Genome-wide identification and expression profiles of ABCB gene family in Chinese hickory (Carya cathayensis Sarg.) during grafting

High-quality genome assembly and genetic transformation system of Lasiodiplodia theobromae strain LTTK16-3, a fungal pathogen of Chinese hickory

Lasiodiplodia theobromae, as one of the causative agents associated with Chinese hickory trunk cankers, has caused huge economic losses to the Chinese hickory industry. Although the biological characteristics of this pathogen and the occurrence pattern of this disease have been well studied, few studies have addressed the related mechanisms due to the poor molecular and genetic study basis of this fungus. In this study, we sequenced and assembled L. theobromae strain LTTK16-3, isolated from a Chinese hickory tree (cultivar of Linan) in Linan, Zhejiang province, China. Phylogenetic analysis and comparative genomics analysis presented crucial cues in the prediction of LTTK16-3, which shared similar regulatory mechanisms of transcription, DNA replication, and DNA damage response with the other four Chinese hickory trunk canker-associated Botryosphaeria strains including, Botryosphaeria dothidea, Botryosphaeria fabicerciana, Botryosphaeria qingyuanensis, and Botryosphaeria corticis. Moreover, it contained 18 strain-specific protein clusters (not conserved in the other L. theobromae strains, AM2As and CITRA15), with potential roles in specific host-pathogen interactions during the Chinese hickory infection. Additionally, an efficient system for L. theobromae protoplast preparation and polyethylene glycol (PEG) -mediated genetic transformation was firstly established as the foundation for its future mechanisms study. Collectively, the high-quality genome data and the efficient transformation system of L. theobromae here set up the possibility of targeted molecular improvements for Chinese hickory canker control.IMPORTANCEFungi with disparate genomic features are physiologically diverse, possessing species-specific survival strategies and environmental adaptation mechanisms. The high-quality genome data and related molecular genetic studies are the basis for revealing the mechanisms behind the physiological traits that are responsible for their environmental fitness. In this study, we sequenced and assembled the LTTK16-3 strain, the genome of Lasiodiplodia theobromae first obtained from a diseased Chinese hickory tree (cultivar of Linan) in Linan, Zhejiang province, China. Further phylogenetic analysis and comparative genomics analysis provide crucial cues in the prediction of the proteins with potential roles in specific host-pathogen interactions during the Chinese hickory infection. An efficient PEG-mediated genetic transformation system of L. theobromae was established as the foundation for the future mechanisms exploration. The above genetic information and tools set up valuable clues to study L. theobromae pathogenesis and assist in Chinese hickory canker control.

Genome-wide identification and expression analysis of AUX/LAX family genes in Chinese hickory (Carya cathayensis Sarg.) Under various abiotic stresses and grafting

Auxin is essential for regulating plant growth and development as well as the response of plants to abiotic stresses. AUX/LAX proteins are auxin influx transporters belonging to the amino acid permease family of proton-driven transporters, and are involved in the transport of indole-3-acetic acid (IAA). However, how AUX/LAX genes respond to abiotic stresses in Chinese hickory is less studied. For the first time identification, structural characteristics as well as gene expression analysis of the AUX/LAX gene family in Chinese hickory were conducted by using techniques of gene cloning and real-time fluorescent quantitative PCR. Eight CcAUX/LAXs were identified in Chinese hickory, all of which had the conserved structural characteristics of AUX/LAXs. CcAUX/LAXs were most closely related to their homologous proteins in Populus trichocarpa , which was in consistence with their common taxonomic character of woody trees. CcAUX/LAXs exhibited different expression profiles in different tissues, indicating their varying roles during growth and development. A number of light-, hormone-, and abiotic stress responsive cis-acting regulatory elements were detected on the promoters of CcAUX/LAX genes. CcAUX/LAX genes responded differently to drought and salt stress treatments to varying degrees. Furthermore, CcAUX/LAX genes exhibited complex expression changes during Chinese hickory grafting. These findings not only provide a valuable resource for further functional validation of CcAUX/LAXs, but also contribute to a better understanding of their potential regulatory functions during grafting and abiotic stress treatments in Chinese hickory.

Expression analysis of PIN family genes in Chinese hickory reveals their potential roles during grafting and salt stress

Grafting is an effective way to improve Chinese hickory while salt stress has caused great damage to the Chinese hickory industry. Grafting and salt stress have been regarded as the main abiotic stress types for Chinese hickory. However, how Chinese hickory responds to grafting and salt stress is less studied. Auxin has been proved to play an essential role in the stress response through its re-distribution regulation mediated by polar auxin transporters, including PIN-formed (PIN) proteins. In this study, the PIN gene family in Chinese hickory (CcPINs) was identified and structurally characterized for the first time. The expression profiles of the genes in response to grafting and salt stress were determined. A total of 11 CcPINs with the open reading frames (ORFs) of 1,026-1,983 bp were identified. Transient transformation in tobacco leaves demonstrated that CcPIN1a, CcPIN3, and CcPIN4 were localized in the plasma membrane. There were varying phylogenetic relationships between CcPINs and homologous genes in different species, but the closest relationships were with those in Carya illinoinensis and Juglans regia. Conserved N- and C-terminal transmembrane regions as well as sites controlling the functions of CcPINs were detected in CcPINs. Five types of cis-acting elements, including hormone- and stress-responsive elements, were detected on the promoters of CcPINs. CcPINs exhibited different expression profiles in different tissues, indicating their varied roles during growth and development. The 11 CcPINs responded differently to grafting and salt stress treatment. CcPIN1a might be involved in the regulation of the grafting process, while CcPIN1a and CcPIN8a were related to the regulation of salt stress in Chinese hickory. Our results will lay the foundation for understanding the potential regulatory functions of CcPIN genes during grafting and under salt stress treatment in Chinese hickory.