Searchable transcriptome databases were derived from weed species sequenced at Auburn University in collaboration with other university partners. Other sequenced transciptomes were derived from the NCBI Transcriptome Shotgun (TSA) Assembly Database (https://www.ncbi.nlm.nih.gov/genbank/tsa/) using the Sequence Set Browser (https://www.ncbi.nlm.nih.gov/Traces/wgs/?term=tsa). Sequences acquired from TSA were annotated using Trinotate by first assigning a fake Trinity assembly identifier and using the autotrinotate script. Full credit is given to the authors of the submitted NCBI submitted transcriptomes. Unless otherwise noted, RNA was extracted and sequenced from a developing leaf.

Species Assesmbled by Dr. McElroy

Species Common Name Sequencing Read Source and Number Assembler Number Contigs Assembled Annotation Software Unannotated Contigs Percent Annotated Contributor Associated publication Download Fasta
Eleusine indica goosegrass Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Multiple assemblers (SoapDeNovo, Trinity, Velvet, and CLC) refined with EvidentialGene 29,774 Blast2Go 7,093 76.2 J.S. McElroy, Auburn University doi:10.3835/plantgenome2014.10.0064
Poa infirma weak bluegrass Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Multiple assemblers (SoapDeNovo, Trinity, Velvet, and CLC) refined with EvidentialGene 38,117 Blast2Go 9,019 76.3 J.S. McElroy, Auburn University doi:10.3835/plantgenome2015.06.0050
Poa supina supine bluegrass Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Multiple assemblers (SoapDeNovo, Trinity, Velvet, and CLC) refined with EvidentialGene 36,429 Blast2Go 9,188 74.8 J.S. McElroy, Auburn University doi:10.3835/plantgenome2015.06.0050
Poa annua - infirma annual bluegrass - I Genome Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Multiple assemblers (SoapDeNovo, Trinity, Velvet, and CLC) refined with EvidentialGene 28,056 Blast2Go 4,729 83.1 J.S. McElroy, Auburn University doi:10.3835/plantgenome2015.06.0050
Poa annua - supina annual bluegrass - S Genome Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Multiple assemblers (SoapDeNovo, Trinity, Velvet, and CLC) refined with EvidentialGene 27,577 Blast2Go 4,536 83.6 J.S. McElroy, Auburn University doi:10.3835/plantgenome2015.06.0050
Cyperus esculentus yellow nutsedge Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 105,768 Trinotate v2.0.2 47,934 54.7 J.S. McElroy, Auburn University, J.K. Norsworthy, Arkansas http://www.bioone.org/doi/abs/10.1614/WS-D-15-00182.1
Cyperus rotundus purple nutsedge Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 96,727 Trinotate v2.0.2 44,202 54.3 J.S. McElroy, Auburn University, J.K. Norsworthy, Arkansas DOI: 10.1002/ps.3922
Paspalum urvillei vaseygrass Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 308,980 Trinotate v2.0.2 190,254 38.4 J.S. McElroy, Auburn University, P.E. McCullough, Georgia No associated publications
Leptochloa panicoides Amazon sprangletop Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 132,266 Trinotate v2.0.2 54,550 58.8 J.S. McElroy, Auburn University, J.K. Norsworthy, Arkansas http://www.sciencedirect.com/science/article/pii/S0048357516300177
Euphorbia maculata (Chamaesyce maculata) spotted spurge Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 147,145 Trinotate v2.0.2 57,775 60.7 J.S. McElroy, Auburn University, P.E. McCullough, Georgia https://doi.org/10.1614/WS-D-15-00142.1
Cyperus difformis small-flower umbrella sedge Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 81,499 Trinotate v2.0.2 32,355 60.3 J.S. McElroy, Auburn University, J.K. Norsworthy, Arkansas https://doi.org/10.1614/WS-D-14-00147.1
Cyperus iria rice-flat sedge Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 98,755 Trinotate v2.0.2 41,147 58.3 J.S. McElroy, Auburn University, J.K. Norsworthy, Arkansas https://doi.org/10.1614/WS-D-15-00014.1
Plantgo lanceolata buckhorn plantain Illumina HiSeq, Hudson Alpha, 100 bp pe reads, 50 million reads Trinity v2.4.0 89,731 Trinotate v2.0.2 46,399 48.3 J.S. McElroy, Auburn University, Aaron Patton, Purdue University No associated publications

Transcriptomes from the NCBI TSA archive

Prefix Type Organism Bioproject Biosample Other Source Total Length (Mbases) Contigs (#) Unannotated Contigs % Annotated Genbank Link
GEOH01 TSA Ambrosia trifida PRJNA267208 SAMN03195640 Leaf, five node stage 174.9 246,544 150,699 38.8 https://www.ncbi.nlm.nih.gov/nuccore/GEOH00000000.1
GEZL01 TSA Ambrosia artemisifolia PRJNA335689
Not available 126.3 218,533 122,981 43.7 https://www.ncbi.nlm.nih.gov/nuccore/GEZL00000000.1
ACQK01 WGS Amaranthus tuberculatus PRJNA38543 SAMN00008865 Leaf 4.1 15,440 13,839 10.4 https://www.ncbi.nlm.nih.gov/nuccore/ACQK00000000.1
GAPX01 TSA Amaranthus tricolor PRJNA202395 SAMN02142107 Young seedling, in vitro plantlet 37.7 45,529 23,108 49.2 https://www.ncbi.nlm.nih.gov/nuccore/GAPX00000000.1
GBXX01 TSA Lolium multiflorum PRJNA266320 SAMN03164177 Leaf 55.5 55,564 28,656 48.4 https://www.ncbi.nlm.nih.gov/nuccore/GBXX00000000.1
GAYX01 TSA Lolium perenne PRJNA222646 SAMN02566648, SAMN02566649, SAMN02566650, SAMN02566651, SAMN02566652, SAMN02566653 Inflorescence, leaf sheath, mature leaf, meristem root, stem 147.1 185,833 101,741 45.3 https://www.ncbi.nlm.nih.gov/nuccore/GAYX00000000.1
GFJI01 TSA Echinochloa colona PRJNA374405 SAMN06323305, SAMN06323306 Not reported 436.8 435,094 232,267 46.6 https://www.ncbi.nlm.nih.gov/nuccore/GFJI00000000.1
GRM01 TSA Digitaria sanguinalis PRJNA392316 SAMN07291349, SAMN07291350 Not reported 80.7 118,167 69,312 41.7 https://www.ncbi.nlm.nih.gov/nuccore/GFRM00000000.1
GABG01 TSA Ipomoea purpurea PRJNA175931 SAMN01729313, SAMN01729314, SAMN01729315, SAMN01729316, SAMN01729317, SAMN01729318 petals, sepals, leaves at varying growth stages (see NCBI submission for more information) 56.2 61,933 25,562 58.7 https://www.ncbi.nlm.nih.gov/nuccore/GABG00000000.1