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

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.

Floral morphology and phenology of Sassafras tzumu (Lauraceae)

“…Cinnamomeae and is nested within Cinnamomum, while the members of the trib. Laureae form a separate clade [4,5,25]. As a result, it must be assumed that the racemose inflorescences of Sassafras and some members of the trib.…”

“…Recent molecular phylogenetic studies have shown that Sassafras is monophyletic, so that there is no need to split it into two or three genera. It is nested within Cinnamomum and the two Asian species S. tzumu and S. randaiense constitute a clade sister to the American species S. albidum [4,5]. As a result, it can be inferred that the ancestor of Sassafras possessed (predominantly) racemose inflorescences and bisexual flowers, and that the two Asian species retained the plesiomorphic bisexual flowers, whereas S. albidum acquired the autapomorphic unisexual flowers after its divergence from the Asian species.…”

“…Cinnamomeae and is closely related to Cinnamomum sect. Camphora Meisn., which causes non-monophyly of the genus Cinnamomum [4,5].…”

“…Camphora Meisn. but not to Actinodaphne [4,5]. To understand the evolution of the genus better, the inflorescences of the second Asian species, Sassafras tzumu, are re-examined here, in order to clarify the general pattern of inflorescence structure in the genus.…”

Comparative analysis of the structure of complete chloroplast genomes in genus Mangifera and accuracy verification about phylogenetic analysis based on gene ycf2 in genus level

“…Furthermore, single copy regions were indicated that they were more divergent than others. In previous studies, many terms provided the evidence, such as the study of Dr. Fu, Dr. Trofimov's team, Dr. Su's team and Dr. Song's team [41][42][43][44]. In their study, all the results of sequence divergent analysis had the same point: the most divergent areas distributed in single copy regions, either large single copy or small single copy.…”