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Aegilops tauschii Coss. chloroplast genome phylogeny

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Abstract

The chloroplast genome phylogeny of Aegilops tauschii was studied. The sequences of four regions of non-coding chloroplast DNA (cpDNA), about 3000 b.p. in total, in 111 Ae. tauschii accessions, 55 of subspecies tauschii (TauL1) and 56 of subspecies strangulata (2 of TauL3 and 54 of TauL2 gene-pool), were used for neighboring joint and maximum likelihood analysis. This revealed that the patterns of cpDNA divergence essentially differ from those of nuclear genome in Ae. tauschii, coinciding only at TauL3, indicating that the chloroplast genome of TauL3 Ae. tauschii differentiated from those of other Ae. tauschii in ancient times. Among the other Ae. tauschii, Taul1 plants have relatively “older” variants of chloroplast genome; moreover, from 55 TauL1 accessions studied, the four accessions originating from the edges of the species area retained the relict variant of cpDNA, with no indels or base pair substitution having taken place in about 3000 b.p. studied, since the differentiation of TauL1 and TauL2 started. Most of TauL1 plants form a cluster with rather similar cpDNA, which also included eight of 54 Taul2 accessions studied, all originating from Caucasia and pre-Caspian Iran. The other 46 TauL2 accessions form a single cluster residing on the tree among the major and several minor, relict, lineages of TauL1. This cluster presents relatively “young”, considerably changed by mutations, and also highly variable cpDNA. It further falls in the two sub-clusters: one presents TauL2 Ae. tauschii from South Caucasia and pre-Caspian Iran, and another—with TauL2 from Caucasia, Continental Iran and Turkmenistan.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

cpDNA:

Chloroplast DNA

DArT:

Diversity arrays technology

ML:

Maximum likelihood

NJ:

Neighbor-joining

PCR:

Polymerase chain reaction

RFLP:

Restriction fragment length polymorphism

SSR:

Simple sequence repeat

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Acknowledgements

I would like to express my sincere gratitude to Miss. Rinata R. Husainova and Dr. Oleg V. Vaulin for the help in the course of this study. I am also very grateful to Dr. Stephen M. Reader for the help in preparation of the manuscript.

Funding

The work was supported by Russian Foundation for Basic Research, Grant 16-04-00106-a.

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Novosibirsk, Russia, 630090

    Alexander Ju. Dudnikov

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  1. Alexander Ju. Dudnikov
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Correspondence to Alexander Ju. Dudnikov.

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Author Alexander Ju. Dudnikov declares that he has no conflict of interest.

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Fig. 1s (supplement).

Neighbor-Joining phylogenetic tree of Aegilops tauschii chloroplast DNA. DNA sequences were treated “as is” by MEGA 6. Gaps were treated using “partial deletion” option. Ae. tauschii accessions k-433, k-1956s, k-1960, k-1961, KU-20-8, KU-2118, KU-2123, KU-2126, KU-2156 have inversion Nf(i)225b (Dudnikov 2012), and since it is treated here de facto as a set of independent base pair substitutions, its impact is overestimated greatly. (See also designations in the caption for Fig. 1). (JPEG 2354 kb)

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Dudnikov, A.J. Aegilops tauschii Coss. chloroplast genome phylogeny. J. Plant Biochem. Biotechnol. 28, 245–252 (2019). https://doi.org/10.1007/s13562-018-0469-3

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