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The complete chloroplast genome of Fraxinus hupehensis and phylogenic analysis of Lamiales.

ABSTRACT: Fraxinus hupehensis is a national rare and Endangered tree in the Oleaceae family, that has high commercial value owing to its slow growth, interlaced roots, intricate tree shape, and easy to shape. Here, we determined the complete chloroplast (cp) genome sequence for F. hupehensis using genome skimming sequencing. The cp genome was 155,698 bp and consisted of a large single copy (LSC) region (86,498 bp), a small single copy (SSC) region (17,803 bp) and two inverted repeats (IRs) (25,694 bp). It encodes 131 genes, including 88 protein-coding genes, 8 rRNAs and 35 tRNAs. Phylogenetic analysis indicates that F. hupehensis was relatively closely related to F. chinensis compared to other species in the Oleaceae family.

SUBMITTER: Zhang W

PROVIDER: S-EPMC7782264 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Background:Phylogenetic relationship within different genera of Lemnoideae, a kind of small aquatic monocotyledonous plants, was not well resolved, using either morphological characters or traditional markers. Given that rich genetic information in chloroplast genome makes them particularly useful for phylogenetic studies, we used chloroplast genomes to clarify the phylogeny within Lemnoideae. Methods:DNAs were sequenced with next-generation sequencing. The duckweeds chloroplast genomes were indirectly filtered from the total DNA data, or directly obtained from chloroplast DNA data. To test the reliability of assembling the chloroplast genome based on the filtration of the total DNA, two methods were used to assemble the chloroplast genome of Landoltia punctata strain ZH0202. A phylogenetic tree was built on the basis of the whole chloroplast genome sequences using MrBayes v.3.2.6 and PhyML 3.0. Results:Eight complete duckweeds chloroplast genomes were assembled, with lengths ranging from 165,775 bp to 171,152 bp, and each contains 80 protein-coding sequences, four rRNAs, 30 tRNAs and two pseudogenes. The identity of L. punctata strain ZH0202 chloroplast genomes assembled through two methods was 100%, and their sequences and lengths were completely identical. The chloroplast genome comparison demonstrated that the differences in chloroplast genome sizes among the Lemnoideae primarily resulted from variation in non-coding regions, especially from repeat sequence variation. The phylogenetic analysis demonstrated that the different genera of Lemnoideae are derived from each other in the following order: Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia. Discussion:This study demonstrates potential of whole chloroplast genome DNA as an effective option for phylogenetic studies of Lemnoideae. It also showed the possibility of using chloroplast DNA data to elucidate those phylogenies which were not yet solved well by traditional methods even in plants other than duckweeds.

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The complete chloroplast genome of Fraxinus hupehensis and phylogenic analysis of Lamiales.

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