Transcriptome sequencing and de novo assembly in arecanut, Areca catechu L elucidates the secondary metabolite pathway genes

Biotechnology Reports - Tập 17 - Trang 63-69 - 2018
Ramaswamy Manimekalai1, Smita Nair2, A. Naganeeswaran2, Anitha Karun2, Suresh Malhotra3, V. Hubbali4
1Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, 641 007, Tamil Nadu, India
2Central Plantation Crops Research institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O., Kasaragod 671 124, Kerala, India
3Indian Council of Agricultural Research (ICAR), KAB II, New Delhi, India
4Directorate of Arecanut and Cocoa Development, Kera Bhavan, Kochi, India

Tài liệu tham khảo

Staples, 2006 Rao, 1982, Introduction, 1 Giri, 2006, A metabolomic approach to the metabolism of the arecanut alkaloids arecoline and aracaidine in the mouse, Chem. Res. Toxicol., 19, 818, 10.1021/tx0600402 Kumar, 2012, Rapid separation of carotenes and evaluation of their in vitro antioxidant properties from ripened fruit waste of Areca catechu –a plantation crop of agro-industrial importance, Ind. Crops Prod., 40, 204, 10.1016/j.indcrop.2012.03.014 Manimekalai, 2012, Molecular marker-based genetic variability among Yellow Leaf Disease (YLD) resistant and susceptible arecanut (Areca catechu L.) genotypes, Indian J. Hortic., 69, 455 Sankaran, 2013, Assessment of genetic diversity among arecanut accessions by using RAPD markers, Indian J. Hortic., 70, 428 Bharath, 2015, Studies on genetic relationships and diversity in arecanut (Areca catechu L.) germplasm utilizing RAPD markers, J. Plant. Crops, 43, 117 Al-Dous, 2011, De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera), Nat. Biotechnol., 29, 521, 10.1038/nbt.1860 Singh, 2013, Oil palm genome sequence reveals divergence of inter fertile species in Old and New worlds, Nature, 500, 335, 10.1038/nature12309 Fan, 2013, RNA-seq analysis of Cocos nucifera: transcriptome sequencing and subsequent functional genomics approaches, PLoS One, e59997, 10.1371/journal.pone.0059997 Luo, 2012, SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, 1, 18, 10.1186/2047-217X-1-18 Langmead, 2012, Fast gapped-read alignment with bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Mortazavi, 2008, Mapping and quantifying mammalian transcriptomes by RNASeq, Nat. Methods, 5, 621, 10.1038/nmeth.1226 Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Kanehisa, 2010, KEGG for representation and analysis of molecular networks involving diseases and drugs, Nucleic Acids Res., 38, 355, 10.1093/nar/gkp896 Moriya, 2007, KAAS: an automatic genome annotation and pathway reconstruction server, Nucleic Acids Res., 35, W182, 10.1093/nar/gkm321 Asari, 2014, Standalone EST microsatellite mining and analysis tool (SEMAT): for automated EST-SSR analysis in plants, Tree Genet. Genomes, 10.1007/s11295-014-0785-2 Ramosa, 2009, Molecular and functional characterization of a cDNA encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase from Dunaliella salina, J. Plant Physiol., 166, 968, 10.1016/j.jplph.2008.11.008 Pfeiffera, 2006, Biosynthesis of flavan 3-ols by leucoanthocyanidin 4-reductases and anthocyanidin reductases in leaves of grape (Vitis vinifera L.), apple (Malus x domestica Borkh.) and other crops, Plant Physiol. Biochem., 44, 323, 10.1016/j.plaphy.2006.06.001 Li, 2012, De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.), BMC Genomics, 13, 192, 10.1186/1471-2164-13-192 Mathew, 2014, A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms, BMC Genomics, 15, 285, 10.1186/1471-2164-15-285