Sequencing and annotation of the chloroplast genome of Amblyopyrum muticum (Poaceae)
UDC 582.542.1+575.133
Keywords:
Aegilops mutica, Aegilops umbellulata, genus Aegilops, section Sitopsis, T genome
Abstract
The complete chloroplast genomes of two Amblyopyrum muticum (syn. Aegilops mutica) accessions, k-3979 and k-3981, were sequenced, measuring 136911 and 136907 bp, respectively. Alignment and analysis of the nucleotide sequences of chloroplast genomes from different representatives of the Triticeae tribe showed similarities between the plastomes of A. muticum and Aegilops umbellulata from the section Aegilops, reaching 99.74 %. A phylogenetic tree constructed based on the alignment of complete chloroplast genomes showed that A. muticum is phylogenetically distinct from species of the section Sitopsis but not from all representatives of the genus Aegilops.
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References
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Badaeva E. D., Friebe B., Gill B. S. 1996. Genome differentiation in Aegilops. 2. Physical mapping of 5S and 18S–26S ribosomal RNA gene families in diploid species. Genome 39: 1150 ‒ 1158.
Baidouri M., Murat F., Veyssiere M., Molinier M., Flores R., Burlot L., l Alaux M., Quesneville H., Pont C., Salse J. 2017. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytol, 213: 1477–1486. https://doi.org/10.1111/nph.14113
Beier S., Thiel T., Munch T., Scholz U., Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16): 2583–2585. https://doi.org/10.1093/bioinformatics/btx198
Bernhardt N., Brassac J., Dong X., Willing E-M., Poskar C. H., Kilian B., Blattner F. R. 2020. Genome-wide sequence information reveals recurrent hybridization among diploid wheat wild relatives. Plant J. 102: 493–506. https://doi.org/10.1111/tpj.14641
Bernhardt N., Brassac J., Kilian B., Blattner F. R. 2017. Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae. B. M. C. Evol. Biol. 17(1): 141. https://doi.org/10.1186/s12862-017-0989-9
Bolger A. M., Lohse M., Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Chennaveeraiah M. S. 1960. Karyomorphologic and cytotaxonomic studies in Aegilops. Acta Horti Gotoburgensis 23: 85–178.
Clayton S. D., Renvoize S. A. 1986. Genera graminum, grasses of the world. Kew Bull. Addit. Ser. 13: 1 389.
Damascus S. 2012. Resolving genetic relationships among Aegilops L. and Triticum L. species using analysis of chloroplast DNA by Cleaved Amplified Polymorphic Sequence (CAPS). Asian J. Agric. Sci. 4(4): 270–279.
Давоян Р. О., Бебякина И. В., Давоян Э. Р., Миков Д. С., Зубанова Ю. С., Болдаков Д. М., Бадаева Е. Д., Адонина И. Г., Салина Е. А., Зинченко А. Н. Создание и изучение интрогрессивных образцов мягкой пшеницы, полученных на основе синтетической формы RS7 // Вавиловский журнал генетики и селекции, 2019. T. 23, №7. С. 827–835. https://doi.org/10.18699/VJ19.556
Dvorak J., Zhang H-B. 1992. Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences. Theor. Appl. Genet. 84: 419–429.
Eig A. 1929a. Amblyopyrum Eig. A new genus separated from the genus Aegilops. PZE Inst. Agric. Nat. Hist. Agric. Res. 2: 199–204.
Eig A. 1929b. Monographisch-kritische ubersicht der gattung Aegilops. Reprium Nov. Spec. Regni. Veg. 55: 12–88.
Feldman M., Levy A. A. 2023. Wheat Evolution and Domestication. Cham: Springer. 673 pp. https://doi.org/10.1007/978-3-031-30175-9
Fellers J. P., Matthews A., Fritz A. K., Rouse M. N., Grewal S., Hubbart-Edwards S., King I. P., King J. 2020. Resistance to wheat rusts identified in wheat/Amblyopyrum muticum chromosome introgressions. Crop. Science 60: 1957–1964. https://doi.org/10.1002/csc2.20120
Giorgi B., Bozzini A. 1969. Karyotype analysis in Triticum. III. Analysis of the presumed diploid progenitors of polyploid wheats. Caryologia 22: 279–287.
Glemin S., Scornavacca C., Dainat J., Burgarella C., Viader V., Ardisson M., Sarah G., Santoni S., David J., Ranwez V. 2019. Pervasive hybridizations in the history of wheat relatives. Sci. Adv. 5(5): eaav9188. https://doi.org/10.1126/sciadv.aav9188
Graham D. E. 1978. The isolation of high molecular weight DNA from whole organisms of large tissue masses. Anal. Biochem. 78: 673–678.
Greiner S., Lehwark P., Bock R. 2019. Organellar Genome DRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 47: W59–W64. https://doi.org/10.1093/nar/gkz238
Grewal S., Yang Cy., Krasheninnikova K., Collins J., Wood J. M. D., Ashling S., Scholefield D., Kaithakottil G. G., Swarbreck D., Yao E., Sen T. Z., King I. P., King J. 2025. Chromosome-level haplotype-resolved genome assembly of bread wheat’s wild relative Aegilops mutica. Sci Data 12, 438. https://doi.org/10.1038/s41597-025-04737-y
Haider N. 2012. Evidence for the origin of the B genome of bread wheat based on chloroplast DNA. Turk. J. Agric. For. 36(1): 13–25. https://doi.org/10.3906/tar-1011-1394
Hammer K. 1980. Vorarbeiten zur monographischen Darstellung von Wildpflanzensortimenten: Aegilops L. Kulturpflanze 28: 33–180. https://doi.org/10.1038/s41597-025-04737-y
Huynh S., Marcussen T., Felber F., Parisod C. 2019. Hybridization preceded radiation in diploid wheats. Mol. Phylogenet. Evol. 139: 106554. https://doi.org/10.1016/j.ympev.2019.106554
Jones J. K., Majisu B. N. 1968. The homoeology of Aegilops mutica chromosomes. Can. J. Genet. Cytol. 10: 620–626.
Katoh K., Standley, D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30(4): 772–780. https://doi.org/10.1093/molbev/mst010
Kimber G., Tsunewaki K. 1988. Genome symbols and plasma types in the wheat group. In: T. E. Miller, R. M. D. Koebner (eds.). Proceedings of the seventh international wheat genetics symposium. Cambridge: Institute of Plant Science Research. Pp. 1209–1210.
King J., Grewal S., Yang C., Hubbart S., Scholefield D., Ashling S., Keith J., Edwards K. J., Allen A. M., Burridge A., Bloor C., Davassi A., da Silva G. J., Chalmers K., King I. P. 2017. A step change in the transfer of interspecific variation into wheat from Amblyopyrum muticum. Plant. Biotech. J. 15(2): 217–226. https://doi.org/10.1111/pbi.12606
Kuluev A. R., Kuluev B. R., Mikhaylova E. V., Chemeris A. V. 2024. Sequencing and analysis of complete chloroplast genomes of einkorn wheats Triticum sinskajae and Triticum monococcum accession k-20970. Genet. Resour. Crop Evol. 71: 3347–3360. https://doi.org/10.1007/s10722-023-01843-x
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. 2009. The sequence alignment/map format and samtools. Bioinformatics 25: 2078–2079.
Li L-F., Liu B., Olsen K. M., Wendel J. F. 2015. Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops–Triticum complex. New Phytol. 208(1): 11–12.
Li L.-F., Zhang Z.-B., Wang Z.-H., Li N., Sha Y., Wang X.-F., Ding N., Li Y., Zhao J., Wu Y., Gong L., Mafessoni F., Levy A.A., Liu B. 2022. Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome. Mol. Plant. 15(3): 488–503. https://doi.org/10.1016/j.molp.2021.12.019
Maan S. S. 1977. Cytoplasmic homology between Aegilops mutica Boiss. and Ae. ovata L. Euphytica 26: 601–613.
Middleton C. P. Senerchia N., Stein N., Akhunov E. D. 2014. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLOS ONE 9(3): e85761. https://doi.org/10.1371/journal.pone.0085761
Murai K., Xu N. Y, Tsunewaki K. 1989. Studies on the origin of crop species by restriction endonuclease analysis of organellar DNA. III. Chloroplast DNA variation and interspecific relationships in the genus Secale. Jpn. J. Genet. 64: 35–47.
Quinlan A. R., Hall I. M. 2010. Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841–842. https://doi.org/10.1093/bioinformatics/btq033
Riley R. 1966. The genetic regulation of meiotic behavior in wheat and its relatives. In: J. Mac Key (ed.) Proceedings of the second international wheat genetics symposium. Sweden, Lund: Genetic Institute, University of Lund, Hereditas (suppl) 2. Pp. 395–406.
Sallares R., Brown T. A. 2004. Phylogenetic analysis of complete 5’ external transcribed spacers of the 18S ribosomal RNA genes of diploid Aegilops and related species (Triticeae, Poaceae). Genet. Resour. Crop Evol. 51: 701–712.
Sandve S. R., Marcussen T., Mayer K., Jakobsen K. S., Heier L., Steuernagel B., Wulf B. H., Olsen O. A. 2015. Chloroplast phylogeny of Triticum/Aegilops species is not incongruent with an ancient homoploid hybrid origin of the ancestor of the bread wheat D genome. New Phytol. 208: 9–10. https://doi.org/10.1111/nph.13487
Sasanuma T., Chabane K., Endo T. R., Valkoun J. 2004. Characterization of genetic variation in and phylogenetic relationships among diploid Aegilops species by AFLP: incongruity of chloroplast and nuclear data. Theor. Appl. Genet. 108: 612–618.
Schoen A., Saripalli G., Hosseinirad S., Sharma P. K., Kajla A., Yadav S. S., Tiwari V. 2024. Genome sequences from diploids and wild relatives of wheat for comparative genomics and alien introgressions. In: R. Appels et al. (eds.). The Wheat Genome. Cham: Springer. Pp. 241–263. https://doi.org/10.1007/978-3-031-38294-9_12
Сенянинова-Корчагина М. Кариосистематическое исследование рода Aegilops // Труды по прикладной ботанике, генетике и селекции, 1932. Серия 2, № 1. С. 1–90.
Shi L., Chen H., Jiang M., Wang L., Wu X., Huang L., Liu C. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47: W65–W73. https://doi.org/10.1093/nar/gkz345
Shi C., Hu N., Huang H., Gao J., Zhao Y.-J., Gao L.-Z. 2012. An improved chloroplast DNA extraction procedure for whole plastid genome sequencing. PLoS ONE 7(2): e31468. https://doi.org/10.1371/journal.pone.0031468
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Published
2025-10-11
How to Cite
Kuluev A. R., Matniyazov R. T., Kuluev B. R., Chemeris A. V. Sequencing and annotation of the chloroplast genome of Amblyopyrum muticum (Poaceae) // Turczaninowia, 2025. Vol. 28, № 3. P. 154–164 DOI: 10.14258/turczaninowia.28.3.18. URL: https://turczaninowia.asu.ru/article/view/18014.
Section
Science articles
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