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

Dimitrij Trofimov,Jonas Schmidt-Chanasit,Jens G Rohwer,Pedro Luís Rodrigues De Moraes,Daniel Cadar

doi:10.1038/s41598-021-04635-4

Dimitrij Trofimov, Jonas Schmidt-Chanasit + Show 3 more

Open Access

https://doi.org/10.1038/s41598-021-04635-4

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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.

Highlights

The Lauraceae are among the most frequent woody plant families in moist tropical areas and include about 55 genera with 2500–3500 species[1,2,3]
The chloroplast genome sequences of the seven Ocotea species range from 152,630 bp in O. porosa (Nees & Mart.) Barroso to 152,685 bp in O. aciphylla (Nees & Mart.) Mez (Table 1)
Contents of nucleotides in the large single copy (LSC), inverted repeats (IRs) and small single copy (SSC) of the plastomes were similar in all species of Ocotea examined (Supplementary Table S2)

Summary

Introduction

The Lauraceae are among the most frequent woody plant families in moist tropical areas and include about 55 genera with 2500–3500 species[1,2,3]. Most of the molecular phylogenetic studies in Lauraceae published so far focused on other genera or on the major evolutionary lineages in the Lauraceae and included only a relatively small number of Ocotea species[9,10,11]. They suggested that Ocotea was paraphyletic with respect to most other New World genera, viz. Aniba Aubl., Damburneya Raf., Dicypellium Nees & Mart., Endlicheria Nees, Kubitzkia van der Werff, Licaria Aubl., Nectandra Rol. ex Rottb., Paraia Rohwer, H.G. Richt. Have been studied so far, plus the North American P. borbonia (L.) Spreng.[24,25,28] These studies considerably improved support values among the major phylogenetic lineages in the Asian Lauraceae, especially among Cassytha, Caryodaphnopsis and Neocinnamomum. In other plant groups, such as the genus Quercus L., Poaceae-Arundinarieae and Rosaceae, they allowed resolving phylogenetic relationships on different levels[34,35,36]

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