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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.

SUBMITTER: Trofimov D

PROVIDER: S-EPMC8782842 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundArtemisia subg. Seriphidium, one of the most species-diverse groups within Artemisia, grows mainly in arid or semi-arid regions in temperate climates. Some members have considerable medicinal, ecological, and economic value. Previous studies on this subgenus have been limited by a dearth of genetic information and inadequate sampling, hampering our understanding of their phylogenetics and evolutionary history. We therefore sequenced and compared the chloroplast genomes of this subgenus, and evaluated their phylogenetic relationships.ResultsWe newly sequenced 18 chloroplast genomes of 16 subg. Seriphidium species and compared them with one previously published taxon. The chloroplast genomes, at 150,586-151,256 bp in length, comprised 133 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and one pseudogene, with GC content of 37.40-37.46%. Comparative analysis showed that genomic structures and gene order were relatively conserved, with only some variation in IR borders. A total of 2203 repeats (1385 SSRs and 818 LDRs) and 8 highly variable loci (trnK - rps16, trnE - ropB, trnT, ndhC - trnV, ndhF, rpl32 - trnL, ndhG - ndhI and ycf1) were detected in subg. Seriphidium chloroplast genomes. Phylogenetic analysis of the whole chloroplast genomes based on maximum likelihood and Bayesian inference analyses resolved subg. Seriphidium as polyphyletic, and segregated into two main clades, with the monospecific sect. Minchunensa embedded within sect. Seriphidium, suggesting that the whole chloroplast genomes can be used as molecular markers to infer the interspecific relationship of subg. Seriphidium taxa.ConclusionOur findings reveal inconsistencies between the molecular phylogeny and traditional taxonomy of the subg. Seriphidium and provide new insights into the evolutionary development of this complex taxon. Meanwhile, the whole chloroplast genomes with sufficiently polymorphic can be used as superbarcodes to resolve interspecific relationships in subg. Seriphidium.

Project description:BackgroundForage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four Urochloa species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels).ResultsWhole plastid genome sizes were 138,765 bp in U. ruziziensis, 138,945 bp in U. decumbens, 138,946 bp in U. brizantha and 138,976 bp in U. humidicola. Each Urochloa chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses. U. brizantha and U. decumbens chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to U. ruziziensis and U. humidicola. Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of U. humidicola from a common ancestor with the three other Urochloa species was estimated at 9.46 mya. U. ruziziensis, U. decumbens, and U. brizantha formed a clade where the U. ruziziensis lineage would have diverged by 5.67 mya, followed by a recent divergence event between U. decumbens and U. brizantha around 1.6 mya.ConclusionLow-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of Urochloa used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of Urochloa. Our results placed the origin of U. humidicola and U. ruziziensis divergence in the Miocene-Pliocene boundary, and the split between U. brizantha and U. decumbens in the Pleistocene.

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

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