The actin multigene family in Populus: Organization, expression and phylogenetic analysis

Molecular Genetics and Genomics

Volumn 284, Issue 2, 2010, Pages 105-119

  Zhang, Deqiang ^a   Du, Qingzhang ^a   Xu, Baohua ^a   Zhang, Zhiyi ^a   Li, Bailian ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

Actin genes; Differential expression; Gene structure; Nucleotide diversity; Phylogeny; Poplar

Indexed keywords

ACTIN; ACTIN 1; ACTIN 2; ACTIN 3; ACTIN 4; ACTIN 5; ACTIN 6; ACTIN 7; ACTIN 8; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; ASPEN; CONTROLLED STUDY; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; GEOGRAPHICAL VARIATION (SPECIES); MICROARRAY ANALYSIS; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHLOEM; PLANT DEVELOPMENT; PLANT GROWTH; PLANT LEAF; PLANT ROOT; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; SPECIES DIVERSITY; SPECIES IDENTIFICATION; XYLEM; GENETICS; GROWTH, DEVELOPMENT AND AGING; MULTIGENE FAMILY; PHYLOGENY; PLANT; PLANT STEM; WOOD;

POPULUS;

ACTINS; MULTIGENE FAMILY; PHYLOGENY; PLANT STEMS; PLANTS; POPULUS; WOOD;

EID: 77955297327     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-010-0552-5     Document Type: Article

References (41)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Blancaflor EB (2002) The cytoskeleton and gravitropism in higher plants. J Plant Growth Regul 21:120-136
3. Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. PNAS 10142:15255-15260
4. Chaffey N, Barlow P, Sundberg B (2002) Understanding the role of the cytoskeleton in wood formation in angiosperm trees: Hybrid aspen (Populus tremula 9 P. tremuloides) as the model species. Tree Physiol 22:239-249
5. Daniel HM, Meyer W (2003) Evaluation of ribosomal RNA and actin gene sequences for the identification of ascomycetous yeasts. Int J Food Microbiol 86:61-78
6. Daniel HM, Sorrell TC, Meyer W (2001) Partial sequence analysis of the actin gene and its potential for studying the phylogeny of Candida species and their teleomorphs. Int J Syst Evol Microbiol 51:1593-1606
7. Djerbi S, Aspeborg H, Nilsson P, Sundberg B, Mellerowicz E, Blomqvist K, Teeri TT (2004) Identification and expression analysis of genes encoding putative cellulose synthases (CesA) in the hybrid aspen, Populus tremula (L.) 9 P. tremuloides (Michx.). Cellulose 11:301-312
8. Droltin G, Dover GA (1990) Independent gene evolution in the potato actin gene family demonstrated by phylogenetic procedures for resolving gene conversions and the phylogeny of angiosperm actin genes. J Mol Evol 31:132-150
9. Foissner I, Lichtscheidl IK, Wasteneys GO (1996) Actin-based vesicle dynamics and exocytosis during wound wall formation in Characean internodal cells. Cell Motil Cytoskeleton 35:35-48
10. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709
11. Fukuda H, Kobayashi H (1989) Dynamic organization of the cytoskeleton during tracheary-element differentiation. Develop Growth Differ 31:9-16
12. Heuertz M, Paoli ED, Källman T, Larsson H, Jurman I, Morgante M et al (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway Spruce [Picea abies (L.) Karst]. Genetics 174:2095-2105
13. Hightower RC, Meagher RB (1985) Divergence and differential expression of soybean actin genes. EMBO J 4:1-8
14. Huang ZH (1992) The study on the climatic regionalization of the distributional region of Populus tomentosa. J Beijing For Univ 14:26-32
15. Huang S, An YQ, McDowell JM, McKinney EC, Meagher RB (1997) The Arabidopsis ACT11 actin gene is strongly expressed in tissues of the emerging inflorescence, pollen, and developing ovules. Plant Mol Biol 33:125-139
16. Hussey PJ, Ketelaar T, Deeks MJ (2006) Control of the actin cytoskeleton in plant cell growth. Annu Rev Plant Biol 57:109-125
17. Ingvarsson PK (2008) Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180:329-340
18. Krutovsky KV, Neale DB (2005) Nucleotide diversity and linkage disequilibrium in cold-hardiness-and wood quality-related candidate genes in Douglas Fir. Genetics 171:2029-2041
19. Li XB, Fan XP, Wang XL, Lin Cai, Yang WC (2005) The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 17:859-875
20. Li X, Wu HX, Dillon SK, Southerton SG (2009) Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don. BMC Genomics 2009(10):41
21. Lukashin AV, Borodovsky M (1998) GeneMark.hmm: New solutions for gene finding. Nucleic Acids Res 26:1107-1115
22. McDowell JM, Huang S, McKinney EC, An YQ, Meagher RB (1996) Structure and evolution of the actin gene family in Arabidopsis thaliana. Genetics 142:587-602 (Pubitemid 26039227)
23. McElroy D, Rothenberg M, Reece KS, Wu R (1990a) Characterization of the rice (Oryza sativa) actin gene family. Plant Mol Biol 15:257-268
24. McElroy D, Zhang W, Cao J, Wu R (1990b) Isolation of an efficient actin promoter for use in rice transformation. Plant Cell 2:163-171
25. McLean BG, Eubanks S, Meagher RB (1990) Tissue specific expression of divergent actins in soybean root. Plant Cell 2:335-344
26. Mellerowicz EJ, Sundberg B (2008) Wood cell walls: Biosynthesis, developmental dynamics and their implications for wood properties. Curr Opin Plant Biol 11:293-300
27. Moniz de Sa M, Drouin G (1996) Phylogeny and substitution rates of angiosperm actin genes. Mol Biol Evol 13:1198-1212
28. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
29. Quang ND, Ikeda S, Harada K (2008) Nucleotide variation in Quercus crispula Blume. Heredity 101:166-174
30. Reece KS, McElroy D, Wu R (1990) Genomic nucleotide sequence of four rice (Oryza sativa) actin genes. Plant Mol Biol 14:621-624
31. Rozas J, Sánchez-Delbarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497
32. Shah DM, Hightower RC, Meagher RB (1983) Genes encoding actin in higher plants: Intron positions are highly conserved but the coding sequences are not. J Mol Appl Genet 2:111-126
33. Sjödin A, Bylesjö M, Skogström O, Eriksson D, Nilsson P, Rydén P, Jansson S et al (2006) UPSC-BASE-Populus transcriptomics online. Plant J 48:806-817
34. Smith LG, Oppenheimer DG (2005) Spatial control of cell expansion by the plant cytoskeleton. Annu Rev Cell Dev Biol 21:271-295
35. Staiger CJ (2000) Signalling to the actin cytoskeleton in plants. Annu Rev Plant Physiol Plant Mol Biol 51:257-288
36. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595
37. Takagi S (2000) Roles for actin filaments in chloroplast motility and anchoring. In: Staiger C (ed) Actin: A dynamic framework for multiple plant cell functions. Kluwer, Dordrecht, pp 203-212
38. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599
39. Timonen S, Peterson RL (2002) Cytoskeleton in mycorrhizal symbiosis. Plant Soil 244:199-210
40. Tuskan GA, DiFazio S, Jansson S et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-1604
41. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:188-193