Chloroplast Genome Differences Between Asian and American Equisetum Arvense (Equisetaceae) and the Origin of the Hypervariable TrnY-trnE Intergenic Spacer

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2014 Aug 27

PMID 25157804

Citations 10

Authors

Hyoung Tae Kim

Ki-Joong Kim

Affiliations

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Abstract

Comparative analyses of complete chloroplast (cp) DNA sequences within a species may provide clues to understand the population dynamics and colonization histories of plant species. Equisetum arvense (Equisetaceae) is a widely distributed fern species in northeastern Asia, Europe, and North America. The complete cp DNA sequences from Asian and American E. arvense individuals were compared in this study. The Asian E. arvense cp genome was 583 bp shorter than that of the American E. arvense. In total, 159 indels were observed between two individuals, most of which were concentrated on the hypervariable trnY-trnE intergenic spacer (IGS) in the large single-copy (LSC) region of the cp genome. This IGS region held a series of 19 bp repeating units. The numbers of the 19 bp repeat unit were responsible for 78% of the total length difference between the two cp genomes. Furthermore, only other closely related species of Equisetum also show the hypervariable nature of the trnY-trnE IGS. By contrast, only a single indel was observed in the gene coding regions: the ycf1 gene showed 24 bp differences between the two continental individuals due to a single tandem-repeat indel. A total of 165 single-nucleotide polymorphisms (SNPs) were recorded between the two cp genomes. Of these, 52 SNPs (31.5%) were distributed in coding regions, 13 SNPs (7.9%) were in introns, and 100 SNPs (60.6%) were in intergenic spacers (IGS). The overall difference between the Asian and American E. arvense cp genomes was 0.12%. Despite the relatively high genetic diversity between Asian and American E. arvense, the two populations are recognized as a single species based on their high morphological similarity. This indicated that the two regional populations have been in morphological stasis.

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References

Cosner M, Raubeson L, Jansen R . Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol Biol. 2004; 4:27. PMC: 516026. DOI: 10.1186/1471-2148-4-27. View

Grewe F, Guo W, Gubbels E, Hansen A, Mower J . Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes. BMC Evol Biol. 2013; 13:8. PMC: 3553075. DOI: 10.1186/1471-2148-13-8. View

Funk H, Berg S, Krupinska K, Maier U, Krause K . Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol. 2007; 7:45. PMC: 2089061. DOI: 10.1186/1471-2229-7-45. View

Jansen R, Raubeson L, Boore J, dePamphilis C, Chumley T, Haberle R . Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol. 2005; 395:348-84. DOI: 10.1016/S0076-6879(05)95020-9. View

Zhang Y, Ma P, Li D . High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS One. 2011; 6(5):e20596. PMC: 3105084. DOI: 10.1371/journal.pone.0020596. View

Gao L, Zhou Y, Wang Z, Su Y, Wang T . Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers. BMC Plant Biol. 2011; 11:64. PMC: 3098776. DOI: 10.1186/1471-2229-11-64. View

Hipkins V, Marshall K, Neale D, Rottmann W, Strauss S . A mutation hotspot in the chloroplast genome of a conifer (Douglas-fir: Pseudotsuga) is caused by variability in the number of direct repeats derived from a partially duplicated tRNA gene. Curr Genet. 1995; 27(6):572-9. DOI: 10.1007/BF00314450. View

Kim K, Lee H . Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 2004; 11(4):247-61. DOI: 10.1093/dnares/11.4.247. View

Lee H, Jansen R, Chumley T, Kim K . Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol. 2007; 24(5):1161-80. DOI: 10.1093/molbev/msm036. View

10.

Xiang Q, Soltis D, Soltis P, Manchester S, Crawford D . Timing the eastern Asian-eastern North American floristic disjunction: molecular clock corroborates paleontological estimates. Mol Phylogenet Evol. 2000; 15(3):462-72. DOI: 10.1006/mpev.2000.0766. View

11.

Young H, Lanzatella C, Sarath G, Tobias C . Chloroplast genome variation in upland and lowland switchgrass. PLoS One. 2011; 6(8):e23980. PMC: 3161095. DOI: 10.1371/journal.pone.0023980. View

12.

Xiang Q, Soltis D, Soltis P . The eastern Asian and eastern and western North American floristic disjunction: congruent phylogenetic patterns in seven diverse genera. Mol Phylogenet Evol. 1999; 10(2):178-90. DOI: 10.1006/mpev.1998.0524. View

13.

Gao L, Yi X, Yang Y, Su Y, Wang T . Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes. BMC Evol Biol. 2009; 9:130. PMC: 2706227. DOI: 10.1186/1471-2148-9-130. View

14.

Wolf P, Rowe C, Sinclair R, Hasebe M . Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res. 2003; 10(2):59-65. DOI: 10.1093/dnares/10.2.59. View

15.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View

16.

Wicker T, Schlagenhauf E, Graner A, Close T, Keller B, Stein N . 454 sequencing put to the test using the complex genome of barley. BMC Genomics. 2006; 7:275. PMC: 1633745. DOI: 10.1186/1471-2164-7-275. View

17.

Zhu Q, Ge S . Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol. 2005; 167(1):249-65. DOI: 10.1111/j.1469-8137.2005.01406.x. View

18.

Saski C, Lee S, Fjellheim S, Guda C, Jansen R, Luo H . Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet. 2007; 115(4):571-90. PMC: 2674615. DOI: 10.1007/s00122-007-0567-4. View

19.

Tang J, Xia H, Cao M, Zhang X, Zeng W, Hu S . A comparison of rice chloroplast genomes. Plant Physiol. 2004; 135(1):412-20. PMC: 429394. DOI: 10.1104/pp.103.031245. View

20.

Morris G, Grabowski P, Borevitz J . Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. Mol Ecol. 2011; 20(23):4938-52. PMC: 3383086. DOI: 10.1111/j.1365-294X.2011.05335.x. View