pubmed.ncbi.nlm.nih.gov

A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex - PubMed

  • ️Sat Jan 01 2022

A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex

Dimitrij Trofimov et al. Sci Rep. 2022.

Abstract

The genus Ocotea (Lauraceae) includes about 450 species, of which about 90% are Neotropical, while the rest is from Macaronesia, Africa and Madagascar. In this study we present the first complete chloroplast genome sequences of seven Ocotea species, six Neotropical and one from Macaronesia. Genome sizes range from 152,630 (O. porosa) to 152,685 bp (O. aciphylla). All seven plastomes contain a total of 131 (114 unique) genes, among which 87 (80 unique) encode proteins. The order of genes (if present) is the same in all Lauraceae examined so far. Two hypervariable loci were found in the LSC region (psbA-trnH, ycf2), three in the SSC region (ycf1, ndhH, trnL(UAG)-ndhF). The pairwise cp genomic alignment between the taxa showed that the LSC and SSC regions are more variable compared to the IR regions. The protein coding regions comprise 25,503-25,520 codons in the Ocotea plastomes examined. The most frequent amino acids encoded in the plastomes were leucine, isoleucine, and serine. SSRs were found to be more frequent in the two dioecious Neotropical Ocotea species than in the four bisexual species and the gynodioecious species examined (87 vs. 75-84 SSRs). A preliminary phylogenetic analysis based on 69 complete plastomes of Lauraceae species shows the seven Ocotea species as sister group to Cinnamomum sensu lato. Sequence divergence among the Ocotea species appears to be much lower than among species of the most closely related, likewise species-rich genera Cinnamomum, Lindera and Litsea.

© 2022. The Author(s).

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1

Gene map of Ocotea species (O. aciphylla, O. daphnifolia, O. foetens, O. guianensis, O. odorifera, O. porosa, and O. tabacifolia) chloroplast genomes. The genes shown on the inside and the outside of the outer circle are transcribed in clockwise and counterclockwise direction, respectively. The coloured bars denote gene functional groups. The dark gray and light gray shading within the inner circle correspond to percentage GC and AT content, respectively. IR inverted repeat, LSC large single copy, SSC small single copy.

Figure 2
Figure 2

Comparison of the nucleotide variability (Pi) values, (a) among the seven Ocotea plastomes and (b) among 69 plastomes of Lauraceae. The linear gene map of Ocotea species is shown below.

Figure 3
Figure 3

Comparison of LSC, IR, and SSC junction positions among seven Ocotea chloroplast genomes.

Figure 4
Figure 4

Visualization of Ocotea chloroplast genomes using mVISTA program with O. aciphylla as reference. CNS conserved non-coding sequence; UTR untranslated region.

Figure 5
Figure 5

Amino acid percentage of protein-coding genes in seven Ocotea plastomes.

Figure 6
Figure 6

Simple sequence repeats (SSRs) in seven chloroplast genomes of Ocotea. (a) Counts of nucleotide repeats; (b) counts of mono-, di-, tri-, tetra-, penta- and hexanucleotides.

Figure 7
Figure 7

Maximum Likelihood phylogeny including 69 complete chloroplast genome sequences of Core Lauraceae. Color codes: blue—Cinnamomeae, incl. pale blue for Ocotea spp.; pink—Laureae; green—Perseeae. Maximum likelihood bootstrap support values (ML-BS) are shown next to the branches.

Similar articles

Cited by

References

    1. Rohwer JG, et al. Lauraceae. In: Kubitzki K, et al., editors. The Families and Genera of Vascular Plants. Springer; 1993.
    1. Trofimov D, Moraes PLR, Rohwer JG. Towards a phylogenetic classification of the Ocotea complex (Lauraceae)—Classification principles and reinstatement of Mespilodaphne. Bot. J. Linn. Soc. 2019;190:25–50. doi: 10.1093/botlinnean/boz010. - DOI
    1. Trofimov D, Rohwer JG. Towards a phylogenetic classification of the Ocotea complex (Lauraceae)—An analysis with emphasis on the Old World taxa and description of the new genus Kuloa. Bot. J. Linn. Soc. 2020;192:510–535. doi: 10.1093/botlinnean/boz088. - DOI
    1. Rohwer JG. Prodromus einer Monographie der Gattung Ocotea Aubl. (Lauraceae), sensu lato. Mitt. Inst. Allg. Bot. Hamburg. 1986;1986(20):3–278.
    1. van der Werff H. Studies in Malagasy Lauraceae II: New taxa. Novon. 1996;6:463–475. doi: 10.2307/3392057. - DOI

Publication types

MeSH terms