Supplementary Table 2. Comparison of assembly outcomes for selected plant transcriptomes performed by 454 pyrosequencing1
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Plant
Number of Reads
Size (Mb)
Assembler
Assembly Summary
____________________________________________________________________________________________________________
Switchgrass2
928,820
analyzed)
Panicum virgatum
217
Buckwheat3
266,782
Fagopyrum esculentum
92.3
Mira
25,435 contigs (17.8Mb) and 56,766 singletons
75.1% contigs and 25.1% singletons had blast hits at E-val 1x10-6
Buckwheat3
229,031
Fagopyrum tataricum
77.9
Mira
25,401 contigs (17.9Mb) and 42,899 singletons
75.1% contigs and 34.2% singeltons had blast hits at E-val 1x10-6
Bracken Fern4
681,722
Pteridium aquilinum
254
Mira+CAP3
56,256 combined contigs and singletons (30.8Mb)
61.8% combined had blast hits at E-val 1x10-10
Chickpea5
Cicer arietinum
435,018
94.0
CAP3
(Assembly included 21,491 Sanger ESTs)
44,845 contigs and 58,370 singletons
58.5% combined had blast hit at E-val 1x10-10
Wild Rice6
337,830
Oryza longistaminata
87.3
CAP3
41,189 contigs (12.3Mb) and 30,178 singletons
48.4% combined had blast hits at E-val 1x10-5
Horseweed7
411,962
Conyza canadensis
95.8
CAP3+
16,102 contigs (7.1Mb) and 15,681 singletons
EGassembler 57.5% contigs had blast hits at E-val 1x10-3
Newbler
27,687 contigs (12.9Mb) and 170,312 singletons (43,094
70.5% contigs and 45.8% singletons had blast hits at E-val 1x10-3
Waterhemp8
483,225
Amaranthus tuberculatus
112
CAP3+
22,035 contigs (9.6Mb) and 22,434 singletons
EGassembler 70.7% contigs and 46.0% singletons had blast hits at E-val 1x10-3
Barbados Nut9
Jatropha curcas
13.1
Newbler
17,457 contigs (16.0Mb) and 54,002 singletons
91.2% contigs had blast hits at E-val of 1x10-10
877
Newbler
25,998 contigs (18.0Mb) and 178,363 singletons (trimmed to
381,597
Amaranth10
2,700,168
5,113)
Amaranthus hypochondriacus
82.0% isotigs had blast hits at e-value of 1x10-10
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1
De novo 454 sequencing of plants with limited or no genome sequences.
2
This study.
3
Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA (2011) De novo sequencing and
characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 12:30.
4
Der JP, Barker MS, Wickett NJ, dePamphilis CW, Wolf PG (2011) De novo characterization of the gametophyte transcriptome in
bracken fern, Pteridium aquilinum. BMC Genomics 12:99.
5
Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, et al. (2011) Large-scale transcriptome analysis in chickpea (Cicer
arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J. 2011 May 25. doi:
10.1111/j.1467-7652.2011.00625.x. [Epub ahead of print]
6
Yang H, Hu L, Hurek T, Reinhold-Hurek B (2010) Global characterization of the root transcriptome of a wild species of rice, Oryza
longistaminata, by deep sequencing. BMC Genomics 11:705.
7
Peng Y, Abercrombie LL, Yuan JS, Riggins CW, Sammons RD, et al. (2010) Characterization of the horseweed (Conyza canadensis)
transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide
resistance genes. Pest Manag Sci 66(10): 1053-62.
8
Riggins CW, Peng Y, Stewart CN Jr, Tranel PJ (2010) Characterization of de novo transcriptome for waterhemp (Amaranthus
tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Manag Sci
66(10):1042-52.
9
Natarajan P, Parani M (2011) De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX
titanium platform of 454 pyrosequencing. BMC Genomics 12:191.
10
Délano-Frier JP, Avilés-Arnaut H, Casarrubias-Castillo K, Casique-Arroyo G, Castrillón-Arbeláez PA, et al. (2011) Transcriptomic
analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus,
expression profiling in stems and in response to biotic and abiotic stress. BMC Genomics 12:363.
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Supplementary Table 2. Comparison of assembly outcomes for