Revisiting the Decoded Genomes to Promptly Reveal their Genomic Perspectives

Post Arabidopsis thaliana , 55 genomes comprising 49 different plant species have been decoded by use of clone-by-clone, whole genome shotgun and next-generation sequencing approaches. The structural outcomes of these sequenced genomes shed light on their genomic constitution, particularly the way genes, transposable elements and genetic markers are orga-nized within the genomes. The functional outcomes provide a brief account of specific phenotypic trait characteristics of crop genomes by digging deep into the genetic make-up of transcription factors, regulato-ry elements and gene families governing multiple ag-ronomic traits in these crop plants. The comparative and evolutionary outcomes deduce the genetic basis of biological diversity and basic process of ge-nome evolution by analysing the syntenic relationships among genes and genomes/chromosomes of the se-quenced crop plants. Therefore, a revisit to published genome sequence landmarks in 30 major cultivated food crops constituting major groups (cereals, leg-umes, vegetables, fruits, oil seeds and fibres) would significantly assist us to gain a detailed insight into their genome organization and dissect the structural, functional, comparative and evolutionary intricacies for identifying species- and lineage-specific genes con-trolling multiple characteristics in crop plants. The es-sential inputs obtained will be helpful in devising efficient strategies to develop high-yielding climate-ready crop varieties through translational genomics.

[1]  Wensheng Wang,et al.  SNP-Seek database of SNPs derived from 3000 rice genomes , 2014, Nucleic Acids Res..

[2]  Hui Xiang,et al.  Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean , 2015, Nature Biotechnology.

[3]  Rod A Wing,et al.  A reference genome for common bean and genome-wide analysis of dual domestications , 2014, Nature Genetics.

[4]  Kun Lu,et al.  The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes , 2014, Nature Communications.

[5]  Andrea Zuccolo,et al.  Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication , 2014, Nature Biotechnology.

[6]  T. Nishio,et al.  Draft Sequences of the Radish (Raphanus sativus L.) Genome , 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

[7]  Marie E. Bolger,et al.  Plant genome sequencing - applications for crop improvement. , 2014, Current opinion in biotechnology.

[8]  Yeisoo Yu,et al.  Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species , 2014, Nature Genetics.

[9]  Hiroaki Sakai,et al.  Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice , 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

[10]  Ying Li,et al.  A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity , 2013, Nature Genetics.

[11]  S. Jackson,et al.  The First 50 Plant Genomes , 2013 .

[12]  Mukesh Jain,et al.  A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). , 2013, The Plant journal : for cell and molecular biology.

[13]  Yadan Luo,et al.  Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation , 2013, Nature.

[14]  Wenlong Yang,et al.  Draft genome of the wheat A-genome progenitor Triticum urartu , 2013, Nature.

[15]  James K. Hane,et al.  Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement , 2013, Nature Biotechnology.

[16]  Ye Yin,et al.  Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution , 2013, Nature Communications.

[17]  Niranjan Nagarajan,et al.  The draft genome of sweet orange (Citrus sinensis) , 2012, Nature Genetics.

[18]  W. J. Lucas,et al.  The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions , 2012, Nature Genetics.

[19]  Mihaela M. Martis,et al.  A physical, genetic and functional sequence assembly of the barley genome. , 2022 .

[20]  Simon Hawkins,et al.  The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. , 2012, The Plant journal : for cell and molecular biology.

[21]  Yaqin Ma,et al.  Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat1[W][OA] , 2012, Plant Physiology.

[22]  P. Kersey,et al.  Analysis of the bread wheat genome using whole genome shotgun sequencing , 2012, Nature.

[23]  A. Fujiyama,et al.  A map of rice genome variation reveals the origin of cultivated rice , 2012, Nature.

[24]  John Z. Yu,et al.  The draft genome of a diploid cotton Gossypium raimondii , 2012, Nature Genetics.

[25]  Saravanaraj N. Ayyampalayam,et al.  The banana (Musa acuminata) genome and the evolution of monocotyledonous plants , 2012, Nature.

[26]  R. Guigó,et al.  The genome of melon (Cucumis melo L.) , 2012, Proceedings of the National Academy of Sciences.

[27]  Jian Wang,et al.  Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential , 2012, Nature Biotechnology.

[28]  Justin N. Vaughn,et al.  Reference genome sequence of the model plant Setaria , 2012, Nature Biotechnology.

[29]  Huanming Yang,et al.  Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers , 2011, Nature Biotechnology.

[30]  The first draft of the pigeonpea genome sequence , 2011, Journal of Plant Biochemistry and Biotechnology.

[31]  Alvaro J. González,et al.  The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.

[32]  J. Poulain,et al.  The genome of the mesopolyploid crop species Brassica rapa , 2011, Nature Genetics.

[33]  David M. A. Martin,et al.  Genome sequence and analysis of the tuber crop potato , 2011, Nature.

[34]  Henry D. Priest,et al.  The genome of woodland strawberry (Fragaria vesca) , 2011, Nature Genetics.

[35]  Roger E Bumgarner,et al.  The genome of the domesticated apple (Malus × domestica Borkh.) , 2010, Nature Genetics.

[36]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[37]  Asan,et al.  The genome of the cucumber, Cucumis sativus L. , 2009, Nature Genetics.

[38]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[39]  M. Freeling,et al.  Conserved noncoding sequences (CNSs) in higher plants. , 2009, Current opinion in plant biology.

[40]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[41]  H. Mori,et al.  Genome Structure of the Legume, Lotus japonicus , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.

[42]  Stephen M. Mount,et al.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) , 2008, Nature.

[43]  J. Salse,et al.  Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution[W] , 2008, The Plant Cell Online.

[44]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[45]  Steven Maere,et al.  Genome duplication and the origin of angiosperms. , 2005, Trends in ecology & evolution.

[46]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica) , 2002, Science.

[47]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[48]  J. Kader.  LIPID-TRANSFER PROTEINS IN PLANTS. , 1996, Annual review of plant physiology and plant molecular biology.

[49]  M. Kuntz,et al.  Metabolism of cyclic carotenoids: a model for the alteration of this biosynthetic pathway in Capsicum annuum chromoplasts. , 1995, The Plant journal : for cell and molecular biology.

[50]  D. J. Bennett,et al.  Constitution and biosynthesis of capsaicin , 1968 .

[51]  Yasuko Takahashi,et al.  Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events , 2022 .