Dataset Information

The complete chloroplast genome of Protea kilimandscharica Engl. (Proteaceae).

ABSTRACT: Protea kilimandscharica is endemic to the heath zone of Mt Kenya, restricted to the rocky slopes of the mountain. The complete chloroplast genome of P. kilimandscharica was determined by next-generation sequencing technology, with a total length of 158,657 bp. The cp genome encodes 115 unique genes, with four rRNA genes, 81 protein-coding genes (PCGs), and 30 tRNA genes. A 3.1 kb inversion was noted in the LSC. Phylogenetic analysis, based on 75 common protein-coding genes revealed P. kilimandscharica as sister to Macadamia integrifolia and Macadamia ternifolia.

SUBMITTER: Nzei JM

PROVIDER: S-EPMC7748779 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Protea kilimandscharica Engl. (Proteaceae).

Nzei John M JM Saina Josphat K JK Mwanzia Virginia M VM Avoga Sheila S Pan Cheng C

Mitochondrial DNA. Part B, Resources 20200114 1

Protea kilimandscharica is endemic to the heath zone of Mt Kenya, restricted to the rocky slopes of the mountain. The complete chloroplast genome of P. kilimandscharica was determined by next-generation sequencing technology, with a total length of 158,657 bp. The cp genome encodes 115 unique genes, with four rRNA genes, 81 protein-coding genes (PCGs), and 30 tRNA genes. A 3.1 kb inversion was noted in the LSC. Phylogenetic analysis, based on 75 common protein-coding genes r ...[more]

PMID: 33366666

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Project description:BackgroundSequence data from the chloroplast genome have played a central role in elucidating the evolutionary history of flowering plants, Angiospermae. In the past decade, the number of complete chloroplast genomes has burgeoned, leading to well-supported angiosperm phylogenies. However, some relationships, particulary among early-diverging lineages, remain unresolved. The diverse Southern Hemisphere plant family Proteaceae arose on the ancient supercontinent Gondwana early in angiosperm history and is a model group for adaptive radiation in response to changing climatic conditions. Genomic resources for the family are limited, and until now it is one of the few early-diverging 'basal eudicot' lineages not represented in chloroplast phylogenomic analyses.ResultsThe chloroplast genome of the Australian nut crop tree Macadamia integrifolia was assembled de novo from Illumina paired-end sequence reads. Three contigs, corresponding to a collapsed inverted repeat, a large and a small single copy region were identified, and used for genome reconstruction. The complete genome is 159,714 bp in length and was assembled at deep coverage (3.29 million reads; ~2000 x). Phylogenetic analyses based on 83-gene and inverted repeat region alignments, the largest sequence-rich datasets to include the basal eudicot family Proteaceae, provide strong support for a Proteales clade that includes Macadamia, Platanus and Nelumbo. Genome structure and content followed the ancestral angiosperm pattern and were highly conserved in the Proteales, whilst size differences were largely explained by the relative contraction of the single copy regions and expansion of the inverted repeats in Macadamia.ConclusionsThe Macadamia chloroplast genome presented here is the first in the Proteaceae, and confirms the placement of this family with the morphologically divergent Plantanaceae (plane tree family) and Nelumbonaceae (sacred lotus family) in the basal eudicot order Proteales. It provides a high-quality reference genome for future evolutionary studies and will be of benefit for taxon-rich phylogenomic analyses aimed at resolving relationships among early-diverging angiosperms, and more broadly across the plant tree of life.

Project description:Background and aimsGlobal plant trait datasets commonly identify trait relationships that are interpreted to reflect fundamental trade-offs associated with plant strategies, but often these trait relationships are not identified when evaluating them at smaller taxonomic and spatial scales. In this study we evaluate trait relationships measured on individual plants for five widespread Protea species in South Africa to determine whether broad-scale patterns of structural trait (e.g. leaf area) and physiological trait (e.g. photosynthetic rates) relationships can be detected within natural populations, and if these traits are themselves related to plant fitness.MethodsWe evaluated the variance structure (i.e. the proportional intraspecific trait variation relative to among-species variation) for nine structural traits and six physiological traits measured in wild populations. We used a multivariate path model to evaluate the relationships between structural traits and physiological traits, and the relationship between these traits and plant size and reproductive effort.Key resultsWhile intraspecific trait variation is relatively low for structural traits, it accounts for between 50 and 100 % of the variation in physiological traits. Furthermore, we identified few trait associations between any one structural trait and physiological trait, but multivariate regressions revealed clear associations between combinations of structural traits and physiological performance (R2 = 0.37-0.64), and almost all traits had detectable associations with plant fitness.ConclusionsIntraspecific variation in structural traits leads to predictable differences in individual-level physiological performance in a multivariate framework, even though the relationship of any particular structural trait to physiological performance may be weak or undetectable. Furthermore, intraspecific variation in both structural and physiological traits leads to differences in plant size and fitness. These results demonstrate the importance of considering measurements of multivariate phenotypes on individual plants when evaluating trait relationships and how trait variation influences predictions of ecological and evolutionary outcomes.

Dataset Information

The complete chloroplast genome of Protea kilimandscharica Engl. (Proteaceae).

Publications

The complete chloroplast genome of <i>Protea kilimandscharica</i> Engl. (Proteaceae).

Similar Datasets

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