Complete Plastome Assemblies from a Panel of 13 Diverse Potato Taxa

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2020 Oct 8

PMID 33031462

Citations 10

Authors

Sai Reddy Achakkagari

Maria Kyriakidou

Helen H Tai

Noelle L Anglin

David Ellis

Martina V Stromvik

Affiliations

Soon will be listed here.

Abstract

The chloroplasts are a crucial part of photosynthesizing plant cells and are extensively utilized in phylogenetic studies mainly due to their maternal inheritance. Characterization and analysis of complete plastome sequences is necessary to understand their diversity and evolutionary relationships. Here, a panel of thirteen plastomes from various potato taxa are presented. Though they are highly similar with respect to gene order and content, there is also a great extent of SNPs and InDels between them, with one of the Solanum bukasovii plastomes (BUK2) having the highest number of SNPs and InDels. Five different potato plastome types (C, S, A, W, W2) are present in the panel. Interestingly, the S. tuberosum subsp. tuberosum (TBR) accession has a W-type plastome, which is not commonly found in this species. The S-type plastome has a conserved 48 bp deletion not found in other types, which is responsible for the divergence of the S-type from the C-type plastome. Finally, a phylogenetic analysis shows that these plastomes cluster according to their types. Congruence between the nuclear genome and the plastome phylogeny of these accessions was seen, however with considerable differences, supporting the hypothesis of introgression and hybridization between potato species.

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References

Johnston S, den Nijs T, Peloquin S, Hanneman Jr R . The significance of genic balance to endosperm development in interspecific crosses. Theor Appl Genet. 2013; 57(1):5-9. DOI: 10.1007/BF00276002. View

Katoh K, Misawa K, Kuma K, Miyata T . MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30(14):3059-66. PMC: 135756. DOI: 10.1093/nar/gkf436. View

San Millan R, Martinez-Ballesteros I, Rementeria A, Garaizar J, Bikandi J . Online exercise for the design and simulation of PCR and PCR-RFLP experiments. BMC Res Notes. 2013; 6:513. PMC: 4029544. DOI: 10.1186/1756-0500-6-513. View

Amiryousefi A, Hyvonen J, Poczai P . IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018; 34(17):3030-3031. DOI: 10.1093/bioinformatics/bty220. View

Rodriguez F, Wu F, Ane C, Tanksley S, Spooner D . Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?. BMC Evol Biol. 2009; 9:191. PMC: 3087518. DOI: 10.1186/1471-2148-9-191. View

Benson G . Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1998; 27(2):573-80. PMC: 148217. DOI: 10.1093/nar/27.2.573. View

Hosaka K, Sanetomo R . Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species. Genes Genet Syst. 2010; 84(5):371-8. DOI: 10.1266/ggs.84.371. View

Greiner S, Lehwark P, Bock R . OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019; 47(W1):W59-W64. PMC: 6602502. DOI: 10.1093/nar/gkz238. View

Sanetomo R, Gebhardt C . Cytoplasmic genome types of European potatoes and their effects on complex agronomic traits. BMC Plant Biol. 2015; 15:162. PMC: 4480903. DOI: 10.1186/s12870-015-0545-y. View

10.

Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S . ycf1, the most promising plastid DNA barcode of land plants. Sci Rep. 2015; 5:8348. PMC: 4325322. DOI: 10.1038/srep08348. View

11.

Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P . Genome sequence and analysis of the tuber crop potato. Nature. 2011; 475(7355):189-95. DOI: 10.1038/nature10158. View

12.

Kurtz S, Choudhuri J, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R . REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001; 29(22):4633-42. PMC: 92531. DOI: 10.1093/nar/29.22.4633. View

13.

Kyriakidou M, Anglin N, Ellis D, Tai H, Stromvik M . Genome assembly of six polyploid potato genomes. Sci Data. 2020; 7(1):88. PMC: 7066127. DOI: 10.1038/s41597-020-0428-4. View

14.

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

15.

Cho K, Cheon K, Hong S, Cho J, Im J, Mekapogu M . Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum. Plant Cell Rep. 2016; 35(10):2113-23. DOI: 10.1007/s00299-016-2022-y. View

16.

Kraemer L, Beszteri B, Gabler-Schwarz S, Held C, Leese F, Mayer C . STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design. BMC Bioinformatics. 2009; 10:41. PMC: 2644677. DOI: 10.1186/1471-2105-10-41. View

17.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

18.

Bi Y, Zhang M, Xue J, Dong R, Du Y, Zhang X . Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria. Sci Rep. 2018; 8(1):1184. PMC: 5775360. DOI: 10.1038/s41598-018-19591-9. View

19.

Chung H, Jung J, Park H, Kim J, Cha H, Min S . The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. Plant Cell Rep. 2006; 25(12):1369-79. DOI: 10.1007/s00299-006-0196-4. View

20.

Hosaka K . Successive domestication and evolution of the Andean potatoes as revealed by chloroplast DNA restriction endonuclease analysis. Theor Appl Genet. 2013; 90(3-4):356-63. DOI: 10.1007/BF00221977. View