Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Jan 9;12(1):92.
doi: 10.3390/life12010092.

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Daqu Liang  1 , Haoyun Wang  1 , Jun Zhang  1 , Yuanxiang Zhao  1 , Feng Wu  1
Affiliations

Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships

Daqu Liang et al. Life (Basel). .

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.

Keywords: F. longipetiolata; chloroplast genome; comparative analysis; phylogenetic analysis; purifying selection.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Gene map of the F. longipetiolata cp genome. The forward coding genes are located on the outside of the circle, and the reverse coding genes are located on the inside of the circle. Genes with different functions are colour-coded. The deeper grey in the inner circle represents the GC content, while the lighter grey represents the AT content.
Figure 2
Figure 2
Counting of relative synonymous codon usage (RSCU) of amino acids in the chloroplast genome of F. longipetiolata. The colors of the histogram correspond to the colors of the codons.
Figure 3
Figure 3
Repeated sequences of the F. longipetiolata cp genome. The abscissa is the length of the repeat sequence, and the ordinate is the number of repeat sequences. F stands for forward repetition, P for palindromic repetition, R for reverse repetition, and C for complementary repetition.
Figure 4
Figure 4
Counting of the types of SSRs. The abscissa represents SSR repetition units, and the ordinate represents the number of SSRs of each type.
Figure 5
Figure 5
Comparative analysis of cp genome structure between Fagus and A. thaliana. The outer two circles describe the gene length and direction of the genome. The five circles inside represent the similarity results of genome alignment between F. longipetiolata and A. thaliana (AP000423), F. engleriana (KX852398), F. crenata (MH171101), F. sylvatica (MK598696), and F. japonica var. multinervis (MN894556). Black circles represent GC content; green circles indicate G > C; purple circles indicate G < C.
Figure 6
Figure 6
Line chart of gene Pi values calculated from 106 loci based on the five Fagus cp genomes. x-axis: gene name, y-axis: Pi value.
Figure 7
Figure 7
Comparisons of IR-SC boundary locations across the cp genomes of the five Fagus and A. thaliana.
Figure 8
Figure 8
The 80 protein-coding genes of the F. longipetiolata cp genome and four Fagus species were used for ka/ka analysis.
Figure 9
Figure 9
The phylogenetic tree was constructed by using the complete cp sequences of F. longipetiolata and 18 Fagaceae species. P. trichocarpa was used as the outgroup.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Renner S.S., Grimm G.W., Kapli P., Denk T. Species relationships and divergence times in beeches: New insights from the inclusion of 53 young and old fossils in a birth–death clock model. Philos. Trans. R. Soc. B. 2016;371:20150135. doi: 10.1098/rstb.2015.0135. - DOI - PMC - PubMed
    1. Guo K., Werger M.-J. Effect of prevailing monsoons on the distribution of beeches in continental East Asia. For. Ecol. Manag. 2010;259:2197–2203. doi: 10.1016/j.foreco.2009.11.034. - DOI
    1. Peters R. Ph.D. Thesis. Wageningen Agricultural University; Wageningen, The Netherlands: 1992. Ecology of Beech Forests in the Northern Hemisphere.
    1. Fang J., Lechowicz M.-J. Climatic limits for the present distribution of beech (Fagus L.) species in the world. J. Biogeogr. 2006;33:1804–1819. doi: 10.1111/j.1365-2699.2006.01533.x. - DOI
    1. Denk T. Phylogeny of Fagus L. (Fagaceae) based on morphological data. Plant Syst. Evol. 2003;240:55–81. doi: 10.1007/s00606-003-0018-x. - DOI

LinkOut - more resources