Length variation of chloroplast simple sequence repeats in the genus Eucalyptus L'Hér.
DOI:
https://doi.org/10.14719/pst.2020.7.3.750Keywords:
Chloroplast, Eucalyptus, Polymorphic, Simple sequence repeats, TransferabilityAbstract
Eucalyptus L'Hér. is an economically important genus of plants with several environmental significances and great industrial advantages. To accelerate breeding and conservation studies, efforts on molecular breeding and molecular genetic analysis are underway in the genus Eucalyptus. Despite these efforts, no sufficient information is available about common, polymorphic and unique chloroplast simple sequence repeats (cpSSRs) in the genus Eucalyptus. . These repeats consist of 1-6 nucleotides and play important role in the development of molecular markers, genetic mapping and plant breeding. In the present study, a total of 920 cpSSRs were detected and length variation of cpSSRs analysed between each pair of species among 31 chloroplast genome sequences of the genus Eucalyptus. Additionally, cross species transferability of common and polymorphic cpSSRs were also observed. The common, unique and putative polymorphic cpSSRs analysed in this study can be used for species identification and genetic diversity studies of Eucalyptus.
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References
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13. Kabra R, Kapil A, Attarwala K, Rai PK, Shanker A. Identification of common unique and polymorphic microsatellites among 73 cyanobacterial genomes. World J Microbiol Biotechnol. 2016;32:71. https://doi.org/10.1007/s11274-016-2061-0
14. Shanker A, Sharma V, Daniell H. Phylogenomic evidence of bryophytes’ monophyly using complete and incomplete data sets from chloroplast proteomes. J Plant Biochem Biot. 2011; 20:288-92. https://doi.org/10.1007/s13562-011-0054-5
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21. Steane DA, Jones RC, Vaillancourt RE. A set of chloroplast microsatellite primers for Eucalyptus (Myrtaceae). Mol Ecol Resour. 2005; 5:538-41. https://doi.org/10.1111/j.1471-8286.2005.00981.x
22. Payn KG, Dvorak WS, Janse BJ, Myburg AA. Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla endemic to seven islands in eastern Indonesia. Tree Genet Genomes. 2008;4:519-30. https://doi.org/10.1007/s11295-007-0128-7
23. Brondani RPV, Brondani C, Tarchini R, Grattapaglia D. Development characterization and mapping of microsatellite markers in Eucalyptus grandis and E urophylla. Theor Appl Genet. 1998; 97:816-27. https://doi.org/10.1007/s001220050961
24. Brondani R, Brondani C, Grattapaglia D. Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers. Mol Genet Genomics. 2002;267:338-47. https://doi.org/10.1007/s00438-002-0665-6
25. Ottewell KM, Donnellan SC, Moran GF, Paton DC. Multiplexed microsatellite markers for the genetic analysis of Eucalyptus leucoxylon (Myrtaceae) and their utility for ecological and breeding studies in other Eucalyptus species. J Hered. 2005; 96:445-51. https://doi.org/10.1093/jhered/esi057
26. Ceresini PC, Silva CLSP, Missio RF, Souza EC, Fischer CN, Guillherme IR, Gregorio I, Silva EHTD, Cicarelli RMB, Silva MTAD, Garcia JF. Satellyptus: Analysis and database of microsatellites from ESTs of Eucalyptus. Genet Mol Biol. 2005;28:589-600. https://doi.org/10.1590/S1415-47572005000400014
27. Rabello E, Souza AND, Saito D, Tsai SM. In silico characterization of microsatellites in Eucalyptus spp: abundance length variation and transposon associations. Genet Mol Biol. 2005;28:582-88. https://doi.org/10.1590/S1415-47572005000400013
28. Yasodha R, Sumathi R, Chezhian P, Kavitha S, Ghosh M. Eucalyptus microsatellites mined in silico: survey and evaluation. J Genet. 2008;87:21-25. https://doi.org/10.1007/s12041-008-0003-9
29. Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PloS one. 2015; 10:e0116528. https://doi.org/10.1371/journal.pone.0116528
30. Andrade MC, Perek M, Pereira FB, Moro M, Tambarussi EV. Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence. Crop Breed Appl Biotechnol. 2018; 18:97-102. https://doi.org/10.1590/1984-70332018v18n1a13
31. Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M. Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol J. 2012; 10:690-702. https://doi.org/10.1111/j.1467-7652.2012.00712.x
32. Duran C, Singhania R, Raman H, Batley J, Edwards D. Predicting polymorphic EST?SSRs in silico. Mol Ecol Resour. 2013; 13:538-45. https://doi.org/10.1111/1755-0998.12078
33. Motta FG, Skowronski L, da Costa JV, da Costa RB. Transferability of microsatellite loci from Croton floribundus Spreng. to Croton urucurana Baill. (Euphorbiaceae). Afr J Biotechnol. 2019; 18:383-89. https://doi.org/10.5897/AJB2019.16810
34. Nagel JH, Cruywagen EM, Machua J, Wingfield MJ, Slippers B. Highly transferable microsatellite markers for the genera Lasiodiplodia and Neofusicoccum. Fungal Ecol. 2020; 44:100903. https://doi.org/10.1016/j.funeco.2019.100903
35. Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93:77-78. https://doi.org/10.1093/jhered/93.1.77
36. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics methods and protocols 2000 (pp. 365-386). Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-192-2:365
37. Cao Y, Wang L, Xu K, Kou C, Zhang Y, Wei G, He J, Wang Y, Zhao L. Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. BMC bioinformatics. 2005; 6:190. https://doi.org/10.1186/1471-2105-6-190
38. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A. Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol. 1998;15:1275-87. https://doi.org/10.1093/oxfordjournals.molbev.a025856
39. Acuña CV, Villalba PV, García M, Pathauer P, Hopp HE, Marcucci Poltri SN. Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus. Electron J Biotechnol. 2012; 15(2):1-17. https://doi.org/10.2225/vol15-issue2-fulltext-3
40. Bradbury D, Smithson A, Krauss SL. Development and testing of new gene-homologous EST-SSRs for Eucalyptus gomphocephala (Myrtaceae). Appl Plant Sci. 2013;1:1300004. https://doi.org/10.3732/apps.1300004
41. Bayly MJ, Rigault P, Spokevicius A, Ladiges PY, Ades PK, Anderson C, Bossinger G, Merchant A, Udovicic F, Woodrow IE, Tibbits J. Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae). Mol Phylogenetics Evol. 2013;69:704-16. https://doi.org/10.1016/j.ympev.2013.07.006
42. Steane DA. Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum Eucalyptus globulus (Myrtaceae). DNA Res. 2005;12:215-20. https://doi.org/10.1093/dnares/dsi006
43. Paiva JA, Prat E, Vautrin S, Santos MD, San-Clemente H, Brommonschenkel S, Fonseca PG, Grattapaglia D, Song X, Ammiraju JS, Kudrna D. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. BMC genomics. 2011;12:137. https://doi.org/10.1186/1471-2164-12-137
2. Luo J, Arnold R, Ren S, Jiang Y, Lu W, Peng Y, Xie Y. Veneer grades recoveries and values from 5-year-old Eucalypt clones. Ann Forest Sci. 2013;70:417-28. https://doi.org/10.1007/s13595-013-0268-x
3. Ahlem S, Khaled H, Wafa M, Sofiane B, Mohamed D and Jean-Claude M. Oral administration of Eucalyptus globulus extract reduces the alloxan-induced oxidative stress in rats. Chem Biol Interact. 2009; 181:71-76. https://doi.org/10.1016/j.cbi.2009.06.006
4. Dessie G. Eucalyptus in East Africa: socio-economic and environmental issues. IWMI; 2011; H043946
5. Eidi A, Eidi M, Givianrad MH, Abaspour N. Hypolipidemic effects of alcoholic extract of Eucalyptus (Eucalyptus globulus Labill) leaves on diabetic and non-diabetic rats. J Diabetes Metab Disord. 2009;8:13
6. Steane DA, West AK, Potts BM, Ovenden JR, Reid JB. Restriction fragment length polymorphisms in chloroplast DNA from six species of Eucalyptus. Aust J Bot. 1991;39:399-414. https://doi.org/10.1071/BT9910399
7. Keil M, Griffin AR. Use of random amplified polymorphic DNA (RAPD) markers in the discrimination and verification of genotypes in Eucalyptus. Theor Appl Genet. 1994;89:442-50. https://doi.org/10.1007/BF00225379
8. Marques CM, Araujo JA, Ferreira JG, Whetten R, O’malley DM, Liu BH, Sederoff R. AFLP genetic maps of Eucalyptus globulus and E. tereticornis. Theor Appl Genet. 1998;96:727-37. https://doi.org/10.1007/s001220050795
9. Byrne M, Marquezgarcia MI, Uren T, Smith DS, Moran GF. Conservation and genetic diversity of microsatellite loci in the genus Eucalyptus. Aust J Bot. 1996;44:331-41. https://doi.org/10.1071/BT9960331
10. Acuña CV, Fernandez P, Villalba PV, García MN, Hopp HE, Poltri SNM. Discovery validation and in silico functional characterization of EST-SSR markers in Eucalyptus globulus. Tree Genet Genomes. 2012;8:289-301. https://doi.org/10.1007/s11295-011-0440-0
11. Shanker A. Identification of microsatellites in chloroplast genome of Anthoceros formosae. Arch Bryol. 2013;191:1-6
12. Shanker A, Bhargava A, Bajpai R, Singh S, Srivastava S, Sharma V. Bioinformatically mined simple sequence repeats in UniGene of Citrus sinensis. Sci Hort. 2007;113:353-61. https://doi.org/10.1016/j.scienta.2007.04.011
13. Kabra R, Kapil A, Attarwala K, Rai PK, Shanker A. Identification of common unique and polymorphic microsatellites among 73 cyanobacterial genomes. World J Microbiol Biotechnol. 2016;32:71. https://doi.org/10.1007/s11274-016-2061-0
14. Shanker A, Sharma V, Daniell H. Phylogenomic evidence of bryophytes’ monophyly using complete and incomplete data sets from chloroplast proteomes. J Plant Biochem Biot. 2011; 20:288-92. https://doi.org/10.1007/s13562-011-0054-5
15. Shanker A. Combined data from chloroplast and mitochondrial genome sequences showed paraphyly of bryophytes. Arch Bryol. 2013;171:1-9
16. Shanker A. Inference of bryophytes paraphyly using mitochondrial genomes. Arch Bryol. 2013;165:1-5
17. Kapil A, Rai PK, Shanker A. ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants. Database. 2014;bau107. https://doi.org/10.1093/database/bau107
18. Kumar M, Kapil A, Shanker A. MitoSatPlant: mitochondrial microsatellites database of viridiplantae. Mitochondrion. 2014;19:334-37. https://doi.org/10.1016/j.mito.2014.02.002
19. Kumar S, Shanker A. Common unique and polymorphic simple sequence repeats in chloroplast genomes of genus Arabidopsis. Vegetos. 2018;31(special):125-31. https://doi.org/10.5958/2229-4473.2018.00043.5
20. Kumar S, Shanker A. Analysis of microsatellites in mitochondrial genome of Aneura pinguis (L.) Dumort. In: Afroz Alam, editor. Recent Advances in Botanical Science: Contemporary Research on Bryophytes 2020 pp. 20-37. Bentham Science Publishers Pte. Ltd. Singapore. https://doi.org/10.2174/9789811433788120010011
21. Steane DA, Jones RC, Vaillancourt RE. A set of chloroplast microsatellite primers for Eucalyptus (Myrtaceae). Mol Ecol Resour. 2005; 5:538-41. https://doi.org/10.1111/j.1471-8286.2005.00981.x
22. Payn KG, Dvorak WS, Janse BJ, Myburg AA. Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla endemic to seven islands in eastern Indonesia. Tree Genet Genomes. 2008;4:519-30. https://doi.org/10.1007/s11295-007-0128-7
23. Brondani RPV, Brondani C, Tarchini R, Grattapaglia D. Development characterization and mapping of microsatellite markers in Eucalyptus grandis and E urophylla. Theor Appl Genet. 1998; 97:816-27. https://doi.org/10.1007/s001220050961
24. Brondani R, Brondani C, Grattapaglia D. Towards a genus-wide reference linkage map for Eucalyptus based exclusively on highly informative microsatellite markers. Mol Genet Genomics. 2002;267:338-47. https://doi.org/10.1007/s00438-002-0665-6
25. Ottewell KM, Donnellan SC, Moran GF, Paton DC. Multiplexed microsatellite markers for the genetic analysis of Eucalyptus leucoxylon (Myrtaceae) and their utility for ecological and breeding studies in other Eucalyptus species. J Hered. 2005; 96:445-51. https://doi.org/10.1093/jhered/esi057
26. Ceresini PC, Silva CLSP, Missio RF, Souza EC, Fischer CN, Guillherme IR, Gregorio I, Silva EHTD, Cicarelli RMB, Silva MTAD, Garcia JF. Satellyptus: Analysis and database of microsatellites from ESTs of Eucalyptus. Genet Mol Biol. 2005;28:589-600. https://doi.org/10.1590/S1415-47572005000400014
27. Rabello E, Souza AND, Saito D, Tsai SM. In silico characterization of microsatellites in Eucalyptus spp: abundance length variation and transposon associations. Genet Mol Biol. 2005;28:582-88. https://doi.org/10.1590/S1415-47572005000400013
28. Yasodha R, Sumathi R, Chezhian P, Kavitha S, Ghosh M. Eucalyptus microsatellites mined in silico: survey and evaluation. J Genet. 2008;87:21-25. https://doi.org/10.1007/s12041-008-0003-9
29. Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PloS one. 2015; 10:e0116528. https://doi.org/10.1371/journal.pone.0116528
30. Andrade MC, Perek M, Pereira FB, Moro M, Tambarussi EV. Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence. Crop Breed Appl Biotechnol. 2018; 18:97-102. https://doi.org/10.1590/1984-70332018v18n1a13
31. Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M. Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol J. 2012; 10:690-702. https://doi.org/10.1111/j.1467-7652.2012.00712.x
32. Duran C, Singhania R, Raman H, Batley J, Edwards D. Predicting polymorphic EST?SSRs in silico. Mol Ecol Resour. 2013; 13:538-45. https://doi.org/10.1111/1755-0998.12078
33. Motta FG, Skowronski L, da Costa JV, da Costa RB. Transferability of microsatellite loci from Croton floribundus Spreng. to Croton urucurana Baill. (Euphorbiaceae). Afr J Biotechnol. 2019; 18:383-89. https://doi.org/10.5897/AJB2019.16810
34. Nagel JH, Cruywagen EM, Machua J, Wingfield MJ, Slippers B. Highly transferable microsatellite markers for the genera Lasiodiplodia and Neofusicoccum. Fungal Ecol. 2020; 44:100903. https://doi.org/10.1016/j.funeco.2019.100903
35. Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93:77-78. https://doi.org/10.1093/jhered/93.1.77
36. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics methods and protocols 2000 (pp. 365-386). Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-192-2:365
37. Cao Y, Wang L, Xu K, Kou C, Zhang Y, Wei G, He J, Wang Y, Zhao L. Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. BMC bioinformatics. 2005; 6:190. https://doi.org/10.1186/1471-2105-6-190
38. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A. Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol. 1998;15:1275-87. https://doi.org/10.1093/oxfordjournals.molbev.a025856
39. Acuña CV, Villalba PV, García M, Pathauer P, Hopp HE, Marcucci Poltri SN. Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus. Electron J Biotechnol. 2012; 15(2):1-17. https://doi.org/10.2225/vol15-issue2-fulltext-3
40. Bradbury D, Smithson A, Krauss SL. Development and testing of new gene-homologous EST-SSRs for Eucalyptus gomphocephala (Myrtaceae). Appl Plant Sci. 2013;1:1300004. https://doi.org/10.3732/apps.1300004
41. Bayly MJ, Rigault P, Spokevicius A, Ladiges PY, Ades PK, Anderson C, Bossinger G, Merchant A, Udovicic F, Woodrow IE, Tibbits J. Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae). Mol Phylogenetics Evol. 2013;69:704-16. https://doi.org/10.1016/j.ympev.2013.07.006
42. Steane DA. Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum Eucalyptus globulus (Myrtaceae). DNA Res. 2005;12:215-20. https://doi.org/10.1093/dnares/dsi006
43. Paiva JA, Prat E, Vautrin S, Santos MD, San-Clemente H, Brommonschenkel S, Fonseca PG, Grattapaglia D, Song X, Ammiraju JS, Kudrna D. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. BMC genomics. 2011;12:137. https://doi.org/10.1186/1471-2164-12-137
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Kumar S, Shanker A. Length variation of chloroplast simple sequence repeats in the genus Eucalyptus L’Hér. Plant Sci. Today [Internet]. 2020 Jul. 1 [cited 2024 May 2];7(3):353-9. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/750
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