10.1186/s41065-016-0007-z (2016). (PMID: 10.1186/s41065-016-0007-z280967665226102)
Shahabzadeh, Z., Mohammadi, R., Darvishzadeh, R. & Jaffari, M. Genetic structure and diversity analysis of tall fescue populations by EST-SSR and ISSR markers. Mol. Biol. Rep. 47, 655–669. https://doi.org/10.1007/s11033-019-05173-z (2020). (PMID: 10.1007/s11033-019-05173-z31707600)
Zavinon, F. et al. Genetic diversity and population structure in Beninese pigeon pea [Cajanus cajan (L.) Huth] landraces collection revealed by SSR and genome wide SNP markers. Genet. Resour. Crop Evol. 67, 191. https://doi.org/10.1007/s10722-019-00864-9 (2020). (PMID: 10.1007/s10722-019-00864-9)
Kim, J. H. et al. Characterization and development of EST-SSR markers in sweet potato (Ipomoea batatas (L.) Lam). 3 Biotech 6, 243. https://doi.org/10.1007/s13205-016-0565-9 (2016). (PMID: 10.1007/s13205-016-0565-9283303155234531)
Yan, L. et al. De novo transcriptome analysis of Fraxinus velutina using Illumina platform and development of EST-SSR markers. Biol. Plant 61, 210–218. https://doi.org/10.1007/s10535-016-0681-8 (2017). (PMID: 10.1007/s10535-016-0681-8)
Zhang, X., Song, C., Zhang, Y., Yang, Y. & Huang, M. Development of EST-SSR in Populus deltoides and P. euramericana. Sci. Silvae Sin. 12, 53–59. https://doi.org/10.11707/j.1001-7488.20090910 (2009). (PMID: 10.11707/j.1001-7488.20090910)
Chen, L. Y. et al. Characterization of transcriptome and development of novel EST-SSR makers based on next-generation sequencing technology in Neolitsea sericea(Lauraceae) endemic to East Asian land-bridge islands. Mol. Breeding 35, 187. https://doi.org/10.1007/s11032-015-0379-1 (2015). (PMID: 10.1007/s11032-015-0379-1)
Wang, J., Li, Z., Guo, Q., Ren, Q. & Wu, Y. Genetic variation within and between populations of a desert poplar (Populus euphratica) revealed by SSR markers. Ann. For. Sci. 68, 1143. https://doi.org/10.1007/s13595-011-0119-6 (2011). (PMID: 10.1007/s13595-011-0119-6)
Ciftci, A. & Kaya, Z. Genetic diversity and structure of Populus nigra populations in two highly fragmented river ecosystems from Turkey. Tree Genet. Genomes 15, 66. https://doi.org/10.1007/s11295-019-1370-5 (2019). (PMID: 10.1007/s11295-019-1370-5)
Wei, Z., Du, Q., Zhang, J., Li, B. & Zhang, D. Genetic diversity and population structure in chinese indigenous poplar (Populus simonii) populations using microsatellite markers. Plant Mol. Biol. Rep. 31, 620–632. https://doi.org/10.1007/s11105-012-0527-2 (2013). (PMID: 10.1007/s11105-012-0527-2)
Saito, Y. et al. Genetic diversity of Populus euphratica populations in northwestern China determined by RAPD DNA analysis. New Forest. 23, 97–103. https://doi.org/10.1023/A:1015605928414 (2002). (PMID: 10.1023/A:1015605928414)
Mutegi, S. M. et al. Genetic diversity of the African poplar (Populus ilicifolia) populations in Kenya. Tree Genet. Genomes 12, 66. https://doi.org/10.1007/s11295-016-1013-z (2016). (PMID: 10.1007/s11295-016-1013-z)
Shen, D.F., Bo, W.H., Xu, F. & Wu, R. Genetic diversity and population structure of the Tibetan poplar (Populus szechuanica var. tibetica) along an altitude gradient. BMC Genet.15, S11. https://www.biomedcentral.com/1471-2156/15/S1/S11 (2014).
Li, J., Wang, S., Yu, J., Wang, L. & Zhou, S. A modified CTAB protocol for plant DNA extraction. Chin. Bull. Bot. 48, 72–78 (2013). (PMID: 10.3724/SP.J.1259.2013.00072)
Ghawana, S. et al. An RNA isolation system for plant tissues rich in secondary metabolites. BMC Res. Notes.4, 85. https://www.biomedcentral.com/1756-0500/4/85 (2011).
Hewitt, G. M. & Johnston, A. Molecular Techniques in Taxonomy 283–293 (Springer, Berlin, 1991). (PMID: 10.1007/978-3-642-83962-7)
Li, W. & Godzik, A. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006). (PMID: 10.1093/bioinformatics/btl158)
Deng, Y. Y. et al. Integrated NR database in protein annotation system and its localization. Computer Eng. 32, 71–74 (2006).
Apweiler, R. et al. UniProt: The Universal Protein knowledgebase. Nucleic Acids Res. 32, D115–D119 (2004). (PMID: 10.1093/nar/gkh131)
Ashburner, M. et al. Gene ontology: Tool for the unification of biology. Nat. Genet. 25, 25–29 (2000). (PMID: 10.1038/75556)
Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: A tool for genome scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000). (PMID: 10.1093/nar/28.1.33)
Koonin, E. V. et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5, R7 (2004). (PMID: 10.1186/gb-2004-5-2-r7)
Finn, R. D. et al. Pfam: The protein families database. Nucleic Acids Res. 42, D222–D230 (2013). (PMID: 10.1093/nar/gkt1223)
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280 (2004). (PMID: 10.1093/nar/gkh063)
Altschul, S. F. et al. Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402. https://doi.org/10.1093/nar/25.17.3389 (1997). (PMID: 10.1093/nar/25.17.3389146917146917)
R Core Team. R: A language and environment for statisticalcomputing. R Foundation for Statistical Computing, Vienna,Austria. https://www.R-project.org/ .(2019). - الرقم المعرف: 0 (Genetic Markers)
- الموضوع: Date Created: 20201002 Date Completed: 20201230 Latest Revision: 20211001
- الموضوع: 20221213
- الرقم المعرف: PMC7530656
- الرقم المعرف: 10.1038/s41598-020-73289-5
- الرقم المعرف: 33004908
- المصدر:
حقوق النشر© 2024، دائرة الثقافة والسياحة جميع الحقوق محفوظة Powered By EBSCO Stacks 3.3.0 [353] | Staff Login
![](https://library.dctabudhabi.ae/sites/default/files/dct_logo_white.png)
حقوق النشر © دائرة الثقافة والسياحة، جميع الحقوق محفوظة
No Comments.