Expression Analysis of 12 miRNA Families Specific to Conifers during Somatic Embryogenesis of Larch

ZHANG Jun-hong; WU Tao; HAN Su-ying; QI Li-wang; ZHANG Shou-gong

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Expression Analysis of 12 miRNA Families Specific to Conifers during Somatic Embryogenesis of Larch

1.
Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2.
Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2012-03-13

Abstract

In order to identify miRNA and investigate it’s expression profile during somatic embryogenesis (SE) of larch, a small RNA library was constructed and sequenced by Solexa technique, and expression analysis of miRNAs and four precursors during eight developmental stages of SE was evaluated by qRT-PCR. The results demonstrated that a total of 87 miRNAs was identified, of which 29 miRNAs from 12 families were specific to conifers, including miR946, miR947, miR950, miR951, miR1311, miR1312, miR1313, miR1314, miR1316, miR3701, miR3702 and miR3704, which could be used for further analysis and next experiment. Of these, 25 miRNAs were 22nt in length, while 4 miRNAs were 21nt. The abundance of miRNAs varied largely in the small RNA library, such as miR1311 was detected by 18 copies, while miR950 with 33 009 copies. 34 potential target genes were predicted for 12 miRNA families, which were linked to many respects of regulation, including plant growth and development, disease resistance, AGO protein feedback regulation. qRT-PCR analysis showed that, for 72% miRNAs, the minor expression peak was at late single embryo or early cotyledonary embryo, the lowest level was at middle cotyledonary embryo, while the major peak was at late cotyledonary embryo, which was consistent with the physiology events of cotyledon formation, embryo pre-mature, and embryo dormancy. However, the expression model of miRNA precursor was differed from that of miRNA, and precursor expression with much smaller extent than that of miRNA. The discovery of miRNAs specific to conifers and their targets using embryogenic tissue could provide references for the study on the growth and development of gymnosperms.
- Larix leptolepis,
- somatic embryo,
- microRNA,
- conifer,
- expression analysis

References

[1]	Juarez M T, Kui J S, Thomas J, et al. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity[J]. Nature, 2004, 428(6978):84-88
[2]	Parry G, Calderon-Villalobos L I, Prigge M et al. Complex regulation of the TIR1/AFB family of auxin receptors[J]. Proc Natl Acad Sci U S A, 2009, 106(52):22540-22545
[3]	Liu H H, Tian X, Li Y J, et al. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana[J]. RNA, 2008, 14(5):836-843
[4]	Jones-Rhoades M W, Bartel D P, Bartel B. MicroRNAs and their regulatory roles in plants[J]. Annu Rev Plant Biol, 2006, 57:19-53
[5]	Lu S f, Sun Y H, Amerson H, et al. MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development [J]. The Plant Journal,2007, 51:1077-1098
[6]	Yakovlev I A, Fossdal C G, Johnsen O. MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce[J]. New Phytol, 2010, 187(4):1154-1169
[7]	孙晓梅,张守攻,齐力旺,等.日本落叶松自由授粉家系纸浆材材性遗传变异的研究[J].林业科学研究,2003,16( 5): 515-522
[8]	Bowe L M, Gwe'nae¨le C, dePamphilis C W. Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales’ closest relatives are conifers [J]. Proc Natl Acad Sci U S A, 2000, 97:4092-4097
[9]	Filonova L H, Bozhkov P V, von Arnold S. Developmental pathway of somatic embryogenesis in Picea abies as revealed by time-lapse tracking[J]. J Exp Bot, 2000, 51(343):249-264
[10]	Cairney J, Pullman G S. The cellular and molecular biology of conifer embryogenesis[J]. New Phytol, 2007, 176(3):511-536
[11]	Kirst M, Johnson A F, Baucom C, et al. Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda) with Arabidopsis thaliana[J]. Proc Natl Acad Sci U S A, 2003, 100(12):7383-7388
[12]	Lorenz W W, Sun F, Liang C, et al. Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries[J]. Tree Physiol, 2006, 26(1):1-16
[13]	Cairney J, Zheng L, Cowels A, et al. Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis[J]. Plant Mol Biol, 2006, 62(4-5):485-501
[14]	Ahuja M R, Neale a D B. Evolution of Genome Size in Conifers[J]. Silvae Genetica, 2005, 54(3):126-137
[15]	Li M, Xia Y, Gu Y, et al. MicroRNAome of porcine pre- and postnatal development[J]. PLoS One, 2010, 5(7):e11541
[16]	Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data[J]. Nucleic Acids Res, 2011, 39(Database issue):D152-157
[17]	Dai X, Zhao a P X. psRNATarget: a plant small RNA target analysis server[J]. Nucleic Acids Research, 2011, 39(Web Server issue):W155-159
[18]	Vaucheret H, Vazquez F, Crete P, et al. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development[J]. Genes Dev, 2004, 18(10):1187-1197
[19]	Yang H, Matsubayashi Y, Nakamura K, et al. Oryza sativa PSK gene encodes a precursor of phytosulfokine-alpha, a sulfated peptide growth factor found in plants[J]. Proc Natl Acad Sci U S A, 1999, 96(23):13560-13565
[20]	Lindsey K, Casson S, Chilley P. Peptides:new signaling molecules in plants[J]. Trends Plant Sci, 2002, 7(2): 78-83
[21]	Allen E, Xie Z X, Gustafson A M, et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants [J]. Cell, 2005, 121(2):207-221
[22]	Howell M D, Fahlgren N, Chapman E J, et al. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting [J]. Plant Cell, 2007, 19(3):926-942
[23]	Allen E, Xie Z X, Gustafson A M, et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana[J]. Nature Genetics, 2004, 36(12):1282-1290
[24]	Vazquez F, Blevins T, Ailhas J, et al. Evolution of Arabidopsis MIR genes generates novel microRNA classes[J]. Nucleic Acids Res, 2008, 36(20):6429-6438
[25]	Braybrook S A, Stone S L, Park S, et al. Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis[J]. Proc Natl Acad Sci U S A, 2006, 103(9):3468-3473
[26]	Holdsworth M J, Bentsink L, Soppe W J. Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination[J]. New Phytol, 2008, 179(1):33-54

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Expression Analysis of 12 miRNA Families Specific to Conifers during Somatic Embryogenesis of Larch

1. Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

2. Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2012-03-13

Available Online: 2012-08-20

Abstract: In order to identify miRNA and investigate it’s expression profile during somatic embryogenesis (SE) of larch, a small RNA library was constructed and sequenced by Solexa technique, and expression analysis of miRNAs and four precursors during eight developmental stages of SE was evaluated by qRT-PCR. The results demonstrated that a total of 87 miRNAs was identified, of which 29 miRNAs from 12 families were specific to conifers, including miR946, miR947, miR950, miR951, miR1311, miR1312, miR1313, miR1314, miR1316, miR3701, miR3702 and miR3704, which could be used for further analysis and next experiment. Of these, 25 miRNAs were 22nt in length, while 4 miRNAs were 21nt. The abundance of miRNAs varied largely in the small RNA library, such as miR1311 was detected by 18 copies, while miR950 with 33 009 copies. 34 potential target genes were predicted for 12 miRNA families, which were linked to many respects of regulation, including plant growth and development, disease resistance, AGO protein feedback regulation. qRT-PCR analysis showed that, for 72% miRNAs, the minor expression peak was at late single embryo or early cotyledonary embryo, the lowest level was at middle cotyledonary embryo, while the major peak was at late cotyledonary embryo, which was consistent with the physiology events of cotyledon formation, embryo pre-mature, and embryo dormancy. However, the expression model of miRNA precursor was differed from that of miRNA, and precursor expression with much smaller extent than that of miRNA. The discovery of miRNAs specific to conifers and their targets using embryogenic tissue could provide references for the study on the growth and development of gymnosperms.

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Reference (26)

[1]	Juarez M T, Kui J S, Thomas J, et al. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity[J]. Nature, 2004, 428(6978):84-88
[2]	Parry G, Calderon-Villalobos L I, Prigge M et al. Complex regulation of the TIR1/AFB family of auxin receptors[J]. Proc Natl Acad Sci U S A, 2009, 106(52):22540-22545
[3]	Liu H H, Tian X, Li Y J, et al. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana[J]. RNA, 2008, 14(5):836-843
[4]	Jones-Rhoades M W, Bartel D P, Bartel B. MicroRNAs and their regulatory roles in plants[J]. Annu Rev Plant Biol, 2006, 57:19-53
[5]	Lu S f, Sun Y H, Amerson H, et al. MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development [J]. The Plant Journal,2007, 51:1077-1098
[6]	Yakovlev I A, Fossdal C G, Johnsen O. MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce[J]. New Phytol, 2010, 187(4):1154-1169
[7]	孙晓梅,张守攻,齐力旺,等.日本落叶松自由授粉家系纸浆材材性遗传变异的研究[J].林业科学研究,2003,16( 5): 515-522
[8]	Bowe L M, Gwe'nae¨le C, dePamphilis C W. Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales’ closest relatives are conifers [J]. Proc Natl Acad Sci U S A, 2000, 97:4092-4097
[9]	Filonova L H, Bozhkov P V, von Arnold S. Developmental pathway of somatic embryogenesis in Picea abies as revealed by time-lapse tracking[J]. J Exp Bot, 2000, 51(343):249-264
[10]	Cairney J, Pullman G S. The cellular and molecular biology of conifer embryogenesis[J]. New Phytol, 2007, 176(3):511-536
[11]	Kirst M, Johnson A F, Baucom C, et al. Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda) with Arabidopsis thaliana[J]. Proc Natl Acad Sci U S A, 2003, 100(12):7383-7388
[12]	Lorenz W W, Sun F, Liang C, et al. Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries[J]. Tree Physiol, 2006, 26(1):1-16
[13]	Cairney J, Zheng L, Cowels A, et al. Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis[J]. Plant Mol Biol, 2006, 62(4-5):485-501
[14]	Ahuja M R, Neale a D B. Evolution of Genome Size in Conifers[J]. Silvae Genetica, 2005, 54(3):126-137
[15]	Li M, Xia Y, Gu Y, et al. MicroRNAome of porcine pre- and postnatal development[J]. PLoS One, 2010, 5(7):e11541
[16]	Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data[J]. Nucleic Acids Res, 2011, 39(Database issue):D152-157
[17]	Dai X, Zhao a P X. psRNATarget: a plant small RNA target analysis server[J]. Nucleic Acids Research, 2011, 39(Web Server issue):W155-159
[18]	Vaucheret H, Vazquez F, Crete P, et al. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development[J]. Genes Dev, 2004, 18(10):1187-1197
[19]	Yang H, Matsubayashi Y, Nakamura K, et al. Oryza sativa PSK gene encodes a precursor of phytosulfokine-alpha, a sulfated peptide growth factor found in plants[J]. Proc Natl Acad Sci U S A, 1999, 96(23):13560-13565
[20]	Lindsey K, Casson S, Chilley P. Peptides:new signaling molecules in plants[J]. Trends Plant Sci, 2002, 7(2): 78-83
[21]	Allen E, Xie Z X, Gustafson A M, et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants [J]. Cell, 2005, 121(2):207-221
[22]	Howell M D, Fahlgren N, Chapman E J, et al. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting [J]. Plant Cell, 2007, 19(3):926-942
[23]	Allen E, Xie Z X, Gustafson A M, et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana[J]. Nature Genetics, 2004, 36(12):1282-1290
[24]	Vazquez F, Blevins T, Ailhas J, et al. Evolution of Arabidopsis MIR genes generates novel microRNA classes[J]. Nucleic Acids Res, 2008, 36(20):6429-6438
[25]	Braybrook S A, Stone S L, Park S, et al. Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis[J]. Proc Natl Acad Sci U S A, 2006, 103(9):3468-3473
[26]	Holdsworth M J, Bentsink L, Soppe W J. Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination[J]. New Phytol, 2008, 179(1):33-54

Expression Analysis of 12 miRNA Families Specific to Conifers during Somatic Embryogenesis of Larch

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通讯作者: 陈斌, bchen63@163.com

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Expression Analysis of 12 miRNA Families Specific to Conifers during Somatic Embryogenesis of Larch

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