Abstract
Conifers are evolutionarily distant from angiosperms, separated by 300 million years of evolution. The genomes of coniferous species are very large, among the largest of any nonpolyploid plant species. Their genomes are characterized by reduced evolutionary rate for coding genes, accumulation of noncoding DNA, and evolutionarily distance from angiosperms. I highlight both the advantages and disadvantages for conifers as model organism for genomics. With advances of new high-throughput sequencing technologies, we are at a watershed in conifer genomics.
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References
Aderkas P, Bonga JM (1993) Plants from haploid tissue culture of Larix decidua. TAG Theor Appl Genet 87:225–228
Allona I, Quinn M, Shoop E, Swope K, Cyr SS, Carlis J, Riedl J, Retzel E, Campbell MM, Sederoff R, Whetten RW (1998) Analysis of xylem formation in pine by cDNA sequencing. Proc Natl Acad Sci U S A 95:9693–9698
Barbazuk WB, Bedell JA, Rabinowicz PD (2005) Reduced representation sequencing: a success in maize and a promise for other plant genomes. BioEssays 27:839–848
Bautista R, Villalobos DP, Díaz-Moreno S, Cantón FR, Cánovas FM, Gonzalo Claros M (2007) Toward a Pinus pinaster bacterial artificial chromosome library. Ann For Sci 64:855–864
Bonfield JK, Whitwham A (2010) Gap5—editing the billion fragment sequence assembly. Bioinformatics 26:1699–1703
Bowe LM, Coat G, dePamphilis CW (2000) Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales’ closest relatives are conifers. Proc Natl Acad Sci U S A 97:4092–4097
Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc Natl Acad Sci U S A 101:15255–15260
Burdon R, Wilcox P (2011) Integration of molecular markers in breeding. In: Plomion C, Bousquet J (eds) Genetics, genomics and breeding of conifers. Science Publishers, Edenbridge
Buschizzo E, Ritland C, Bohlmann J, Ritland K (2012) Slow but not low: genomic comparisons reveals slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol 12:8
Cairney J, Xu N, Mackay J, Pullman J (2000) Special symposium: in vitro plant recalcitrance transcript profiling: a tool to assess the development of conifer embryos. In Vitro Cell Dev Biol Plant 36:155–162
Chagné D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera M, Vendramin G, Garcia V, Frigerio JM, Echt C, Richardson T, Plomion C (2004) Cross-species transferability and mapping of genomic and cDNA SSRs in pines. TAG Theor Appl Genet 109:1204–1214
Chaw S-M, Chun-Chieh Shih A, Wang D, Wu Y-W, Liu S-M, Chou T-Y (2008) The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Mol Biol Evol 25:603–615
Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier M-C, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anderson JA, Gill BS, Appels R, Keller B, Feuillet C (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22:1686–1701
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e122
Dauwe R, Robinson A, Mansfield S (2011) Recent advances in proteomics and metabolomics in gymnosperms. In: Plomion C, Bousquet J (eds) Genetics, genomics and breeding of conifers. Science Publishers, Edenbridge
Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132
Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467
Futamura N, Totoki Y, Toyoda A, Igasaki T, Nanjo T, Seki M, Sakaki Y, Mari A, Shinozaki K, Shinohara K (2008) Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili. BMC Genomics 9:383
García-Gil M (2008) Evolutionary aspects of functional and pseudogene members of the phytochrome gene family in Scots pine. J Mol Evol 67:222–232
Group CPW, Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, Graham SW, James KE, Kim K-J, Kress WJ, Schneider H, van AlphenStahl J, Barrett SCH, van den Berg C, Bogarin D, Burgess KS, Cameron KM, Carine M, Chacón J, Clark A, Clarkson JJ, Conrad F, Devey DS, Ford CS, Hedderson TAJ, Hollingsworth ML, Husband BC, Kelly LJ, Kesanakurti PR, Kim JS, Kim Y-D, Lahaye R, Lee H-L, Long DG, Madriñán S, Maurin O, Meusnier I, Newmaster SG, Park C-W, Percy DM, Petersen G, Richardson JE, Salazar GA, Savolainen V, Seberg O, Wilkinson MJ, Yi D-K, Little DP (2009) A DNA barcode for land plants. Proc Natl Acad Sci 106:12794–12797
Hamberger B, Hall D, Yuen M, Oddy C, Hamberger B, Keeling C, Ritland C, Ritland K, Bohlmann J (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 Biol 9:106
Heuertz M, De Paoli E, Kallman T, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174:2095–2105
Kinlaw CS, Neale DB (1997) Complex gene families in pine genomes. Trends Plant Sci 2:356–359
Kinlaw CS, Ho T, Gerttula SM, Gladstone E, Harry DE, Quintana L, Baysdorfer C (1996) Gene discovery in loblolly pine through cDNA sequencing. In: Ahuja MR, Boerjan W, Neale DB (eds) Somatic cell genetics and molecular genetics of trees. Kluwer Academic Publishers, Dordrecht, pp 175–182
Knoop V, Volkmar U, Hecht J, Grewe F (2011) Mitochondrial genome evolution in the plant lineage. In: Kempken F (ed) Plant mitochondria. Springer, New York, pp 3–29
Kovach A, Wegrzyn J, Parra G, Holt C, Bruening G, Loopstra C, Hartigan J, Yandell M, Langley C, Korf I, Neale D (2010) The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 11:420
Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB (2004) Comparative mapping in the Pinaceae. Genetics 168:447–461
Krutovsky K, Elsik C, Matvienko M, Kozik A, Neale D (2006) Conserved ortholog sets in forest trees. Tree Genet Genomes 3:61–70
Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS (2005) The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.). Genome 48:1120–1126
Leitch IJ, Hanson L, Winfield M, Parker J, Bennett MD (2001) Nuclear DNA C-values complete familial representation in gymnosperms. Ann Bot 88:843–849
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC-C, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT-Y, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam T-W, Yiu S-M, Liuand S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK-S, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J (2010a) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010b) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272
Liang C, Wang G, Liu L, Ji G, Fang L, Liu Y, Carter K, Webb J, Dean J (2007) ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). BMC Genomics 8:134
Liewlaksaneeyanawin C, Ritland CE, El-Kassaby YA, Ritland K (2004) Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. TAG Theor Appl Genet 109:361–369
Liewlaksaneeyanawin C, Zhuang J, Tang M, Farzaneh N, Lueng G, Cullis C, Findlay S, Ritland C, Bohlmann J, Ritland K (2009) Identification of COS markers in the Pinaceae. Tree Genet Genomes 5:247–255
Lippert D, Zhuang J, Ralph S, Ellis DE, Gilbert M, Olafson R, Ritland K, Ellis B, Douglas CJ, Bohlmann J (2005) Proteome analysis of early somatic embryogenesis in Picea glauca. Proteomics 5:461–473
Liu W, Magbanua ZV, Orzkan S, Chouvarine P, Bartlett BD, Peterson DG (2009) BAC libraries for two distantly related conifers, loblolly pine and bald cypress. In: Plant and animal genomes XVII conference, San Diego, USA
Lorenz WW, Sun F, Liang C, Kolychev D, Wang H, Zhao X, Cordonnier-Pratt M-M, Pratt LH, Dean JFD (2006) Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiol 26:1–16
Mackay J, Dean J (2011) Transcriptomics. In: Plomion C, Bousquet J (eds) Genetics, genomics and breeding of conifers. Science Publishers, Edenbridge
Magbanua ZV, Ozkan S, Bartlett BD, Chouvarine P, Saski CA, Liston A, Cronn RC, Nelson CD, Peterson DG (2011) Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS One 6:e16214
Miksche JP, Hotta Y (1973) DNA base composition and repetitious DNA in several conifers. Chromosoma 41:29–36
Morgante M, De Paoli E (2011) Toward the conifer genome sequence. In: Plomion C, Bousquet J (eds) Genetics, genomics and breeding of conifers. Science Publishers, Edenbridge
Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nat Rev Genet 12:111–122
Paterson AH (2006) Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nat Rev Genet 7:174–184
Pavy N, Parsons L, Paule C, MacKay J, Bousquet J (2006) Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 7:1–14
Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J (2006) Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-scale changes of the host transcriptome. Plant Cell Environ 29:1545–1570
Ralph S, Chun H, Kolosova N, Cooper D, Oddy C, Ritland C, Kirkpatrick R, Moore R, Barber S, Holt R, Jones S, Marra M, Douglas C, Ritland K, Bohlmann J (2008) A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics 9:484
Ritland K, Krutovsky K, Tsumura Y, Pelgas B, Bousquet J (2011) Genetic mapping in conifers. In: Plomion C, Bousquet J (eds) Genetics, genomics and breeding of conifers. Science Publishers, Edenbridge
Rungis D, Bérubé Y, Zhang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J, Ritland K (2004) Robust simple sequence repeat (SSR) markers for spruce (Picea spp.) from expressed sequence tags (ESTs). Theor Appl Genet 109:1283–1294
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh C-T, Emrich SJ, Jia Y, Kalyanaraman A, Hsia A-P, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia J-M, Deragon J-M, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145
Simola LK, Santanen A (1990) Improvement of nutrient medium for growth and embryogenesis of megagametophyte and embryo callus lines of Picea abies. Physiol Plant 80:27–35
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol İ (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117–1123
Springer NM, Xu X, Barbazuk WB (2004) Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiol 136:3023–3033
Tulsieram LK, Glaubitz JC, Kiss G, Carlson JE (1992) Single tree genetic linkage mapping in conifers using haploid DNA from megagametophytes. Nat Biotechnol 10:686–690
von Aderkas P, Anderson P (1993) Aneuploidy and polyploidization in haploid tissue cultures of Larix decidua. Physiol Plant 88:73–77
Warren RL, Sutton GG, Jones SJM, Holt RA (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500–501
Wen W, Mei H, Feng F, Yu S, Huang Z, Wu J, Chen L, Xu X, Luo L (2009) Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theor Appl Genet 119:459–470
Acknowledgments
I thank David Neale and Bert Abbott for their comments on drafts, John MacKay for discussions about conifer genomics, Steven Jones and Inanc Birol for teaching me the latest about sequence assembly, Carol Ritland for support at both work and home, and Genome BC/ Genome Canada for their support of conifer genome projects.
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Communicated by A. Abbott
A contribution to the Special Issue “The genomes of the giants: a walk through the forest of tree genomes”
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Ritland, K. Genomics of a phylum distant from flowering plants: conifers. Tree Genetics & Genomes 8, 573–582 (2012). https://doi.org/10.1007/s11295-012-0497-4
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DOI: https://doi.org/10.1007/s11295-012-0497-4