Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

Molecular Ecology Resources

Volumn 15, Issue 3, 2015, Pages 601-612

  Karam, M J ^a   Lefevre F ^a   Dagher Kharrat, M Bou ^b   Pinosio, S ^c,d   Vendramin, G G ^d  

^a French National Institute for Agriculture   (France)

^b SAINT JOSEPH UNIVERSITY   (Lebanon)

^c Istituto di Genomica Applicata (IGA)   (Italy)

^d CNR   (Italy)

Author keywords

Cedrus atlantica; Next generation sequencing; RADseq; SNP; SSR; Transcriptome

Indexed keywords

CEDRUS ATLANTICA; CONIFEROPHYTA;

GENETIC MARKER; PLANT DNA;

CEDRUS; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETIC MARKER; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; PLANT GENOME; SINGLE NUCLEOTIDE POLYMORPHISM;

CEDRUS; DNA, PLANT; GENETIC MARKERS; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84926520352     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12329     Document Type: Article

References (60)

1. Ahuja M, Neale D (2005) Evolution of genome size in conifers. Silvae Genetica, 54, 126-137.
2. Alberto FJ, Aitken SN, Alia R et al. (2013) Potential for evolutionary responses to climate change evidence from tree populations. Global Change Biology, 19, 1645-1661.
3. Arnold B, Corbett-Detig RB, Hartl D, Bomblies K (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, 22, 3179-3190.
4. Baird NA, Etter PD, Atwood TS, et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3, e3376.
5. Birol I, Raymond A, Jackman SD et al. (2013) Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics, 29, 1492-1497.
6. Bou Dagher-Kharrat M, Grenier G, Bariteau M et al. (2001) Karyotype analysis reveals interspecific differentiation in the genus Cedrus despite genome size and base composition constancy. Theoretical and Applied Genetics, 103, 846-854.
7. Bou Dagher-Kharrat M, Mariette S, Lefèvre F et al. (2007) Geographical diversity and genetic relationships among Cedrus species estimated by AFLP. Tree Genetics & Genomes, 3, 275-285.
8. Chancerel E, Lepoittevin C, Le Provost G et al. (2011) Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics, 12, 368.
9. Chen C, Mitchell S, Elshire R et al. (2013) Mining conifers' mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform. Tree Genetics & Genomes, 9, 1537-1544.
10. Conesa A, Götz S, García-Gómez JM et al. (2005) blast2go: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
11. Cutler DJ, Jensen JD (2010) To pool, or not to pool? Genetics, 186, 41-43.
12. Davey JL, Blaxter MW (2010) radseq: next-generation population genetics. Briefings in Functional Genomics, 9, 416-423.
13. Davey JW, Hohenlohe PA, Etter PD, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
14. Eaton DAR, Ree RH (2013) Inferring Phylogeny and introgression using radseq Data: an example from flowering plants (Pedicularis: Orobanchaceae). Systematic Biology, 62, 689-706.
15. Eckert AJ, Pande B, Ersoz ES et al. (2009) High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genetics & Genomes, 5, 225-234.
16. Elsik C, Williams C (2000) Retroelements contribute to the excess low-copy-number DNA in pine. Molecular and General Genetics, 264, 47-55.
17. Emberton J, Ma J, Yuan Y, SanMiguel P, Bennetzen JL (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Research, 15, 1441-1446.
18. Friesen N, Brandes A, Heslop-Harrison JS (Pat) (2001) Diversity, origin, and distribution of retrotransposons (Gypsy and Copia) in conifers. Molecular Biology and Evolution, 18, 1176-1188.
19. Fumagalli M (2013) Assessing the effect of sequencing depth and sample size in population genetics inferences. PLoS ONE, 8, e79667.
20. Gautier M, Gharbi K, Cezard T et al. (2013) The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology, 22, 3165-3178.
21. Grattapaglia D, Silva-Junior O, Kirst M et al. (2011) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biology, 11, 65.
22. Hamberger B, Hall D, Yuen M et al. (2009) Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome. BMC Plant Biology, 9, 106.
23. Henson J, Tischler G, Ning Z (2012) Next-generation sequencing and large genome assemblies. Pharmacogenomics, 13, 901-915.
24. Hohenlohe PA, Day MD, Amish SJ et al. (2013) Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Molecular Ecology, 22, 3002-3013.
25. Howe GT, Yu J, Knaus B et al. (2013) A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. BMC Genomics, 14, 137.
26. Huang Y, Niu B, Gao Y, Fu L, Li W (2010) cd-hit Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-682.
27. Jurka J, Kapitonov V, Pavlicek A et al. (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research, 110, 462-467.
28. Kovach A, Wegrzyn JL, Parra G et al. (2010) The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics, 11, 420.
29. Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.
30. Larsson H, De Paoli E, Morgante M, Lascoux M, Gyllenstrand N (2013) The Hypomethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies). Tree Genetics & Genomes, 9, 601-612.
31. Leitch IJ, Soltis DE, Soltis PS, Bennett MD (2005) Evolution of DNA amounts across land plants (Embryophyta). Annals of Botany, 95, 207-217.
32. Lepoittevin C, Frigerio J-M, Garnier-Géré P et al. (2010) In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species? PLoS ONE, 5, e11034.
33. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
34. Li W, Godzik A (2006) cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
35. Li H, Handsaker B, Wysoker A et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
36. Liu W, Thummasuwan S, Sehgal SK, Chouvarine P, Peterson DG (2011) Characterization of the genome of bald cypress. BMC Genomics, 12, 553.
37. Lorenz WW, Ayyampalayam S, Bordeaux J et al. (2012) Conifer dbmagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species. Tree Genetics & Genomes, 8, 1477-1485.
38. Meglécz E, Costedoat C, Dubut V et al. (2010) qdd: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics, 26, 403-404.
39. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17, 240-248.
40. Morgante M, De Paoli E (2011) Toward the conifer genome sequence. Genetics, Genomics and Breeding of Conifers, pp. 389-403. CRC Press, New York.
41. Müller T, Ensminger I, Schmid K (2012) A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings. BMC Genomics, 13, 673.
42. Murray B, Leitch I, Bennett M (2012) Gymnosperm DNA C-values database (release 5.0, Dec. 2012). Available from http://www.kew.org/cvalues/ Accessed March 2014.
43. Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nature Reviews Genetics, 12, 111-122.
44. Neale D, Wegrzyn J, Stevens K et al. (2014) Decoding the massive genome of Loblolly pine using haploid DNA and novel assembly strategies. Genome Biology, 15, R59.
45. Neves LG, Davis JM, Barbazuk WB, Kirst M (2013) Whole-exome targeted sequencing of the uncharacterized pine genome. The Plant Journal, 75, 146-156.
46. Nystedt B, Street NR, Wetterbom A et al. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature, 497, 579-584.
47. Panetsos KP, Christou A, Scaltsoyiannes A (1992) First analysis on allozyme variation in cedar species (Cedrus sp.). Silvae Genetica, 41-6, 339-342.
48. Parchman T, Geist K, Grahnen J, Benkman C, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics, 11, 180.
49. Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q (2013) De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. BMC Genomics, 14, 556.
50. Pinosio S, González-Martínez SC, Bagnoli F et al. (2014) First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill. Molecular Ecology Resources, 14, 846-856.
51. Rake JP, Adrian V, Hall RB, Hansen KM (1980) DNA reassociation kinetics of four conifers. Canadian Journal of Genetics and Cytology, 22, 69-79.
52. Rocheta M, Cordeiro J, Oliveira M, Miguel C (2007) PpRT1: the first complete gypsy-like retrotransposon isolated in Pinus pinaster. Planta, 225, 551-562.
53. Roschanski AM, Fady B, Ziegenhagen B, Liepelt S (2013) Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba. Applications in Plant Sciences, 1, 1200179.
54. Savolainen O, Pyhäjärvi T (2007) Genomic diversity in forest trees. Current Opinion in Plant Biology, 10, 162-167.
55. Sena JS, Giguère I, Boyle B et al. (2014) Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC Plant Biology, 14, 95.
56. Stuart-Rogers C, Flavell AJ (2001) The evolution of Ty1-copia group retrotransposons in gymnosperms. Molecular Biology and Evolution, 18, 155-163.
57. Terrab A, Paun O, Talavera S et al. (2006) Genetic diversity and population structure in natural populations of Moroccan Atlas cedar (Cedrus atlantica; Pinaceae) determined with cpSSR markers. American Journal of Botany, 93, 1274-1280.
58. Wang N, Thomson M, Bodles WJA et al. (2013) Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Molecular Ecology, 22, 3098-3111.
59. Wegrzyn JL, Liechty JD, Stevens KA et al. (2014) Unique features of the Loblolly Pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics, 196, 891-909.
60. Zerbino DR, Birney E (2008) velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18, 821-829.