IsoSeq transcriptome assembly of C IsoSeq transcriptome assembly of C 33 panicoid grasses provides panicoid grasses provides tools to study evolutionary change in the Panicoideae tools to study evolutionary change in the Panicoideae

The number of plant species with genomic and transcriptomic data has been increas-ing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C 4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C 3 panicoid grass species: Dichanthelium oligosanthes ,

[1]  R. Leegood.  C 4 Photosynthesis , 2021, eLS.

[2]  James C. Schnable,et al.  Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize. , 2019, The Plant journal : for cell and molecular biology.

[3]  Ying Li,et al.  Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis , 2019, BMC Plant Biology.

[4]  J. Bennetzen,et al.  Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia , 2019, bioRxiv.

[5]  Hui Zhang,et al.  The genome of broomcorn millet , 2019, Nature Communications.

[6]  Songnian Hu,et al.  PacBio full‐length cDNA sequencing integrated with RNA‐seq reads drastically improves the discovery of splicing transcripts in rice , 2018, The Plant journal : for cell and molecular biology.

[7]  Anna Lipzen,et al.  The genomic landscape of molecular responses to natural drought stress in Panicum hallii , 2018, Nature Communications.

[8]  J. Keilwagen,et al.  A chromosome‐scale assembly of the model desiccation tolerant grass Oropetium thomaeum , 2018, bioRxiv.

[9]  B. Simmons,et al.  A mosaic monoploid reference sequence for the highly complex genome of sugarcane , 2018, Nature Communications.

[10]  Wenqin Wang,et al.  Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes , 2018, Genes.

[11]  James C. Schnable,et al.  Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses , 2017, Scientific Reports.

[12]  C. Osborne,et al.  Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis , 2017, Molecular biology and evolution.

[13]  O. P. Yadav,et al.  Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments , 2017, Nature Biotechnology.

[14]  David L Adelson,et al.  Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis , 2017, Cell Discovery.

[15]  Shailaja Hittalmani,et al.  Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties , 2017, BMC Genomics.

[16]  Kevin L. Schneider,et al.  Improved maize reference genome with single-molecule technologies , 2017, Nature.

[17]  Rebecca L. Roston,et al.  Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize[OPEN] , 2017, Plant Cell.

[18]  E. Kellogg,et al.  The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes , 2016, Genome Biology.

[19]  James C. Schnable,et al.  Cross species selection scans identify components of C4 photosynthesis in the grasses , 2016, Journal of experimental botany.

[20]  Saravanaraj N. Ayyampalayam,et al.  A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales , 2016, Genome biology and evolution.

[21]  Haibao Tang,et al.  Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum , 2015, Nature.

[22]  James C. Schnable,et al.  Phylogeny and photosynthesis of the grass tribe Paniceae. , 2015, American journal of botany.

[23]  C. Osborne,et al.  Genetic enablers underlying the clustered evolutionary origins of C4 photosynthesis in angiosperms. , 2015, Molecular biology and evolution.

[24]  L. Farinelli,et al.  Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef) , 2014, BMC Genomics.

[25]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[26]  Xiandong Meng,et al.  A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing , 2014, Scientific Reports.

[27]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

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

[29]  D. Schwartz,et al.  Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data , 2013, Rice.

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

[31]  J. Schmutz,et al.  The Switchgrass Genome: Tools and Strategies , 2011 .

[32]  J. Hibberd,et al.  The role of proteins in C(3) plants prior to their recruitment into the C(4) pathway. , 2011, Journal of experimental botany.

[33]  Brent S. Pedersen,et al.  Screening synteny blocks in pairwise genome comparisons through integer programming , 2011, BMC Bioinformatics.

[34]  Sai Guna Ranjan Gurazada,et al.  Genome sequencing and analysis of the model grass Brachypodium distachyon , 2010, Nature.

[35]  Pamela J Green,et al.  Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses , 2010, Genome Biology.

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

[37]  Haibao Tang,et al.  Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses , 2009, Genome Biology.

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

[39]  M. Freeling,et al.  How to usefully compare homologous plant genes and chromosomes as DNA sequences. , 2008, The Plant journal : for cell and molecular biology.

[40]  Gerard Talavera,et al.  Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.

[41]  V. Savolainen,et al.  C4 Photosynthesis Evolved in Grasses via Parallel Adaptive Genetic Changes , 2007, Current Biology.

[42]  Dawei Li,et al.  The Genomes of Oryza sativa: A History of Duplications , 2005, PLoS biology.

[43]  E. Kellogg,et al.  A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. , 2001, American journal of botany.

[44]  J. Sheen.  Molecular mechanisms underlying the differential expression of maize pyruvate, orthophosphate dikinase genes. , 1991, The Plant cell.

[45]  C. Glackin,et al.  Organ-specific transcripts of different size and abundance derive from the same pyruvate, orthophosphate dikinase gene in maize. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[46]  H. O. Yates.  Revision of Grasses Traditionally Referred to Uniola, II. Chasmanthium , 1966 .

[47]  H. O. Yates.  REVISION OF GRASSES TRADITIONALLY REFERRED TO UNIOLA, I. UNIOLA AND LEPTOCHLOOPSIS' , 1966 .

[48]  T. Brutnell,et al.  Setaria viridis as a Model for C 4 Photosynthesis , 2017 .

[49]  M. Gonzalez-Garay.  Introduction to Isoform Sequencing Using Pacific Biosciences Technology (Iso-Seq) , 2016 .

[50]  E. Kellogg.  VIII. Subfamily Panicoideae Link (1827) , 2015 .

[51]  H. Ellegren.  Genome sequencing and population genomics in non-model organisms. , 2014, Trends in ecology & evolution.

[52]  T. Hodkinson,et al.  New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. , 2012, The New phytologist.

[53]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[54]  H. Kibbler,et al.  Physiological adaptations of Hymenachne amplexicaulis to flooding , 1999 .