Rooting gene trees without outgroups: EP rooting

Identification of MYC genes in four Cucurbitaceae species and their roles in the response to temperature stress

BACKGROUND

Myelocytomatosis (MYC) transcription factors are crucial mediators of the response of plants to environmental stresses through via binding to DNA regulatory regions. However, few systematic characterizations of MYC genes are available in Cucurbitaceae species.

RESULTS

In this study, we identified 10, 8, 12, and 10 MYC genes in Cucumis sativus, Cucumis melo, Citrullus lanatus, and Benincasa hispida, respectively. Characterization revealed that all of the MYC proteins contain a highly conserved H4-V5-E6-E8-R9-R11-R12 sequence, which is essential for the binding of DNA regulatory regions. Evolutionary analysis enabled us to categorize 40 predicted MYC proteins from seven species into five distinct groups and revealed that the expansion of the MYC genes occurred before the divergence of monocots and dicots. The upstream promoter regions of the MYC genes contain a variety of developmental, stress, and hormone-responsive regulatory elements. The expression of cucumber MYC genes varies significantly across organs, with particularly high expression of CsaV3_3G001710 observed across all organs. Transcriptomic analysis revealed that certain cucumber MYC genes undergo specific upregulation or downregulation in response to both biotic and abiotic stressors. In particular, under temperature stress, the cucumber genes CsaV3_3G007980 and CsaV3_3G001710 were significantly upregulated. Interestingly, the homologs of these two genes in C. lanatus presented a similar expression pattern to that in C. sativus, whereas in B. hispida, they presented the opposite pattern, i.e., significant downregulation. These findings indicated that these two genes indeed respond to temperature stress but with different expression patterns, highlighting the divergent functions of homologous genes across different species.

CONCLUSIONS

This study analyzed the size and composition of the MYC gene family in four Cucurbitaceae species and investigated stress-responsive expression profiles, especially under temperature stress. All the results showed that MYC genes play important roles in development and stress responses, laying a theoretical foundation for further investigations of these response mechanisms.

Genome-wide analysis of a putative lipid transfer protein LTP_2 gene family reveals CsLTP_2 genes involved in response of cucumber against root-knot nematode (Meloidogyne incognita)

Plant lipid transfer proteins (LTPs) are small basic proteins that play important roles in the regulation of various plant biological processes as well as the response to biotic and abiotic stresses. However, knowledge is limited on how this family of proteins is regulated in response to nematode infection in cucumber. In the present study, a total of 39 CsLTP_2 genes were identified by querying databases for cucumber-specific LTP_2 using a Hidden Markov Model approach and manual curation. The family has a five-cysteine motif (5CM) with the basic form CC-Xn-CXC-Xn-C, which differentiates it from typical nsLTPs. The members of CsLTP_2 were grouped into six families according to their structure and their phylogenetic relationships. Expression data of CsLTP_2 genes in 10 cucumber tissues indicated that they were tissue-specific genes. Two genes showed significant expression change in roots of resistant and susceptible lines during nematode infection, indicating their involvement in response to Meloidogyne incognita. This systematic analysis provides a foundation of knowledge for future studies of the biological roles of CsLTP_2 genes in cucumber in response to nematode infection and may help in the efforts to improve M. incognita-resistance breeding in cucumber.