Genome-Wide Analysis of the GDSL Genes in Pecan (Carya illinoensis K. Koch): Phylogeny, Structure, Promoter Cis-Elements, Co-Expression Networks, and Response to Salt Stresses

Abstract

The Gly-Asp-Ser-Leu (GDSL)-lipase family is a large subfamily of lipolytic enzymes that plays an important role in plant growth and defense against environmental stress. However, little is known about their function in pecans (Carya illinoensis K. Koch). In this study, 87 CilGDSLs were identified and divided into 2 groups and 12 subgroups using phylogenetic analysis; members of the same sub-branch had conserved gene structure and motif composition. The majority of the genes had four introns and were composed of an α-helix and a β-strand. Subcellular localization analysis revealed that these genes were localized in the extracellular matrix, chloroplasts, cytoplasm, nucleus, vacuole, and endoplasmic reticulum, and were validated by transient expression in tobacco mesophyll cells. Furthermore, the analysis of the promoter cis-elements for the CilGDSLs revealed the presence of plant anaerobic induction regulatory, abscisic acid response, light response elements, jasmonic acid (JA) response elements, etc. The qRT-PCR analysis results in “Pawnee” with salt treatment showed that the CilGDSL42.93 (leaf) and CilGDSL39.88 (root) were highly expressed in different tissues. After salt stress treatment, isobaric tags for relative and absolute quantitation (iTRAQ) analysis revealed the presence of a total of ten GDSL proteins. Moreover, the weighted gene co-expression network analysis (WGCNA) showed that one set of co-expressed genes (module), primarily CilGDSL41.11, CilGDSL39.49, CilGDSL34.85, and CilGDSL41.01, was significantly associated with salt stress in leaf. In short, some of them were shown to be involved in plant defense against salt stress in this study.

The binding pocket properties were fundamental to functional diversification of the GDSL-type esterases/lipases gene family in cotton

“…The results highlighted notable differences in the structures of the 16 GELPs. Similar results were reported by Jiao et al. (2022) , in which the spatial structures of CilGDSL in pecans were also different.…”

“…The results highlighted notable differences in the structures of the 16 GELPs. Similar results were reported by Jiao et al (2022), in which the spatial structures of CilGDSL in pecans were also different. Our molecular docking experiment revealed that the number of docking ligands varied greatly between individual proteins.…”

“…A large number of GELP genes are present in plants. Different numbers (65–194) of GDSL genes have been reported in different plants ( Chepyshko et al., 2012 ; Dong et al., 2016 ; Lai et al., 2017 ; Cao et al., 2018 ; An et al., 2019 ; Li et al., 2019 ; Ni et al., 2020 ; Su et al., 2020 ; Lv et al., 2021 ; Ren et al., 2021 ; Zhang et al., 2021 ; Jiao et al., 2022 ; Sun et al., 2022 ; Zhang et al., 2022 ). Therefore, it was not difficult to find that allotetraploid cotton harboured a larger number of GELP genes.…”

Genome-wide exploration of the GDSL-type esterase/lipase gene family in rapeseed reveals several BnGELP proteins active during early seedling development

“…A crucial first step in transferring the knowledge acquired for model species to non-model species is homology identification. To date, the GELP family has been identified in diverse plant species including many with fully sequenced genomes, such as Arabidopsis thaliana (105 members) , Dasypyrum villosum (193) , Sedum alfredii (80), Nicotiana tabacum (159), Glycine max (194) , Oryza sativa (114) , Dendrobium catenatum (52), Carya illinoensis (87) , Zea mays (103) , Vitis vinifera (83), Brassica rapa (121), and six species in the Rosaceae family ( Pyrus bretschneideri , Malus domestica , Prunus mume , Prunus persica , Fragaria vesca and Prunus avium ; for a total of 597 GELP s) ( Chepyshko et al., 2012 ; Dong et al., 2016 ; Lai et al., 2017 ; Ding et al., 2019b ; Su et al., 2020 ; Lv et al., 2021 ; Wang et al., 2021 ; Zhang et al., 2021 ; Cenci et al., 2022 ; Jiao et al., 2022 ; Shen et al., 2022 ). Some GELP genes have been cloned and functionally characterized in B. napus , such as BnLIP2 ( Ling et al., 2006 ), Bn SCE3 ( Clauss et al., 2008 ), BnGDSL1 ( Ding et al., 2019a ), and BnSFAR1 - 5 ( Karunarathna et al., 2020 ).…”

Nitrogen Allocation Tradeoffs Within-Leaf between Photosynthesis and High-Temperature Adaptation among Different Varieties of Pecan (Carya illinoinensis [Wangenh.] K. Koch)

“…Throughout those habitats, pecans generally develop under a range of climatic conditions with complicated and volatile temperature ranges and cumulative precipitation during the growing season [ 24 , 26 ]. Meanwhile, climate change has also been altering the situation and a growing number of reports have been published on various responses of pecan to environmental factors to understand its decreased growth or survival [ 24 , 27 , 28 ]. Variety identification, including dramatic phenotypic and physiological diversifications, is one of the crop-domestication processes for increasing yield and high-quality crops [ 29 ].…”