A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica

Abstract

BackgroundThe obligate parasitic plant witchweed (Striga hermonthica) infects major cereal crops such as sorghum, maize, and millet, and is the most devastating weed pest in Africa. An understanding of the nature of its parasitism would contribute to the development of more sophisticated management methods. However, the molecular and genomic resources currently available for the study of S. hermonthica are limited.ResultsWe constructed a full-length enriched cDNA library of S. hermonthica, sequenced 37,710 clones from the library, and obtained 67,814 expressed sequence tag (EST) sequences. The ESTs were assembled into 17,317 unigenes that included 10,319 contigs and 6,818 singletons. The S. hermonthica unigene dataset was subjected to a comparative analysis with other plant genomes or ESTs. Approximately 80% of the unigenes have homologs in other dicotyledonous plants including Arabidopsis, poplar, and grape. We found that 589 unigenes are conserved in the hemiparasitic Triphysaria species but not in other plant species. These are good candidates for genes specifically involved in plant parasitism. Furthermore, we found 1,445 putative simple sequence repeats (SSRs) in the S. hermonthica unigene dataset. We tested 64 pairs of PCR primers flanking the SSRs to develop genetic markers for the detection of polymorphisms. Most primer sets amplified polymorphicbands from individual plants collected at a single location, indicating high genetic diversity in S. hermonthica. We selected 10 primer pairs to analyze S. hermonthica harvested in the field from different host species and geographic locations. A clustering analysis suggests that genetic distances are not correlated with host specificity.ConclusionsOur data provide the first extensive set of molecular resources for studying S. hermonthica, and include EST sequences, a comparative analysis with other plant genomes, and useful genetic markers. All the data are stored in a web-based database and freely available. These resources will be useful for genome annotation, gene discovery, functional analysis, molecular breeding, epidemiological studies, and studies of plant evolution.

Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum

“…The currently available EST sequences in parasitic plants are still limited to several species; ESTs for three members of the Orobanchaceae family, i.e., S. hermonthica, P. aegyptiaca, and T. versicolor (Yoshida et al, 2010;Yang et al, 2014), the root parasite in Santalales, S. album (sandalwood), and the stem parasite Cuscuta pentagona (Kim et al, 2014;Ranjan et al, 2014) have been reported. The P. japonicum sequences analyzed in this study provide a valuable addition to parasitic plant gene databases and are suitable for conducting comparative analyses with other parasitic species.…”

“…RNA was extracted using a CTAB/LiCl based-protocol as previously reported (Yoshida et al, 2010). Genomic DNA was removed from the RNA samples by treatment with DNase I, Amplification Grade (Life Technologies; Cat.…”

“…In addition, Pirin, a nuclear protein associated with transcription factor activity, was reported to play regulatory roles in haustorium formation in T. versicolor (Bandaranayake et al, 2012). Accumulating information about the genes expressed in the parasitic Orobanchaceae, including ESTs of S. hermonthica (Yoshida et al, 2010), Phelipanche aegyptiaca, and T. versicolor (http://ppgp.huck.psu.edu/) (Yang et al, 2014;Torres et al, 2005), has contributed to our knowledge of the molecular basis of plant parasitism. Recent significant advances in this field include the identification of core parasitism genes through the sequencing of different tissues of three parasitic species in Orobanchaceae (Yang et al, 2014).…”

Characterization of West and Central African accessions from a pearl millet reference collection for agro-morphological traits and Striga resistance

“…Haussmann et al (2001) tested 50 sorghum varieties at two locations in both Mali and Kenya and showed that varieties having high resistance to Striga at one test location were possibly susceptible at another test location. Furthermore, Yoshida et al (2010) used SSR markers to reveal a wide genetic diversity in Striga itself. Therefore, resistant accessions identified in the present Striga resistance trial in Niger should be re-evaluated before being used as resistance source, especially in other countries than our test country Niger.…”

The WRKY45-Dependent Signaling Pathway Is Required For Resistance against Striga hermonthica Parasitism

“…In addition, S. hermonthica seeds and seedlings germinated without hosts were sampled as controls. Total RNA was extracted as reported previously (Yoshida et al, 2010). For quality control of total RNAs, the 260:280 ratio (over 1.8) and the RNA integrity number (over 7) were measured by NanoDrop 1000 (Thermo Scientific) and 2100 Bioanalyzer (Agilent Technologies), respectively.…”