Gene set by de novo assembly of Perilla species and expression profiling between P. frutescens (L.) var. frutescens and var. crispa

Gene

Volumn 559, Issue 2, 2015, Pages 155-163

  Tong, Wei ^a   Kwon, Soon Jae ^b   Lee, Jeongsoo ^c   Choi, Ik Young ^c   Park, Yong Jin ^a   Choi, Seung Hun ^d   Sa, Kyu Jin ^d   Kim, Byeong Wan ^d   Lee, Ju Kyong ^d  

^a Kongju National University   (South Korea)

^b Korea Atomic Energy Research Institute   (South Korea)

^c Seoul National University   (South Korea)

^d Kangwon National University   (South Korea)

Author keywords

DEG profiling; Leaf color; Perilla; Transcriptome; Weedy and cultivar

Indexed keywords

TRANSCRIPTOME; PLANT RNA; VEGETABLE PROTEIN;

ARTICLE; COLOR; CULTIVAR; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE SEQUENCE; NONHUMAN; PERILLA FRUTESCENS; PLANT LEAF; PRIORITY JOURNAL; UPREGULATION; VARIETAS; COMPARATIVE STUDY; CONTIG MAPPING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; SEQUENCE ANALYSIS;

PERILLA; PERILLA FRUTESCENS; PERILLA FRUTESCENS VAR. FRUTESCENS;

CONTIG MAPPING; GENE EXPRESSION REGULATION, PLANT; MOLECULAR SEQUENCE ANNOTATION; PERILLA FRUTESCENS; PLANT PROTEINS; RNA, PLANT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84922432252     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2015.01.028     Document Type: Article

References (38)

1. Gong Z.Z., et al. Cloning and molecular analysis of structural genes involved in anthocyanin biosynthesis and expressed in a forma-specific manner in Perilla frutescens. Plant Mol. Biol. 1997, 35:915-927.
2. Gong Z.Z., et al. A constitutively expressed Myc-like gene involved in anthocyanin biosynthesis from Perilla frutescens: molecular characterization, heterologous expression in transgenic plants and transactivation in yeast cells. Plant Mol. Biol. 1999, 41(1):33-44.
3. Honda G., et al. Genetic studies of fruit color and hardness in Perilla frutescens. Jpn. J. Breed. 1990, 40:469-474.
4. Honda G., et al. Chemotaxonomic and cytogenetic studies on Perilla frutescens var. citriodora ("Lemon Egoma"). Nat. Med. 1994, 48:185-190.
5. Hong L.Z., et al. Digital gene expression for non-model organisms. Genome Res. 2011, 21:1905-1915.
6. Jiang W.B., et al. Brassinosteroid regulates seed size and shape in Arabidopsis. Plant Physiol. 2013, 162:1965-1977.
7. Jofuku K.D., et al. Control of seed mass and seed yield by the floral homeotic gene APETALA2. Proc. Natl. Acad. Sci. U. S. A. 2005, 102(8):3117-3122.
8. Jung J.N., et al. Variation of seed germination among cultivated and weedy types of Perilla crop in Korea and Japan. Kor. J. Crop Sci. 2009, 54:270-278.
9. Kim J.A., et al. Characteristics of seed germination among accessions of cultivated Perilla crop and their weedy types. Kor. J. Breed. Sci. 2011, 43:220-228.
10. Kristiansson E., et al. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics 2009, 10:345.
11. Kwon S.J., et al. Isolation and characterization of microsatellite markers in Perilla frutescens Britt. Mol. Ecol. Notes 2005, 5:454-456.
12. Lee J.K., Kim N.S. Genetic diversity and relationships of cultivated and weedy types of Perilla frutescens collected from East Asia revealed by microsatellite markers. Kor. J. Breed. Sci. 2007, 39:491-499.
13. Lee J.K., Ohnishi O. Geographical differentiation of morphological characters among Perilla crops and their weedy types in East Asia. Breed. Sci. 2001, 51:247-255.
14. Lee J.K., Ohnishi O. Genetic relationships among cultivated types of Perilla frutescens and their weedy types in East Asia revealed by AFLP markers. Genet. Resour. Crop. Evol. 2003, 50:65-74.
15. Lee J.K., et al. Genetic diversity of Perilla and related weedy types in Korea determined by AFLP analyses. Crop Sci. 2002, 42:2161-2166.
16. Li Y.H., et al. Control of final seed and organ size by the DA1 gene family in Arabidopsis thaliana. Genes Dev. 2007, 22:1331-1336.
17. Luo M., et al. MINI-SEED3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine-rich repeat (LRR) KINASE gene, are regulators of seed size in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:17531-17536.
18. McIntyre L.M., Lopiano K.K., Morse A.M., et al. RNA-seq: technical variability and sampling. BMC Genomics 2011, 12(1):293.
19. Meyer E., et al. Sequencing and de novo analysis of a coral larval transcriptome using 454 GS FLX. BMC Genomics 2009, 10:219.
20. Morozova O., et al. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 2009, 10:135-151.
21. Mortazavi A., et al. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 2008, 5:621-628.
22. Nitta M., Ohnishi O. Genetic relationships among two Perilla crops, shiso and egoma, and the weedy type revealed by RAPD markers. Genes Genet. Syst. 1999, 74:43-48.
23. Nitta M., et al. Asian Perilla crops and their weedy forms: their cultivation, utilization and genetic relationships. Econ. Bot. 2003, 57:245-253.
24. Nitta M., et al. Diversification of multipurpose plant, Perilla frutescens. Genet. Resour. Crop. Evol. 2005, 52:663-670.
25. Oshlack A., Wakefield M.J. Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct 2009, 4:14.
26. Pandey A., et al. Diversity distribution and collection of genetic resources of cultivated and weedy type in Perilla frutescens (L.) Britton var. frutescens and their uses in Indian Himalaya. Genet. Resour. Crop. Evol. 2008, 55:883-892.
27. Park Y.J., et al. On-farm conservation strategy to ensure crop genetic diversity in changing agro-ecosystems in the Republic of Korea. J. Agron. Crop Sci. 2005, 191:401-410.
28. Sa K.J., et al. Comparison of seed characteristics between the cultivated and the weedy types of Perilla species. Hortic. Environ. Biotechnol. 2012, 53:310-315.
29. Simon S.A., et al. Short-read sequencing technologies for transcriptional analyses. Annu. Rev. Plant Biol. 2009, 60:305-333.
30. Tanaka Y., et al. Metabolic engineering to modify flower color. Plant Cell Physiol. 1998, 39:1119-1126.
31. Vera J.C., et al. Rapid transcriptome characterization for a non-model organism using 454 pyrosequencing. Mol. Ecol. 2008, 17:1636-1647.
32. Verma N., et al. Assessment of genetic diversity in Indian Perilla [Perilla frutescens (L.) Britton] landraces using STMS markers. Indian J. Biotechnol. 2010, 09(1):43-49.
33. Wang L., Wang X. DEGseq: Identify Differentially Expressed Genes From RNA-seq Data. R Package Version 1.20.0 2013.
34. Wang Z., et al. RNA-seq a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
35. Wang X.W., et al. De novo characterization of a whitefly transcriptome and analysis its gene expression during development. BMC Genomics 2010, 11:400.
36. Wold B., Myers R.M. Sequence census methods for functional genomics. Nat. Methods 2008, 5:19-21.
37. Yamazaki M., et al. Differential gene expression profiles of red and green forms of Perilla frutescens leading to comprehensive identification of anthocyanin biosynthetic genes. FEBS 2008, 275:3494-3502.
38. Yang Y., et al. Identification of novel and conserved microRNAs in Rehmannia glutinosa L. by Solexa sequencing. Plant Mol. Biol. Report. 2011, 29(4):986-996.