The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

The main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter was used as a selectable marker. Molecular analysis confirmed the integration, copy number, and the level of expression of the chi26 gene in four independent transgenic events. Chitinase enzyme activity was detected using a standard enzymatic assay. The expression levels of chi26 gene in the different transgenic lines, compared to their respective controls, were determined using qRT-PCR. The transgene was silenced in some transgenic families across generations. Gene silencing in the present study seemed to be random and irreversible. The homozygous transgenic plants of T4, T5, T6, T8, and T9 generations were tested in the field for five growing seasons to evaluate their resistance against rusts and powdery mildew. The results indicated high chitinase activity at T0 and high transgene expression levels in few transgenic families. This resulted in high resistance against wheat rusts and powdery mildew under field conditions. It was indicated by proximate and chemical analyses that one of the transgenic families and the non-transgenic line were substantially equivalent. Transgenic wheat with barley chi26 was found to be resistant even after five generations under artificial fungal infection conditions. One transgenic line was proved to be substantially equivalent as compared to the non-transgenic control.

The pBY520 containing theHordeum vulgare HVA1regulated by the rice actin promoter (Act1 5′) or the JS101 containing the bacterial mannitol-1-phosphate dehydrogenase (mtlD) also regulated by riceAct1 5′and a combination of these two plasmids were transferred into the maize genome, and their stable expressions were confirmed through fourth generations. Plants transcribing a combination of theHVA1+mtlDshowed higher leaf relative water content (RWC) and greater plant survival as compared with their single transgene transgenic plants and with their control plants under drought stress. When exposed to various salt concentrations, plants transcribing theHVA1+mtlDshowed higher fresh and dry shoot and dry root matter as compared with single transgene transgenic plants and with their control plants. Furthermore, the leaves of plants expressing themtlDaccumulated higher levels of mannitol. Plants expressing theHVA1+mtlDimproved plant survival rate under drought stress and enhanced shoot and root biomass under salt stress when compared with single transgene transgenic plants and with their wild-type control plants. The research presented here shows the effectiveness of coexpressing of two heterologous abiotic stress tolerance genes in the maize genome. Future field tests are needed to assure the application of this research.

Wheat is considered the most important cereal crop all over the world. The wheat weevil Sitophilus granarius is a serious insect pests in much of the wheat growing area worldwide and is responsible for significant loss of yield. Avidin proteins has been proposed to function as plant defense agents against insect pests. A synthetic avidin gene was introduced into spring wheat (Triticum aestivum L.) cv. Giza 168 using a biolistic bombardment protocol. The presence and expression of the transgene in six selected T0 transgenic wheat lines were confirmed at the molecular level. Accumulation of avidin protein was detected in transgenic plants compared to non-transgenic plants. Avidin transgene was stably integrated, transcribed and translated as indicated by Southern blot, ELISA, and dot blot analyses, with a high level of expression in transgenic wheat seeds. However, no expression was detected in untransformed wheat seeds. Functional integrity of avidin was confirmed by insect bioassay. The results of bioassay using transgenic wheat plants challenged with wheat weevil revealed 100 % mortality of the insects reared on transgenic plants after 21 days. Transgenic wheat plants had improved resistance to Sitophilus granarius.

Black cutworm (BCW) is an economically important lepidopteran insect. The control of this insect by a Bt toxin and the understanding of the interaction between the Bt toxin and its receptor molecule were the objectives of this research work. A gene coding for a Vip3A receptor molecule was identified, characterized, and cloned, from the brush border membrane vesicles (BBMV) of the BCW. The nucleotide sequence analysis of the cloned putative Vip3A-receptor gene revealed that the gene was 1.3-kb long and exhibited no homology with any gene in the gene bank. We succeeded in identifying and characterizing most of the Vip3A-receptor gene sequence; and the nucleotide sequence analysis of the cloned putative Vip3A-receptor gene (accession no. KX858809) revealed about 92% of the expected sequence was recovered, which exhibited no homology with any gene in the GenBank.