Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data. Liu Kai,Zhao Shugang,Wang Shuang,Wang Hongxia,Zhang Zhihua BMC genomics BACKGROUND:Walnut kernels contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids for humans and have important effects on growth and health. The main function of fatty acid desaturase (FAD), which is widely distributed in organisms, is to remove hydrogen from carbon chains in the biosynthesis of unsaturated fatty acids to generate C=C bonds. RESULTS:By performing a series of bioinformatics analysis, 24 members of the JrFAD gene family were identified from the genome database of walnut, and then compared with the homologous genes from Arabidopsis. Phylogenetic analysis showed that JrFADs were classified into four subfamilies: the SAD desaturase subfamily, Δ7/Δ9 desaturase subfamily, Δ12/ω-3 desaturase subfamily and "front-end" desaturase subfamily. Meanwhile, the expression of fatty acid synthesis genes in walnut kernels at different developmental stages was analysed by transcriptome sequencing, with expression of JrFAD3-1, which encodes an enzyme involved in linolenic acid synthesis, being particularly prominent. The relative expression level of JrFAD3-1 changed dramatically with the kernel development stages and exhibited a Bell-Shaped Curve. A significant positive correlation was observed between the expression of JrFAD3-1 during 70-100 DAF (Days after flowering) and the content of alpha-linolenic acid during 100-130 DAF, with a correlation coefficient of 0.991. Additionally, JrFAD3-1 was proved closely related to homologous genes in Betula pendula and Corylus heterophylla, indicating that the conserved structure of FADs is consistent with classical plant taxonomy. CONCLUSION:Twenty-four members JrFADs in walnut were identified and classified into four subfamilies. JrFAD3-1 may play significant roles in the biosynthesis of polyunsaturated fatty acids in walnut. 10.1186/s12864-020-6692-z

Transcriptome Analysis of Walnut ( L.) Embryos Reveals Key Developmental Stages and Genes Involved in Lipid Biosynthesis and Polyunsaturated Fatty Acid Metabolism. Huang Ruimin,Zhou Ye,Zhang Junpei,Ji Feiyang,Jin Feng,Fan Wei,Pei Dong Journal of agricultural and food chemistry Walnut ( L.) is a widely cultivated woody oilseed tree species, and its embryo is rich in polyunsaturated fatty acids. Thus far, the pathways and essential genes involved in oil biosynthesis in developing walnut embryos remain largely unclear. Our analyses revealed that a mature walnut embryo accumulated 69% oil, in which 71% were polyunsaturated fatty acids with 64% linoleic acid and 7% linolenic acid. RNA sequencing generated 39 384 unigenes in 24 cDNA libraries prepared from walnut embryos collected at 49, 63, 77, 91, 105, 119, 133, and 147 days after pollination (DAP). The principal components analysis (PCA) of samples and cluster analysis of differentially expressed genes (DEGs) showed that the total samples were divided into three main groups: 49 DAP, 63-119 DAP, and 133-147 DAP. We identified 108 unigenes associated with lipid biosynthesis, including 60 unigenes for fatty acid biosynthesis, 33 for triacylglycerol biosynthesis, 7 for oil bodies, and 8 for transcription factors. The expression levels of the genes encoding WRI1, ACCase, ACP, KASII, SAD, FAD2, FAD3, and PDAT were upregulated at 63-119 DAP relative to the levels at 49 DAP. Additionally, the lipid biosynthesis in walnut embryos began to increase while oil contents increased from 15 to 69%. We identified eight , three , one , one , one , and three genes. In addition, , , and were highly abundantly expressed in the walnut embryo, and their FPKM values achieved were 834, 2205, and 9038, respectively. High expression levels of and may be the reason why walnuts are rich in polyunsaturated fatty acids. Subcellular localization confirmed that the JrFAD3 protein played a role in the endoplasmic reticulum rather than the plastid, suggesting that linolenic acid was mainly synthesized in the endoplasmic reticulum. Weighted gene coexpression network analysis (WGCNA) showed that , , , and were coexpressed with . Our study provides large-scale and comprehensive transcriptome data of walnut embryo development. These data lay the foundation for the metabolic engineering of walnuts to increase oil contents and modify fatty acid compositions. 10.1021/acs.jafc.0c05598

Integrated Analysis of Seed microRNA and mRNA Transcriptome Reveals Important Functional Genes and microRNA-Targets in the Process of Walnut () Seed Oil Accumulation. Zhao Xinchi,Yang Guiyan,Liu Xiaoqiang,Yu Zhongdong,Peng Shaobing International journal of molecular sciences Walnut () is known as a promising woody oil crop with abundant polyunsaturated fatty acids in its kernel. However, the regulation mechanism of walnut oil accumulation and fatty acid metabolism is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. To reveal the molecular mechanism of walnut oil accumulation, considering the potential regulation of microRNA (miRNA) in seed development, in this study, the oil content of walnut kernel on the 80th, 100th and 120th day after flowering (DAF) was tested and the corresponding proportions are 11.51%, 40.40% and 53.20%. Between DAF of 80th~120th, the content of stearic acid and oleic acid tended to increase, but the proportion of other fatty acids tended to decrease. Meanwhile, comparative transcriptome and sRNA-seq analysis on three stages (80th, 100th and 120th DAF), found 204 conserved miRNAs and 554 novel miRNAs in walnut kernels, among which 104 key genes related to walnut oil accumulation were screened. The phospholipid:diacylglycerol acyltransferase metabolic pathway may contribute more to oil accumulation in walnut. 16 miRNA-mRNA regulatory modules related to walnut oil accumulation and fatty acid synthesis were constructed. 8 known miRNAs and 9 novel miRNAs regulate 28 genes involved in fatty acid (FA) metabolism and lipid synthesis. Among them, jre-miRn105, jre-miRn434, jre-miR477d and jre-miR156a.2 are key miRNAs that regulate walnut FA synthesis. Jre-miRn411 and jre-miR399a.1 are closely related to oil accumulation. These data provide new insights and lay the foundation for subsequent studies on walnut FA synthesis and oil accumulation. 10.3390/ijms21239093

Improved de novo chromosome-level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode. Yan Feng,Xi Rui-Min,She Rui-Xue,Chen Peng-Peng,Yan Yu-Jie,Yang Ge,Dang Meng,Yue Ming,Pei Dong,Woeste Keith,Zhao Peng Molecular ecology resources Manchurian walnut (Juglans mandshurica Maxim.) is a synonym of J. cathayensis, a diploid, vulnerable, temperate deciduous tree valued for its wood and nut. It is also valued as a rootstock for Juglans regia because of its reported tolerance of lesion nematode. Reference genomes are available for several Juglans species, our goal was to produce a de novo, chromosome-level assembly of the J. mandshurica genome. Here, we reported an improved assembly of J. mandshurica with a contig N50 size of 6.49 Mb and a scaffold N50 size of 36.1 Mb. The total genome size was 548 Mb encoding 29,032 protein coding genes which were annotated. The collinearity analysis showed that J. mandshurica and J. regia originated from a common ancestor, with both species undergoing two WGD events. A genomic comparison showed that J. mandshurica was missing 1657 genes found in J. regia, and J. mandshurica includes 2827 genes not found in of the J. regia genome. The J. mandshurica contained 1440 unique paralogues that were highly enriched for flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction. Four gene families related to disease resistance notable contraction (rapidly evolving; LEA, WAK, PPR, and PR) in J. mandshurica compared to eight species. JmaPR10 and JmaPR8 contained three orthologous gene pairs with J. regia that were highly expressed in root bark. JmaPR10 is a strong candidate gene for lesion nematodes resistance in J. mandshurica. The J. mandshurica genome should be a useful resource for study of the evolution, breeding, and genetic variation in walnuts (Juglans). 10.1111/1755-0998.13394