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Radhika DH, Nandan M, Gunnaiah R, Doddaraju P, Dumble P, Manjunatha G, Vikram Singh N. Genome and transcriptome exploration reveals receptor-like kinases as potential resistance gene analogs against bacterial blight in pomegranate. Mol Biol Rep 2024; 51:735. [PMID: 38874770 DOI: 10.1007/s11033-024-09670-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/22/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Pomegranate (Punica granatum L.) is a tropical fruit crop of pharma-nutritional importance. However, it faces farming challenges due to pests and diseases, particularly bacterial blight and wilt. Developing resistant cultivars is crucial for sustainable pomegranate cultivation, and understanding resistance's genetic basis is essential. METHODS AND RESULTS We used an extensive resistance gene analogues (RGA) prediction tool to identify 958 RGAs, classified into Nucleotide Binding Site-leucine-rich repeat (NBS-LRR) proteins, receptor-like kinases (RLKs), receptor-like proteins (RLPs), Transmembrane coiled-coil (TM-CC), and nine non-canonical RGAs. RGAs were distributed across all eight chromosomes, with chromosome 02 containing the most RGAs (161), and chromosome 08 having the highest density (4.42 RGA/Mb). NBS-LRR genes were predominantly present on chromosomes 08 and 02, whereas RLKs and RLPs were primarily located on chromosomes 04 and 07. Gene ontology analysis revealed that 475 RGAs were associated with defence against various biotic stresses. Using RNAseq, we identified 120 differentially expressed RGAs, with RLKs (74) being prominent among the differentially expressed genes. CONCLUSION The discovery of these RGAs is a significant step towards breeding pomegranates for pest and disease resistance. The differentially expressed RLKs hold promise for developing resistant cultivars against bacterial blight, thereby contributing to the sustainability of pomegranate cultivation.
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Affiliation(s)
- Dattatraya Hegde Radhika
- Dept. of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, 587104, India
| | - M Nandan
- Dept. of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, 587104, India
| | - Raghavendra Gunnaiah
- Dept. of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, 587104, India.
| | - Pushpa Doddaraju
- Biocontrol Laboratory, Directorate of Research, University of Horticultural Sciences, Bagalkot, 587104, India
| | - Pavan Dumble
- Biocontrol Laboratory, Directorate of Research, University of Horticultural Sciences, Bagalkot, 587104, India
- Research and Development Division-Biodefense, Sea6Energy Private Limited, C-CAMP, NCBS-TIFR Campus, GKVK, Bengaluru, 560065, India
| | - Girigowda Manjunatha
- Biocontrol Laboratory, Directorate of Research, University of Horticultural Sciences, Bagalkot, 587104, India
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Zhao J, Chao K, Wang A. Integrative analysis of metabolome, proteome, and transcriptome for identifying genes influencing total lignin content in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2023; 14:1244020. [PMID: 37771490 PMCID: PMC10525687 DOI: 10.3389/fpls.2023.1244020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
Lignin, a component of plant cell walls, possesses significant research potential as a renewable energy source to replace carbon-based products and as a notable pollutant in papermaking processes. The monolignol biosynthetic pathway has been elucidated and it is known that not all monolignol genes influence the total lignin content. However, it remains unclear which monolignol genes are more closely related to the total lignin content and which potential genes influence the total lignin content. In this study, we present a combination of t-test, differential gene expression analysis, correlation analysis, and weighted gene co-expression network analysis to identify genes that regulate the total lignin content by utilizing multi-omics data from transgenic knockdowns of the monolignol genes that includes data related to the transcriptome, proteome, and total lignin content. Firstly, it was discovered that enzymes from the PtrPAL, Ptr4CL, PtrC3H, and PtrC4H gene families are more strongly correlated with the total lignin content. Additionally, the co-downregulation of three genes, PtrC3H3, PtrC4H1, and PtrC4H2, had the greatest impact on the total lignin content. Secondly, GO and KEGG analysis of lignin-related modules revealed that the total lignin content is not only influenced by monolignol genes, but also closely related to genes involved in the "glutathione metabolic process", "cellular modified amino acid metabolic process" and "carbohydrate catabolic process" pathways. Finally, the cinnamyl alcohol dehydrogenase genes CAD1, CADL3, and CADL8 emerged as potential contributors to total lignin content. The genes HYR1 (UDP-glycosyltransferase superfamily protein) and UGT71B1 (UDP-glucosyltransferase), exhibiting a close relationship with coumarin, have the potential to influence total lignin content by regulating coumarin metabolism. Additionally, the monolignol genes PtrC3H3, PtrC4H1, and PtrC4H2, which belong to the cytochrome P450 genes, may have a significant impact on the total lignin content. Overall, this study establishes connections between gene expression levels and total lignin content, effectively identifying genes that have a significant impact on total lignin content and offering novel perspectives for future lignin research endeavours.
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Affiliation(s)
- Jia Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, China
| | - Kairui Chao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Achuan Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, China
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Bhattarai R, Liu H, Siddique KHM, Yan G. Transcriptomic profiling of near-isogenic lines reveals candidate genes for a significant locus conferring metribuzin resistance in wheat. BMC PLANT BIOLOGY 2023; 23:237. [PMID: 37142987 PMCID: PMC10161546 DOI: 10.1186/s12870-023-04166-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Weeds reduce wheat yields in dryland farming systems. Herbicides such as metribuzin are commonly used to control weeds. However, wheat has a narrow safety margin against metribuzin. Standing crops such as wheat with weeds in the same field can also be killed by the same dose of metribuzin. Therefore, it is important to identify metribuzin resistance genes and understand the resistance mechanism in wheat for sustainable crop production. A previous study identified a significant metribuzin resistance wheat QTL, Qsns.uwa.4 A.2, explaining 69% of the phenotypic variance for metribuzin resistance. RESULTS Two NIL pairs with the most contrasting performance in the metribuzin treatment and different in genetic backgrounds were compared using RNA sequence analysis, identifying nine candidate genes underlying Qsns.uwa.4 A.2 responsible for metribuzin resistance. Quantitative RT-qPCR further validated the candidate genes, with TraesCS4A03G1099000 (nitrate excretion transporter), TraesCS4A03G1181300 (aspartyl protease), and TraesCS4A03G0741300 (glycine-rich proteins) identified as key factors for metribuzin resistance. CONCLUSION Identified markers and key candidate genes can be used for selecting metribuzin resistance in wheat.
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Affiliation(s)
- Rudra Bhattarai
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia.
| | - Kadambot H M Siddique
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, 6009, Perth, WA, Australia
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Nawae W, Naktang C, Charoensri S, U-thoomporn S, Narong N, Chusri O, Tangphatsornruang S, Pootakham W. Resequencing of durian genomes reveals large genetic variations among different cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1137077. [PMID: 36875624 PMCID: PMC9978785 DOI: 10.3389/fpls.2023.1137077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Salisa Charoensri
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Sonicha U-thoomporn
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Nattapol Narong
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Orwintinee Chusri
- Chantaburi Horticulture Research Center, Horticulture Research Institute, Department of Agriculture, Chantaburi, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani, Thailand
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Chelliah A, Arumugam C, Suthanthiram B, Raman T, Subbaraya U. Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp. Funct Integr Genomics 2022; 23:7. [PMID: 36538175 DOI: 10.1007/s10142-022-00925-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.
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Affiliation(s)
- Anuradha Chelliah
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India.
| | - Chandrasekar Arumugam
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Backiyarani Suthanthiram
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Thangavelu Raman
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Uma Subbaraya
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
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Ali MZ, Farid A, Ahmad S, Muzammal M, Mohaini MA, Alsalman AJ, Al Hawaj MA, Alhashem YN, Alsaleh AA, Almusalami EM, Maryam M, Khan MA. In Silico Analysis Identified Putative Pathogenic Missense nsSNPs in Human SLITRK1 Gene. Genes (Basel) 2022; 13:672. [PMID: 35456478 PMCID: PMC9030497 DOI: 10.3390/genes13040672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
Human DNA contains several variations, which can affect the structure and normal functioning of a protein. These variations could be single nucleotide polymorphisms (SNPs) or insertion-deletions (InDels). SNPs, as opposed to InDels, are more commonly present in DNA and may cause genetic disorders. In the current study, several bioinformatic tools were used to prioritize the pathogenic variants in the SLITRK1 gene. Out of all of the variants, 16 were commonly predicted to be pathogenic by these tools. All the variants had very low frequency, i.e., <0.0001 in the global population. The secondary structure of all filtered variants was predicted, but no structural change was observed at the site of variation in any variant. Protein stability analysis of these variants was then performed, which determined a decrease in protein stability of 10 of the variants. Amino acid conservation analysis revealed that all the amino acids were highly conserved, indicating their structural and functional importance. Protein 3D structure of wildtype SLITRK1 and all of its variants was predicted using I-TASSER, and the effect of variation on 3D structure of the protein was observed using the Missense3D tool, which presented the probable structural loss in three variants, i.e., Asn529Lys, Leu496Pro and Leu94Phe. The wildtype SLITRK1 protein and these three variants were independently docked with their close interactor protein PTPRD, and remarkable differences were observed in the docking sites of normal and variants, which will ultimately affect the functional activity of the SLITRK1 protein. Previous studies have shown that mutations in SLITRK1 are involved in Tourette syndrome. The present study may assist a molecular geneticist in interpreting the variant pathogenicity in research as well as diagnostic setup.
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Affiliation(s)
- Muhammad Zeeshan Ali
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Arshad Farid
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Safeer Ahmad
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Muhammad Muzammal
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
| | - Mohammed Al Mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Al Ahsa 31982, Saudi Arabia;
- King Abdullah International Medical Research Center, Al Ahsa 31982, Saudi Arabia
| | - Abdulkhaliq J. Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia;
| | - Maitham A. Al Hawaj
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al Ahsa 31982, Saudi Arabia;
| | - Yousef N. Alhashem
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Sciences Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia; (Y.N.A.); (A.A.A.)
| | | | - Mahpara Maryam
- Department of Zoology, Government College No.1, Dera Ismail Khan 29111, Pakistan;
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan; (M.Z.A.); (A.F.); (S.A.); (M.M.)
- Department of Human Genetics, Sidra Medical and Research Centre, Doha 26999, Qatar
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Cortaga CQ, Lachica JAP, Lantican DV, Ocampo ETM. Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing. J Genet Eng Biotechnol 2022; 20:46. [PMID: 35275322 PMCID: PMC8917249 DOI: 10.1186/s43141-022-00326-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/27/2022] [Indexed: 11/16/2022]
Abstract
Background The Philippines is among the top 10 major exporters of mango worldwide. However, genomic studies of Philippine mangoes remain largely unexplored and lacking. Here, we sequenced the whole genome of the three Philippine mango species, namely, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica “Carabao” variety using Illumina HiSeq 2500, to identify and analyze their genome-wide variants (SNPs and InDels). Results The high confidence variants were identified by successfully mapping 93–95% of the quality-filtered reads to the Alphonso and Tommy Atkins mango reference genomes. Using these two currently available mango genomes, most variants were observed in M. odorata (4,353,063 and 4,277,287), followed by M. altissima (3,392,763 and 3,449,917), and lastly, M. indica Carabao (2,755,267 and 2,852,480). Approximately 50, 46, and 38% of the variants were unique in the three Philippine mango genomes. The analysis of variant effects and functional annotation across the three mango species revealed 56,982 variants with high-impact effects mapped onto 37,746 genes, of which 25% were found to be novel. The affected mango genes include those with potential economic importance such as 6945 genes for defense/resistance/immune response, 323 genes for fruit development, and 338 genes for anthocyanin production. Conclusions To date, this is the first sequencing effort to comprehensively analyze genome-wide variants essential for the development of genome-wide markers specific to these mango species native to the Philippines. This study provides an important genomic resource that can be used for the genetic improvement of mangoes. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00326-3.
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Affiliation(s)
- Cris Q Cortaga
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines. .,Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines.
| | - John Albert P Lachica
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines.,Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Darlon V Lantican
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Eureka Teresa M Ocampo
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines.,Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
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