An International Open Access Journal
News Scroll
E-mail Alerts
Subscribe for TOC Alerts
Search Articles
sidebar
Creative Commons License

References


Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM (2019) Transposable elements contribute to dynamic genome content in maize. BioRxiv 547398.

Baránek M, Meszáros M, Sochorová J, ?echová J, Raddová J (2012) Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická. Scientia Horticulturae 143: 1-6.

Bergman CM, Quesneville H (2007) Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics 8: 382-392.

Contreras B, Vives C, Castells R, Casacuberta JM (2015) The impact of transposable elements in the evolution of plant genomes: from selfish elements to key players. In Evolutionary biology: Biodiversification from genotype to phenotype ,. Springer, Cham, Pp. 93-105.

Cui Y, Barampuram S, Stacey MG, Hancock CN, Findley S, Mathieu M, Zhang Z, Parrott WA, Stacey G, (2013) Tnt1 retrotransposon mutagenesis: a tool for soybean functional genomics. Plant Physiology, 161:36-47.

Du J, Grant D, Tian Z, Nelson, RT, Zhu L, Shoemaker RC, Ma J (2010) Soy TEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11: 113.

Fedoroff  NV (2012) Transposable elements, epigenetics, and genome evolution. Science 338: 758-767.

Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends in Genetics 5: 103-107.

Gao D, Abernathy B, Rohksar D, Schmutz J, Jackson SA (2014) Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris). Frontiers in Plant Science 5: 339.

Grzebelus D (2018) The functional impact of transposable elements on the diversity of plant genomes. Diversity 10: 18.

Jiang C, Chen C, Huang Z, Liu R, Verdier J (2015) ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. BMC Bioinformatics 16: 72.

Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genetics 33: 102.

Kolade O, Raji A, Fawole I, Ingelbrecht I (2015) Molecular Characterization of Type II Transposable Elements in Cowpea [Vigna unguiculata (L.) Walp]. American Journal of Plant Sciences 6: 767.

Lall I, Upadhyaya K (2002) Panzee, a copia-like retrotransposon from the grain legume, pigeonpea (Cajanus cajan L.). Molecular Genetics and Genomics 267:  271-280.

Lin JY, Stupar RM, Hans C, Hyten DL, Jackson SA (2010) Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris. The Plant Cell 22:2545-2561. doi: 10.1105/tpc.110.074229.

McClean PE, Mamidi S, McConnell M, Chikara S, Lee R (2010) Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics 11: 184.

Nemli S, Kianoosh T, Tanyolac MB (2015) Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turkish Journal of Agriculture and Forestry 39: 940-948.

Ouyang S, Buell CR (2004) The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Research 32: D360-D363.

Panaud O (2009) The molecular bases of cereal domestication and the history of rice. Comptesrendus Biologies 332: 267-272.

Patil PG, Byregowda M, Agbagwa IO, Shashidhar HE (2015) Characterization of Ty1/copia-like retrotransposon families from pigeonpea genome. Genetics and Molecular Research 14: 5812-5822.

Pearce SR, Stuart-Rogers C, Knox MR, Kumar A, Ellis TH, Flavell AJ (1999) Rapid isolation of plant Ty1-copia group retrotransposon LTR sequences for molecular marker studies. The Plant Journal 19: 711-717.

Sandhu D, Bhattacharyya MK (2017) Transposon-Based Functional Characterization of Soybean Genes. In: The Soybean Genome  Springer, Cham, Pp. 183-192.

Sandhu D, Ghosh J, Johnson C, Baumbach J, Baumert E, Cina T, Grant D, Palmer RG, Bhattacharyya MK (2017) The endogenous transposable element Tgm9 is suitable for generating knockout mutants for functional analyses of soybean genes and genetic improvement in soybean. PloS one 12: e0180732.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178.

Singh NK, Gupta DK, Jayaswal PK, Mahato AK, Dutta S, Singh S, Bhutani S, Dogra V, Singh BP, Kumawat G, Pal JK (2011) The first draft of the pigeonpea genome sequence. Journal of Plant Biochemistry and Biotechnology 20: 15.

Staginnus C, Huettel B, Desel C, Schmidt T, Kahl G (2001) A PCR-based assay to detect En/Spm-like transposon sequences in plants. Chromosome Research 9: 591-605.

Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends in Plant Science, 15: 471-478.

Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, Fan G, Whaley AM, Farmer AD  (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 30: 83.

Wawrzynski A, Ashfield T, Chen NW, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, (2008) Replication of nonautonomous retroelements in soybean appears to be both recent and common. Plant Physiology, 148: 1760-1771.

Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proceedings of the National Academy of Sciences 103: 17600-17601.

Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E (2007) A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 8: 973.

Xu M, Brar HK, Grosic S, Palmer RG, Bhattacharyya MK (2009) Excision of an active CACTA-like transposable element from DFR2 causes variegated flowers in soybean [Glycine max (L.) Merr.] Genetics 184:53-63. doi: 10.1534/genetics.109.107904.

Zabala G, Vodkin L (2008) A putative autonomous 20.5 kb-CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max. BMC plant biology 8: 124.

Zabala G, Vodkin LO (2014) Methylation affects transposition and splicing of a large CACTA transposon from a MYB transcription factor regulating anthocyanin synthase genes in soybean seed coats. PLoS One 9: e111959.

Zhang Y, Fan C, Li S, Chen Y, Wang RR, Zhang X, Han F, Hu Z  (2017) The diversity of sequence and chromosomal distribution of new transposable element-related segments in the rye genome revealed by FISH and lineage annotation. Frontiers in Plant Science 8:1706.

Zhao M, Ma J (2017) Transposable Elements. In The Soybean Genome, Springer, Cham, pp. 171-181.

Used Online Resource  

https://www.uniprot.org/blast/

http://www.clustal.org/clustal2/

http://evolution.genetics.washington.edu/phylip.html

Users Online: 59
Editorial Board
Indexed & Listed In
Track manuscript
Manuscript Statistics
Articles Statistics
Publication Statistics