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Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f)

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Abstract

Availability of comprehensive phylogenetic tree for flowering plants which includes many of the economically important crops and trees is one of the essential requirements of plant biologists for diverse applications. It is the first study on the use of chloroplast genome of 3265 Angiosperm taxa to identify evolutionary relationships among the plant species. Sixty genes from chloroplast genome was concatenated and utilized to generate the phylogenetic tree. Overall the phylogeny was in correspondence with Angiosperm Phylogeny Group (APG) IV classification with very few taxa occupying incongruous position either due to ambiguous taxonomy or incorrect identification. Simple sequence repeats (SSRs) were identified from almost all the taxa indicating the possibility of their use in various genetic analyses. Large proportion (95.6%) of A/T mononucleotide was recorded while the di, tri, tetra, penta and hexanucleotide amounted to less than 5%. Ambiguity of the taxonomic status of Tectona grandis L.f was assessed by comparing the chloroplast genome with closely related Lamiaceae members through nucleotide diversity and contraction/expansion of inverted repeat regions. Although the gene content was highly conserved, structural changes in the genome was evident. Phylogenetic analysis suggested that Tectona could qualify for a subfamily Tectonoideae. Nucleotide diversity in intergenic and genic sequences revealed prominent hyper-variable regions such as, rps16-trnQ, atpH-atpI, psc4-psbJ, ndhF, rpl32 and ycf1 which have high potential in DNA barcoding applications.

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Acknowledgements

The authors acknowledge the Department of Biotechnology (DBT), India, for financial support. Junior Research Fellowship provided to PM by DBT is acknowledged.

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Authors and Affiliations

  1. Institute of Forest Genetics and Tree Breeding, Coimbatore, 641 002, India

    P Maheswari, C Kunhikannan & R Yasodha

Authors
  1. P Maheswari
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  2. C Kunhikannan
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  3. R Yasodha
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Corresponding author

Correspondence to R Yasodha.

Additional information

Communicated by Manchikatla Venkat Rajam.

Corresponding editor: Manchikatla Venkat Rajam

Supplementary Information

Below is the link to the electronic supplementary material.

12038_2021_166_MOESM1_ESM.docx

Fifty percent maximum parsimony majority rule consensus tree of Angiospermae with major clades inferred from 60 chloroplast protein coding genes. Terminals with a circle represent collapsed clades with ≥ 2 taxa (DOCX 15 kb)

12038_2021_166_MOESM2_ESM.pdf

Fifty percent maximum parsimony majority rule consensus tree of Angiospermae with major clades inferred from 60 chloroplast protein coding genes. Terminals with a circle represent collapsed clades with ≥ 2 taxa (PDF 287 kb)

12038_2021_166_MOESM3_ESM.pdf

Phylogenetic tree of 3265 taxa data set with two outgroups based on 60 chloroplast protein coding genes using maximum parsimony (MP). The coloured strips indicate the clustering of the MP tree at the family and ordinal level. Ordinal and higher-level group names follow APG IV (PDF 1643 kb)

12038_2021_166_MOESM4_ESM.pdf

Phylogenetic tree of Lamiaceae members. Dendrogram generated based on whole chloroplast genome using maximum parsimony (MP) with 50% majority‐rule consensus principle (PDF 2610 kb)

12038_2021_166_MOESM5_ESM.pdf

Identity plot comparing 10 Lamiaceae members chloroplast genome sequences with annotations, using mVISTA. The vertical scale indicates the percentage of identity, ranging from 50 to 100%. The horizontal scale indicates the coordinates within the chloroplast genomes. Grey arrows represent the genes and their orientations. Blue boxes represent exon regions and red boxes represent non-coding sequence (CNS) regions (PDF 4420 kb)

Supplementary file5 (XLSX 478 kb)

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Maheswari, P., Kunhikannan, C. & Yasodha, R. Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f). J Biosci 46, 43 (2021). https://doi.org/10.1007/s12038-021-00166-2

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  • DOI: https://doi.org/10.1007/s12038-021-00166-2

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