Abstract
Fagus longipetiolata Seemen is a deciduous tree of the Fagus genus in Fagaceae, which is endemic to China. In this study, we successfully sequenced the cp genome of F. longipetiolata, compared the cp genomes of the Fagus genus, and reconstructed the phylogeny of Fagaceae. The results showed that the cp genome of F. longipetiolata was 158,350 bp, including a pair of inverted repeat (IRA and IRB) regions with a length of 25,894 bp each, a large single-copy (LSC) region of 87,671 bp, and a small single-copy (SSC) region of 18,891 bp. The genome encoded 131 unique genes, including 81 protein-coding genes, 37 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs), and 5 pseudogenes. In addition, 33 codons and 258 simple sequence repeats (SSRs) were identified. The cp genomes of Fagus were relatively conserved, especially the IR regions, which showed the best conservation, and no inversions or rearrangements were found. The five regions with the largest variations were the rps12, rpl32, ccsA, trnW-CCA, and rps3 genes, which spread over in LSC and SSC. The comparison of gene selection pressure indicated that purifying selection was the main selective pattern maintaining important biological functions in Fagus cp genomes. However, the ndhD, rpoA, and ndhF genes of F. longipetiolata were affected by positive selection. Phylogenetic analysis revealed that F. longipetiolata and F. engleriana formed a close relationship, which partially overlapped in their distribution in China. Our analysis of the cp genome of F. longipetiolata would provide important genetic information for further research into the classification, phylogeny and evolution of Fagus.
Highlights
The Fagus genus is mainly composed of deciduous trees and is a genus of the Fagaceae family [1]
The complete cp genome sequence of F. longipetiolata was assembled de novo and uploaded to the NCBI database (GenBank accession number MZ562567)
The cp genomes of F. longipetiolata and other Fagus were substantially similar in terms of genome structure, gene content, and gene sequences, some hot spots could be found in large single-copy (LSC) and small single-copy (SSC) regions, which would provide informative markers for the phylogenetic analysis of Fagus
Summary
The Fagus genus is mainly composed of deciduous trees and is a genus of the Fagaceae family [1]. Because Fagus tree species are widely distributed around Eurasia, the study of the evolutionary history of the genus is conducive to revealing the impact of global climate change on vegetation, as well as the geological and biological connections of this group [4]. Most of the previous studies on the classification of Fagus were based on external morphological characteristics, such as the total stem length, involucre bract type and shape, and leaf textural and structural characteristics [5,6]. The external morphological characteristics of the members of the genus Fagus often vary greatly under the influence of environmental factors, and some characteristics are crossed, leading to confusion in their classification [5]. There is still a debate about the number of species in the genus
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