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Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple
ZHANG Li-hua, ZHU Ling-cheng, XU Yu, LÜ Long, LI Xing-guo, LI Wen-hui, LIU Wan-da, MA Feng-wang, LI Ming-jun, HAN De-guo
2023, 22 (7): 2080-2093.   DOI: 10.1016/j.jia.2023.05.024
Abstract241)      PDF in ScienceDirect      

Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality.  However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking.  In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1.  The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological functions and biochemical properties were analyzed.  A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion.  The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication.  Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies.  In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development.  Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit.  The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.

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Genome-wide analysis of OVATE family proteins in cucumber (Cucumis sativus L.)
HAN Li-jie, SONG Xiao-fei, WANG Zhong-yi, LIU Xiao-feng, YAN Li-ying, HAN De-guo, ZHOU Zhao-yang, ZHANG Xiao-lan
2022, 21 (5): 1321-1331.   DOI: 10.1016/S2095-3119(21)63788-7
Abstract245)      PDF in ScienceDirect      
OVATE family proteins (OFPs) are plant-specific proteins with a conserved OVATE domain that regulate plant growth and development.  Although OFPs have been studied in several species, their biological functions remain largely unknown in cucumber (Cucumis sativus L.).  This study identified 19 CsOFPs distributed on seven chromosomes in cucumber.  Most CsOFP genes were expressed in reproductive organs, but with different expression patterns.  Ectopic expression of CsOFP12-16c in Arabidopsis resulted in shorter and blunt siliques.  The overall results indicated that CsOFP12-16c regulates silique development in Arabidopsis and may have a similar function in cucumber.
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Genome-wide identification and expression analysis of asparagine synthetase family in apple
YUAN Xi-sen, YU Zi-peng, LIU Lin, XU Yang, ZHANG Lei, HAN De-guo, ZHANG Shi-zhong
2020, 19 (5): 1261-1273.   DOI: 10.1016/S2095-3119(20)63171-9
Abstract106)      PDF in ScienceDirect      
Asparagine is an efficient nitrogen transport and storage carrier.  Asparagine synthesis occurs by the amination of aspartate which is catalyzed by asparagine synthetase (ASN) in plants.  Complete genome-wide analysis and classifications of the ASN gene family have recently been reported in different plants.  However, systematic analysis and expression profiles of these genes have not been performed in apple (Malus domestica).  Here, a comprehensive bioinformatics approach was applied to identify MdASNs in apple.  Then, plant phylogenetic tree, chromosome location, conserved protein motif, gene structure, and expression pattern of MdASNs were analyzed.  Five members were identified and distributed on 4 chromosomes with conserved GATase-7 and ASN domains.  Expression analysis indicated that all MdASNs mRNA accumulated at the highest level in reproductive organs, namely flowers or fruits, which may be associated with the redistribution of free amino acids in plant metabolic organs and reservoirs.  Additionally, most of MdASNs were dramatically up-regulated under various nitrogen supplies, especially in the aboveground part.  Taken together, MdASNs may be assigned to be responsible for the nitrogen metabolism and asparagine synthesis in apple.
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