The Norway spruce genome sequence and conifer genome evolution

被引：1106

作者：

Nystedt, Bjorn ^{[1
]}

Street, Nathaniel R. ^{[2
]}

Wetterbom, Anna ^{[3
]}

Zuccolo, Andrea ^{[4
,5
]}

Lin, Yao-Cheng ^{[6
,7
]}

Scofield, Douglas G. ^{[2
,8
]}

Vezzi, Francesco ^{[9
]}

Delhomme, Nicolas ^{[2
]}

Giacomello, Stefania ^{[4
,10
]}

Alexeyenko, Andrey ^{[11
]}

Vicedomini, Riccardo ^{[4
,10
]}

Sahlin, Kristoffer ^{[9
]}

Sherwood, Ellen ^{[1
]}

Elfstrand, Malin ^{[12
]}

Gramzow, Lydia ^{[13
]}

Holmberg, Kristina ^{[11
]}

Hallman, Jimmie ^{[11
]}

Keech, Olivier ^{[2
]}

Klasson, Lisa ^{[14
]}

Koriabine, Maxim ^{[15
]}

Kucukoglu, Melis ^{[16
]}

Kaller, Max ^{[11
]}

Luthman, Johannes ^{[3
]}

Lysholm, Fredrik ^{[3
]}

Niittyla, Totte ^{[16
]}

Olson, Ake ^{[12
]}

Rilakovic, Nemanja ^{[11
]}

Ritland, Carol ^{[17
]}

Rossello, Josep A. ^{[18
,19
]}

Sena, Juliana ^{[20
,21
]}

Svensson, Thomas ^{[22
]}

Talavera-Lopez, Carlos ^{[3
]}

Theissen, Guenter ^{[13
]}

Tuominen, Hannele ^{[2
]}

Vanneste, Kevin ^{[6
,7
]}

Wu, Zhi-Qiang ^{[8
]}

Zhang, Bo ^{[2
]}

Zerbe, Philipp ^{[23
]}

Arvestad, Lars ^{[9
,24
]}

Bhalerao, Rishikesh ^{[16
]}

Bohlmann, Joerg ^{[17
,23
]}

Bousquet, Jean ^{[20
,21
]}

Gil, Rosario Garcia ^{[16
]}

Hvidsten, Torgeir R. ^{[2
,25
]}

de Jong, Pieter ^{[15
]}

MacKay, John ^{[20
,21
]}

Morgante, Michele ^{[4
,10
]}

Ritland, Kermit ^{[17
]}

Sundberg, Bjorn ^{[16
]}

Thompson, Stacey Lee ^{[8
]}

机构：

[1] Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-17121 Solna, Sweden

[2] Umea Univ, Dept Plant Physiol, Umea Plant Sci Ctr, S-90187 Umea, Sweden

[3] Karolinska Inst, Sci Life Lab, Dept Cell & Mol Biol, S-17177 Stockholm, Sweden

[4] Ist Genom Applicata, I-33100 Udine, Italy

[5] Scuola Super Sant Anna, Inst Life Sci, I-56127 Pisa, Italy

[6] Univ Ghent, Dept Plant Syst Biol VIB, B-9052 Ghent, Belgium

[7] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

[8] Umea Univ, Dept Ecol & Environm Sci, Umea Plant Sci Ctr, S-90187 Umea, Sweden

[9] KTH Royal Inst Technol, Sch Comp Sci & Commun, Sci Life Lab, S-17121 Solna, Sweden

[10] Univ Udine, I-33100 Udine, Italy

[11] KTH Royal Inst Technol, Sci Life Lab, Sch Biotechnol, S-17121 Solna, Sweden

[12] Swedish Univ Agr Sci, Uppsala Bioctr, Dept Forest Mycol & Plant Pathol, S-75007 Uppsala, Sweden

[13] Univ Jena, Dept Genet, D-07743 Jena, Germany

[14] Uppsala Univ, Dept Cell & Mol Biol, S-75237 Uppsala, Sweden

[15] Childrens Hosp Oakland, Res Inst, BACPAC Resources, Oakland, CA 94609 USA

[16] Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, S-90183 Umea, Sweden

[17] Univ British Columbia, Dept Forest & Conservat Sci, Vancouver, BC V6T 1Z4, Canada

[18] Univ Valencia, Jardi Bot, Valencia 46008, Spain

[19] Carl Faust Fdn, Marimurtra Bot Garden, Blanes 17300, Spain

[20] Univ Laval, Canada Res Chair Forest & Environm Genom, Ctr Forest Res, Quebec City, PQ G1V 0A6, Canada

[21] Univ Laval, Inst Syst & Integrat Biol, Quebec City, PQ G1V 0A6, Canada

[22] Karolinska Inst, Sci Life Lab, Dept Biosci & Nutr, S-17121 Solna, Sweden

[23] Univ British Columbia, Michael Smith Labs, Vancouver, BC V6T 1Z4, Canada

[24] Stockholm Univ, Swedish E Sci Res Ctr, Dept Numer Anal & Comp Sci, S-17121 Solna, Sweden

[25] Norwegian Univ Life Sci, Dept Chem Biotechnol & Food Sci, N-1432 As, Norway

来源：

NATURE | 2013年 / 497卷 / 7451期

基金：

瑞典研究理事会;

关键词：

LONG NONCODING RNAS; TRANSPOSABLE ELEMENTS; SIZE VARIATION; GENE FAMILY; RECOMBINATION; PLANTS; AMPLIFICATION; POLYPLOIDY; COMPLEXITY; SLOW;

D O I：

10.1038/nature12211

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

引用

页码：579 / 584

页数：6

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