A sweet potato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers.
BACKGROUND
Sweetpotato (Ipomoea batatas (L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpotato is in striking contrast to its importance for human nutrition. Previously existing sequence data were restricted to around 22,000 expressed sequence tag (EST) sequences and ~ 1,500 GenBank sequences. We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species.


RESULTS
Two quarter 454 pyrosequencing runs used two normalized cDNA collections from stems and leaves from drought-stressed sweetpotato clone Tanzania and yielded 524,209 reads, which were assembled together with 22,094 publically available expressed sequence tags into 31,685 sets of overlapping DNA segments and 34,733 unassembled sequences. Blastx comparisons with the UniRef100 database allowed annotation of 23,957 contigs and 15,342 singletons resulting in 24,657 putatively unique genes. Further, 27,119 sequences had no match to protein sequences of UniRef100database. On the basis of this gene index, we have identified 1,661 gene-based microsatellite sequences, of which 223 were selected for testing and 195 were successfully amplified in a test panel of 6 hexaploid (I. batatas) and 2 diploid (I. trifida) accessions.


CONCLUSIONS
The sweetpotato gene index is a useful source for functionally annotated sweetpotato gene sequences that contains three times more gene sequence information for sweetpotato than previous EST assemblies. A searchable version of the gene index, including a blastn function, is available at http://www.cipotato.org/sweetpotato_gene_index.
Schafleitner
Roland
R
Germplasm Enhancement and Crop Improvement Division, International Potato Center, La Molina, Lima, Peru. roland.schafleitner@worldveg.org
Tincopa
Luz R
LR
Palomino
Omar
O
Rossel
Genoveva
G
Robles
Ronald F
RF
Alagon
Rocio
R
Rivera
Carlos
C
Quispe
Cynthia
C
Rojas
Luis
L
Pacheco
Jaime A
JA
Solis
Julio
J
Cerna
Diogenes
D
Kim
Ji Young
JY
Hou
Jack
J
Simon
Reinhard
R
D001483:Base Sequence; D020451:Contig Mapping; D057225:Data Mining; D020224:Expressed Sequence Tags; D017343:Genes, Plant / Q000235:genetics*; D027723:Ipomoea batatas / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA / Q000379:methods*; D013696:Temperature