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
Comparative Study
. 2018 Apr 4;19(1):235.
doi: 10.1186/s12864-018-4633-x.

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

Luxian Liu  1 , Yuewen Wang  1 , Peizi He  1 , Pan Li  2 , Joongku Lee  3 , Douglas E Soltis  4 , Chengxin Fu  5
Affiliations
Comparative Study

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

Luxian Liu et al. BMC Genomics. .

Abstract

Background: Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce.

Results: The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure.

Conclusions: In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae.

Keywords: Chloroplast genome; Cp hotspot; East Asia; Population genetics; SSR.

PubMed Disclaimer

Conflict of interest statement

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Chloroplast genome maps of Mukdenia and Oresitrophe: (a) M. rossii, (b) O. rupifraga-BJCP and (C) O. rupifraga-HNYD. Genes inside the circle are transcribed clockwise, genes outside are transcribed counter-clockwise. The light gray inner circle corresponds to the AT content, the dark gray to the GC content. Genes belonging to different functional groups are shown in different colors
Fig. 2
Fig. 2
Visualization of alignment of the five Saxifragaceae chloroplast genome sequences, with Penthorum chinense as the reference. The horizontal axis indicates the coordinates within the chloroplast genome. The vertical scale indicates the percentage of identity, ranging from 50 to 100%. Genome regions are color coded as protein coding, intron, mRNA, and conserved non-coding sequences (CNS)
Fig. 3
Fig. 3
MAUVE alignment of five Saxifragaceae chloroplast genomes. The Penthorum chinense genome is shown at top as the reference. Within each of the alignment, local collinear blocks are represented by blocks of the same color connected by lines
Fig. 4
Fig. 4
Comparison of the borders of large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions among the five Saxifragaceae chloroplast genomes, with the Penthorum chinense genome is shown at top as the reference. The location of two parts of inverted repeat region (IRA and IRB) was referred to Fig. 1
Fig. 5
Fig. 5
The distribution, type, and presence of simple sequence repeats (SSRs) and analysis of repeated sequences in the cp genome of Oresitrophe rupifraga and Mukdenia rossii: (a) Presence of SSRs in the different region of O. rupifraga-BJCP cp genome, (b) Presence of polymers in the cp genome of O. rupifraga and M. rossii, (c) Frequency of repeat types, (d) Frequency of repeats by length
Fig. 6
Fig. 6
Comparative analysis of the nucleotide variability (Pi) values between Mukdenia rossii and Oresitrophe rupifraga (a), and within O. rupifraga (b)
Fig. 7
Fig. 7
The distribution of polymorphic genomic simple sequence repeats (gSSRs) between Mukdenia rossii and Oresitrophe rupifraga (a), and within O. rupifraga (b)
Fig. 8
Fig. 8
The probability of membership and geographical distribution of gene pools in Mukdenia rossii and Oresitrophe rupifraga, detected by STRUCTURE analysis: K = 2 (a) and K = 3 (b). Each vertical bar represents one individual (N = 47), with populations arranged by collection site from Northeast to Central China
See this image and copyright information in PMC

References

    1. Petit R, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, et al. Glacial refugia: hotspots but not melting pots of genetic diversity. Science. 2003;300(5625):1563–1565. - PubMed
    1. Hewitt GM. Genetic consequences of climatic oscillations in the quaternary. Philos Trans R Soc Lond Ser B Biol Sci. 2004;359(1442):183–195. - PMC - PubMed
    1. Hewitt G. The genetic legacy of the quaternary ice ages. Nature. 2000;405:907. - PubMed
    1. Lascoux M, Palme AE, Cheddadi R, Latta RG. Impact of ice ages on the genetic structure of trees and shrubs. Philos Trans R Soc Lond Ser B Biol Sci. 2004;359(1442):197–207. - PMC - PubMed
    1. Bao L, Kudureti A, Bai W, Chen R, Wang T, Wang H, Ge J. Contributions of multiple refugia during the last glacial period to current mainland populations of Korean pine (Pinus koraiensis) Sci Rep. 2015;5:18608. - PMC - PubMed

Publication types

LinkOut - more resources