Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies

Plant Journal

Volumn 89, Issue 3, 2017, Pages 617-635

  Michael, Todd P ^a,b   Bryant, Douglas ^b,c   Gutierrez, Ryan ^a   Borisjuk, Nikolai ^a,h   Chu, Philomena ^a   Zhang, Hanzhong ^a   Xia, Jing ^d,e,i   Zhou, Junfei ^d   Peng, Hai ^d   El Baidouri, Moaine ^f   ten Hallers, Boudewijn ^g   Hastie, Alex R ^g   Liang, Tiffany ^g   Acosta, Kenneth ^a   Gilbert, Sarah ^a   McEntee, Connor ^b   Jackson, Scott A ^f   Mockler, Todd C ^c   Zhang, Weixiong ^d,e   Lam, Eric ^a  

^a RUTGERS UNIVERSITY   (United States)

^b Ibis Biosciences Inc   (United States)

^c DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^d JIANGHAN UNIVERSITY   (China)

^e WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^f UNIVERSITY OF GEORGIA   (United States)

^g USA   (United States)

^h HUAIYIN NORMAL UNIVERSITY   (China)

ⁱ YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

BioNano Genomics; duckweed; methylome; next generation sequencing; rDNA repeats; Spirodela polyrhiza; structure variation

Indexed keywords

ALKYLATION; BIOLOGY; CHROMOSOMES; DNA; DNA SEQUENCES; GENE ENCODING; METHYLATION; NUCLEIC ACIDS; PALM OIL; PROTEINS; RNA;

DUCKWEED; GENOMICS; METHYLOME; NEXT-GENERATION SEQUENCING; RDNA REPEATS; SPIRODELA POLYRHIZA; STRUCTURE VARIATION;

GENES;

GENES; NUCLEIC ACIDS; SEEDS;

PLANT PROTEIN;

ARACEAE; CHROMOSOMAL MAPPING; DNA METHYLATION; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETIC VARIATION; GENETICS; PLANT CHROMOSOME; PLANT GENE; PLANT GENOME; PROCEDURES;

ARACEAE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; DNA METHYLATION; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENES, PLANT; GENETIC VARIATION; GENOME, PLANT; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 85013006970     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.13400     Document Type: Article

References (51)

1. van der Biezen, E.A. and Jones, J.D.G. (1998) The NB-ARC domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals. Curr. Biol. 8, R226–R228.
2. Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. and Pirovano, W. (2011) Scaffolding preassembled contigs using SSPACE. Bioinformatics, 27, 578–579.
3. Bog, M., Lautenschlager, U., Landrock, M.F., Landolt, E., Fuchs, J., Sree, S.K., Oberprieler, C. and Appenroth, K.J. (2015) Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP). Hydrobiologia, 749, 169–182.
4. Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I.A., Belmonte, M.K., Lander, E.S., Nusbaum, C. and Jaffe, D.B. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18, 810–820.
5. Cantarel, B.L., Korf, I., Robb, S.M., Parra, G., Ross, E., Moore, B., Holt, C., Sánchez Alvarado, A. and Yandell, M. (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188–196.
6. Cao, H., Hastie, A.R. and Cao, D. et al. (2014) Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience, 3, 34.
7. Cao, H.X., Vu, G.T., Wang, W., Messing, J. and Schubert, I. (2015) Chromatin organization in duckweed interphase nuclei in relation to the nuclear DNA content. Plant Biol. 17(suppl.), 120–124.
8. Cao, H.X., Vu, G.T., Wang, W., Messing, J. and Schubert, I. (2016) The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. New Phytol. 209, 354–363.
9. Devos, K.M., Brown, J.K. and Bennetzen, J.L. (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075–1079.
10. Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755–763.
11. El Baidouri, M., Kim, K.D., Abernathy, B., Arikit, S., Maumus, F., Panaud, O., Meyers, B.C. and Jackson, S.A. (2015) A new approach for annotation of transposable elements using small RNA mapping. Nucleic Acids Res. 43, e84.
12. Ellinghaus, D., Kurtz, S. and Willhoeft, U. (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9, 18.
13. Fahlgren, N. and Carrington, J.C. (2010) miRNA target prediction in plants. Methods Mol. Biol. 592, 51–57.
14. Flutre, T., Duprat, E., Feuillet, C. and Quesneville, H. (2011) Considering transposable element diversification in de novo annotation approaches. PLoS One, 6, e16526. doi:10.1371/journal.pone.0016526.
15. Freeling, M., Xu, J., Woodhouse, M. and Lisch, D. (2015) A Solution to the C-Value Paradox and the Function of Junk DNA: the Genome Balance Hypothesis. Mol. Plant. 8, 899–910.
16. Grabherr, M.G., Haas, B.M. and Yassour, M. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652.
17. Haas, B.J., Delcher, A.L., Wortman, J.R. and Salzberg, S.L. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics, 20, 3643–3646.
18. Hastie, A.R., Dong, L., Smith, A. et al. (2013) Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS One, 8, e55864.
19. Howell, M.D., Fahlgren, N., Chapman, E.J., Cumbie, J.S., Sullivan, C.M., Givan, S.A., Kasschau, K.D. and Carrington, J.C. (2007) Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell, 19, 926–942.
20. Ibarra-Laclette, E., Lyons, E. and Hernández-Guzmán, G. et al. (2013) Architecture and evolution of a minute plant genome. Nature, 498, 94–98.
21. Johnson, C., Kasprzewska, A., Tennessen, K., Fernandes, J., Nan, G.L., Walbot, V., Sundaresan, V., Vance, V. and Bowman, L.H. (2009) Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res. 19, 1429–1440.
22. Kellis, M., Wold, B. and Snyder, M.P. et al. (2014) Defining functional DNA elements in the human genome. Proc. Natl Acad. Sci. USA, 111, 6131–6138.
23. Kim, M.Y. and Zilberman, D. (2014) DNA methylation as a system of plant genomic immunity. Trends Plant Sci. 19, 320–326.
24. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R. and Salzberg, S.L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36. doi:10.1186/gb-2013-14-4-r36.
25. Kobayashi, T. (2014) Ribosomal RNA gene repeats, their stability and cellular senescence. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 90, 119–129.
26. Konishi, N., Ishiyama, K., Matsuoka, K., Maru, I., Hayakawa, T., Yamaya, T. and Kojima, S. (2014) NADH-dependent glutamate synthase plays a crucial role in assimilating ammonium in the Arabidopsis root. Physiol. Plantarum, 152, 138–151.
27. Krueger, F. and Andrews, S.R. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571–1572.
28. Kuehdorf, K., Jetschke, G., Ballani, L. and Appenroth, K.J. (2014) The clonal dependence of turion formation in the duckweed Spirodela polyrhiza – an ecogeographical approach. Physiol. Plant. 150, 46–54.
29. Lam, E.T., Hastie, A., Lin, C., Ehrlich, D., Das, S.K., Austin, M.D., Deshpande, P., Cao, H., Nagarajan, N., Xiao, M. and Kwok, P.Y. (2012) Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat. Biotechnol. 30, 771–776.
30. Lam, E., Appenroth, K.J., Michael, T., Mori, K. and Fakhoorian, T. (2014) Duckweed in bloom: the 2nd International Conference on Duckweed Research and Applications heralds the return of a plant model for plant biology. Plant Mol. Biol. 84, 737–742.
31. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
32. Li, R., Zhu, H. and Ruan, J. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272.
33. Lyons, E., Pedersen, B., Kane, J. and Freeling, M. (2008) The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Tropical Plant Biol. 1, 181–190.
34. Maumus, F. and Quesneville, H. (2014) Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat. Commun. 5, 4104.
35. Melters, D.P., Bradnam, K.R. and Young, H.A. et al. (2013) Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 14, R10. doi:10.1186/gb-2013-14-1-r10.
36. Michael, T.P. (2014) Plant genome size variation: bloating and purging DNA. Brief Funct. Genomics, 13, 308–317.
37. Morris, P.F., Layzell, D.B. and Canvin, D.T. (1988) Ammonia production and assimilation in glutamate synthase mutants of Arabidopsis thaliana. Plant Physiol. 87, 148–154.
38. Mugal, C.F., Arndt, P.F., Holm, L. and Ellegren, H. (2015) Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes. G3, 5, 441–447.
39. Murray, M.G. and Thompson, W.F. (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321–4325.
40. Parra, G., Bradnam, K. and Korf, I. (2007) GEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics, 23, 1061–1067.
41. Price, A.L., Jones, N.C. and Pevzner, P.A. (2005) De novo identification of repeat families in large genomes. Bioinformatics, 21(suppl.), 351–358.
42. Punta, M., Coggill, P.C. and Eberhardt, R.Y. et al. (2012) The Pfam protein families database. Nucleic Acids Res. 40, 290–301.
43. Tang, H., Lyons, E. and Town, C.D. (2015) Optical mapping in plant comparative genomics. Gigascience, 4, 3.
44. Thomas, C.A. (1971) The genetic organization of chromosomes. Annu. Rev. Genet. 5, 237–256.
45. Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B.C., Remm, M. and Rozen, S.G. (2012) Primer3 – new capabilities and interfaces. Nucleic Acids Res. 40, e115. Epub 2012 Jun 22.
46. Van Buren, R., Bryant, D., Edger, P.P. et al. (2015) Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature, 527, 508–11.
47. Wang, W., Kerstetter, R.A. and Michael, T.P. (2011) Evolution of genome size in Duckweeds (Lemnaceae). J. Bot. 2011, 1–9.
48. Wang, W., Haberer, G. and Gundlach, H. et al. (2014) The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat. Commun. 5, 3311.
49. Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829.
50. Zhang, W., Gao, S., Zhou, X., Xia, J., Chellappan, P., Zhou, X., Zhang, X. and Jin, H. (2010) Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol. 11, R81.
51. Zhang, W., Zhou, X., Xia, J. and Zhou, X. (2012) Identification of microRNAs and natural antisense transcript-originated endogenous siRNAs from small-RNA deep sequencing data. Methods Mol. Biol. 883, 221–227.