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The complete chloroplast genome of Celtis julianae (Ulmaceae).

ABSTRACT: Celtis julianae C.K. Schneid. is a large deciduous tree of Ulmaceae. In this study, the chloroplast genome sequence of C. julianae was 159,064 bp in length, consisting of a large single-copy (LSC) region with 86,139 bp, a small single-copy (SSC) region with 19,137 bp, and two inverted repeat regions (IRs) with 26,894 bp. The GC content in the chloroplast genome of C. julianae was 36.3%. The chloroplast genome of C. julianae contained 127 genes, including 86 protein-coding genes, 37 tRNA genes, and four rRNA genes. Phylogenetic tree showed that C. julianae was clustered with C. tetrandra.

SUBMITTER: Wang X

PROVIDER: S-EPMC7889233 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundUlmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species.ResultsOur results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 - 88,408 bp, a small single copy (SSC) region of 18,650 - 19,038 bp and an inverted repeat (IR) region of 26,288 - 26,546 bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections.ConclusionsFeatures of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus.

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The complete chloroplast genome of Celtis julianae (Ulmaceae).

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