Characterization of variability of the intergenic spacers cpDNA trnH–psbA, trnY–trnT AND rpoB–trnC in representatives of Pisum L. (Tribe Fabeae)

Cover Page
Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access

Abstract


Background. Plant chloroplast genome have conservative structure, but its nucleotide sequence is polymorphous due to which cpDNA fragments are often used in taxonomic and phylogenetic studies. Despite the widespread distribution and use of Fabeae species, mainly peas (Pisum), data on the intraspecific diversity of cpDNA fragments are almost absent. The aim of the work was to analyze the intraspecific variability of three cpDNA spacers in Pisum.

Materials and methods. As a result of the work, intergenic spacers trnYtrnT, trnHpsbA and rpoBtrnC in 38 accessions of the Pisum and related Fabeae species were sequenced. Despite the fact that the selected chloroplast fragments are generally considered to be sufficiently variable in plants and are often used for phylogenetic studies, Pisum accessions have been found to have no intraspecific differences in two of the three spacers sequences analyzed.

Results and conclusion. A total 97 SNPs were detected in Pisum accessions, seven of them distinguished P. sativum from P. fulvum. The most variable of the analyzed fragments was the intergenic spacer rpoB–trnC. Based on rpoB–trnC sequence 17 haplotypes in P. sativum and four haplotypes in P. fulvum were revealed. The cpDNA sequencing data were used for a phylogenetic analysis. On the obtained tree Vavilovia formosa accession formed a separate branch from pea accessions. All Pisum accessions fall in one cluster, split into distinct P. sativum and P. fulvum subclusters (BI = 99%).


Full Text

Restricted Access

About the authors

Elena A. Dyachenko

Federal State Institution Research Center of Biotechnology of the Russian Academy of Sciences

Author for correspondence.
Email: dyachenko-el@yandex.ru
ORCID iD: 0000-0002-0570-9751
SPIN-code: 4525-9700

Russian Federation, Moscow

PhD, Researcher, Laboratory of Plant System Biology

Elena V. Semenova

Federal State Budgetary Scientific Institution Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources

Email: e.semenova@vir.nw.ru
ORCID iD: 0000-0002-2637-1091
SPIN-code: 4667-9935

Russian Federation, Saint Petersburg

PhD, Main Researcher, Department of Leguminous Crops Genetic Resources

Elena Z. Kochieva

Federal State Institution Research Center of Biotechnology of the Russian Academy of Sciences

Email: ekochieva@yandex.ru
ORCID iD: 0000-0002-6091-0765

Russian Federation, Moscow

Dr. Sci. (Biol.), Main Researcher, Laboratory of Plant System Biology

References

  1. Davis CC, Anderson WR, Donoghue MJ. Phylogeny Malpighiaceae: Evidence from chloroplast ndhF and trnL-F nucleotide sequences. Am J Bot. 2001;88(10):1830-1846. https://doi.org/10.2307/3558360.
  2. Borsch T, Quandt D. Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Syst Evol. 2009;282(3-4):169-199. https://doi.org/10.1007/s00606-009-0210-8.
  3. Feldberg K, Vána J, Krusche J, et al. A phylogeny of Cephaloziaceae (Jungermanniopsida) based on nuclear and chloroplast DNA markers. Org Divers Evol. 2016;16(4):727-742. https://doi.org/10.1007/s13127-016-0284-4.
  4. Palmer J, Jorgensen R, Thompson W. Chloroplast DNA variation and evolution in pisum: patterns of change and phylogenetic analysis. Genetics. 1985;109(1):195-213.
  5. Kim KJ, Lee HL. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 2004;11(4):247-261. https://doi.org/10.1093/dnares/11.4.247.
  6. Jansen R, Cai Z, Raubeson L, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA. 2007;104(49):19369-19374. https://doi.org/10.1073/pnas.0709121104.
  7. Magee A, Aspinall S, Rice D, et al. Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res. 2010;20(12):1700-1710. https://doi.org/ 10.1101/gr.111955.110.
  8. Jansen RK, Wojciechowski MF, Sanniyasi E, et al. Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Mol Phylogenet Evol. 2008;48(3):1204-1217. https://doi.org/10.1016/j.ympev.2008.06.013.
  9. Sabir J, Schwarz E, Ellison N, et al. Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnology J. 2014;12(6):743-754. https://doi.org/10.1111/pbi.12179.
  10. Wu CS, Chaw SM. Large-Scale Comparative analysis reveals the mechanisms driving plastomic compaction, reduction, and inversions in conifers II (Cupressophytes). Genome Biol Evol. 2016;8(12):3740-3750. https://doi.org/10.1093/gbe/evw278.
  11. Sveinsson S, Cronk Q. Conserved gene clusters in the scrambled plastomes of IRLC legumes (Fabaceae: Trifolieae and Fabeae). bioRxiv. 2016;040188. https://doi.org/10.1101/040188.
  12. Вишнякова М.А., Бурляева М.О., Алпатьева Н.В., Чесноков Ю.В. RAPD анализ видового полиморфизма рода чина Lathyrus L. семейства Fabaceae Lindl // Информационный вестник ВОГиС. – 2008. – T. 12. – № 4. – С. 595-607. [Vishnyakova MA, Burlyaeva MO, Alpatieva NV, Chesnokov YuV. RAPD-analysis of intrageneric polymorphism in Lathyrus L. from Fabaceae Lindl. Informatsionnyi vestnik VOGiS. 2008;12(4):595-607. (In Russ.)]
  13. Говоров Л.И. Горох // Культурная флора СССР. Т. 4. Зерновые бобовые / Под ред. Н.И. Вавилова, Е.В. Вульф. – М.-Л.: Гос. изд. совхозной и колхозной лит-ры, 1937. – 680 с. [Govorov LI. Gorokh. Kulturnaya flora SSSR. Vol. 4. Zernovye bobovye. Ed. by N.I. Vavilov, E.V. Vul’f. Moscow-Leningrad: State ed. state farm and collective farm literature; 1937. 680 р. (In Russ.)]
  14. Oskoueiyan R, Kazempour OS, Maassoumi AA, et al. Phylogenetic status of Vavilovia formosa (Fabaceae-Fabeae) based on nrDNA ITS and cpDNA sequences. Biochem Syst Ecol. 2010;38(3):313-319. https://doi.org/10.1016/j.bse.2010.01.011.
  15. Schaefer H, Hechenleitner P, Santos-Guerra A, et al. Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages. BMC Evol Biol. 2012;12:250. https://doi.org/10.1186/1471-2148-12-250.
  16. Mikič A, Smýkal P, Kenicer G, et al. The bicentenary of the research on ‘beautiful’ vavilovia (Vavilovia formosa), a legume crop wild relative with taxonomic and agronomic potential. Bot J Linn Soc. 2013;172(4):524-531. https://doi.org/10.1111/boj.12060.
  17. Coulot P, Rabaute P. Monographie de Leguminosae de France. 4. Tribus des Fabeae, des Cicereae et des Genisteae. Bulletin de la Société Botanique du Centre-Ouest. 2016;46:1-902.
  18. Li C, Zhao Y, Huang H, et al. The complete chloroplast genome of an inverted-repeat-lacking species, Vicia sepium, and its phylogeny. Mitochondrial DNA. 2018;3(1):137-138. https://doi.org/10.1080/23802359.2018.1431071.
  19. Макашева Р.Х. Культурная флора СССР. Т. 4. Зерновые бобовые культуры. Ч. 1. Горох / Под ред. Д.Д. Брежнева, О.Н. Коровиной. – Л.: Колос, 1979. – 324 с. [Makasheva RKh. Kul’turnaya flora SSSR Vol. 4. Zernovye bobovye kul’tury. Ch. 1. Gorokh. Ed. by D.D. Brezhnev, O.N. Korovina. Leningrad: Kolos; 1979. 324 р. (In Russ.)]
  20. Maxted N, Ambrose M. Peas (Pisum L.). In: Maxted N, Bennett SJ, eds. Plant genetic resources of Legumes in the Mediterranean. Kluwer Acad., Dordrecht: Current plant science and biotechnology in agriculture; 2001. Р. 181-190. https://doi.org/10.1007/978-94-015-9823-1_10.
  21. Kosterin OE, Zaytseva OO, Bogdanova VS, Ambrose MJ. New data on three molecular markers from different cellular genomes in Mediterranean accessions reveal new insights into phylogeography of Pisum sativum L. sbsp. elatius (Bieb.) Schmalh. Genet Resour Crop Evol. 2010;57(5):733-739. https://doi.org/10.1007/s10722-009-9511-6.
  22. Zaytseva OO, Gunbin KV, Mglinets AV, Kosterin OE. Divergence and population traits in evolution of the genus Pisum L. as reconstructed using genes of two histone H1 subtypes showing different phylogenetic resolution. Gene. 2015;556(2):235-244. https://doi.org/10.1016/j.gene.2014.11.062.
  23. Vershinin AV, Allnutt TR, Knox MR, et al. Transposable elements reveal the impact of introgression, rather than transposition, in Pisum diversity, evolution, and domestication. Mol Biol Evol. 2003;20(12):2067-2075. https://doi.org/10.1093/molbev/msg220.
  24. Jing R, Vershinin A, Grzebyta J, et al. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol. 2010;10(1):44. https://doi.org/10.1186/1471-2148-10-44.
  25. Jing R, Ambrose MA, Knox MR, et al. Genetic diversity in European Pisum germplasm collections. Theor App Genet. 2012;125(2):367-380. https://doi.org/10.1007/s00122-012-1839-1.
  26. Cupic T, Tucak M, Popovic S, et al. Genetic diversity of pea (Pisum sativum L.) genotypes assessed by pedigree, morphological and molecular data. J Food Agric Environ. 2009;7(3-4): 343-348. https://doi.org/10.1234/4.2009.2572.
  27. Pavan S, Schiavulli A, Appiano M, et al. Pea powdery mildew er1 resistance is associated to loss-of-function mutations at a MLO homologous locus. Theor Appl Genet. 2011;123(8): 1425-1431. https://doi.org/10.1007/s00122-011-1677-6.
  28. Дьяченко Е.А., Рыжова Н.Н., Вишнякова М.А., Кочиева Е.З. Молекулярно-генетическое разнообразие гороха (Pisum sativum L.) из коллекции ВИР на основе данных AFLP-анализа // Генетика. – 2014. – Т. 50. – № 9. – С. 1040–1049. [Dyachenko EA, Ryzhova NN, Vishnyakova MA, Kochieva EZ. Molecular genetic diversity of the Pea (Pisum sativum L.) from the Vavilov Research Institute collection detected by the AFLP analysis. Russ J Genet. 2014;50(9): 1040-1049. (In Russ.)]. https://doi.org/10.1134/s1022795414090045.
  29. Wojciechowski MF, Sanderson MJ, Steele KP, Liston A. Molecular phylogeny of the “temperate herbaceous tribes” of papilionoid legumes: a supertree approach. In: Herendeen P, Bruneau A, eds. Advances in Legume Systematics 9. Royal Botanic Garden, Kew; 2000. Р. 277-298.
  30. Zaytseva OO, Bogdanova VS, Mglinets AV, Kosterin OE. Refinement of the collection of wild peas (Pisum L.) and search for the area of pea domestication with a deletion in the plastidic psbA-trnH spacer. Genet Resour Crop Evol. 2017;64(6):1417-1430. https://doi.org/ 10.1007/s10722-016-0446-4.
  31. Oskoueiyan R, Osaloo SK, Amirahmadi A. Molecular phylogeny of the genus Lathyrus (Fabaceae-Fabeae) based on cpDNA matK sequence in Iran. Iran J Biotechnol. 2014;12(2):e10315. https://doi.org/10.5812/ijb.10315.
  32. Bogdanova VS, Zaytseva OO, Mglinets AV, et al. Nuclear-cytoplasmic conflict in pea (Pisum sativum L.) is associated with nuclear and plastidic candidate genes encoding Acetyl-CoA carboxylase subunits. PLoS One. 2015;10(3): e0119835. http://doi.org/10.1371/journal.pone.0119835.
  33. Gao L, Zhou Y, Wang ZW, et al. Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers. BMC Plant Biol. 2011;11(1):64. https://doi.org/10.1186/1471-2229-11-64.
  34. Bieniek W, Mizianty M, Szklarczyk M. Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species. Plant Syst Evol. 2015;301(4):1275-1286. https://doi.org/10.1007/s00606-014-1138-1.
  35. Shaw J, Lickey E, Beck JT, et al. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot. 2005;92(1):142-166. https://doi.org/10.3732/ajb.92.1.142.
  36. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7): 1870-1874. https://doi.org/10.1093/molbev/msw054.
  37. Kenicer GJ, Kajita T, Pennington RT, Murata J. Systematics, biogeography of Lathyrus (Leguminosae) based on internal transcribed spacer, cpDNA sequence data. Am J Bot. 2005;92(7): 1199-1209. https://doi.org/10.3732/ajb.92.7. 1199.
  38. Zaytseva OO, Bogdanova VS, Kosterin OE. Phylogenetic reconstruction at the species and intraspecies levels in the genus Pisum (L.) (Peas) using a histone H1 gene. Gene. 2012;504(2):192-202. https://doi.org/10.1016/j.gene.2012.05.026.

Supplementary files

Supplementary Files Action
1.
Figure: 1. Identified haplotypes in the rpoB – trnC sequence in the pea species P. sativum (Ps) (a) and P. fulvum (Pf) (b). EL - samples of P. sativum subsp. elatius; T - samples of P. sativum subsp. transcaucasicum

Download (369KB) Indexing metadata
2.
Figure: 2. Dendrogram of genetic similarity of 38 samples of the genus Pisum and species of the genera Lathyrus and Vavilovia of the tribe Fabeae based on the total sequence of the analyzed regions of the chloroplast genome (trnH – psbA, trnY – trnT, rpoB – trnC) (ML method, model T92 + G)

Download (177KB) Indexing metadata

Statistics

Views

Abstract - 50

PDF (Russian) - 1

PDF (English) - 0

Cited-By


Article Metrics

Metrics Loading ...

PlumX

Dimensions


Copyright (c) 2021 Dyachenko E.A., Semenova E.V., Kochieva E.Z.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies