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Wan W, Zhao H, Yu K, Xiang Y, Dai W, Du C, Tian E. Exploration into Natural Variation Genes Associated with Determinate and Capitulum-like Inflorescence in Brassica napus. Int J Mol Sci 2023; 24:12902. [PMID: 37629083 PMCID: PMC10454214 DOI: 10.3390/ijms241612902] [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: 07/16/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Brassica napus is a globally important vegetable and oil crop. The research is meaningful for the yield and plant architecture of B. napus. In this study, one natural mutant line with determinate and capitulum-like inflorescence was chosen for further study. Genetic analysis indicated that the segregation patterns of inflorescences in the F2 populations supported a digenic inheritance model, which was further approved via the BSA-Seq technique. The BSA-Seq method detected two QTL regions on C02 (14.27-18.41 Mb) and C06 (32.98-33.68 Mb) for the genetic control of determinate inflorescences in MT plants. In addition, the expression profile in MT compared with WT was analyzed, and a total of 133 candidate genes for regulating the flower development (75 genes, 56.4%), shoot meristem development (29 genes, 21.8%), and inflorescence meristem development (13 genes, 9.8%) were identified. Then one joint analysis combing BSA-Seq and RNA-Seq identified two candidate genes of BnaTFL1 and BnaAP1 for regulating the MT phenotype. Furthermore, the potential utilization of the MT plants was also discussed.
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Affiliation(s)
- Wei Wan
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
| | - Haifei Zhao
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
| | - Kunjiang Yu
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
| | - Yang Xiang
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Y.X.); (W.D.); (C.D.)
| | - Wendong Dai
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Y.X.); (W.D.); (C.D.)
| | - Caifu Du
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Y.X.); (W.D.); (C.D.)
| | - Entang Tian
- Agricultural College, Guizhou University, Guiyang 550004, China; (W.W.); (H.Z.); (K.Y.)
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Hussin NA, Najimudin N, Ab Majid AH. The de novo transcriptome of workers head of the higher group termite Globitermes sulphureus Haviland (Blattodea: Termitidae). Heliyon 2019; 5:e02969. [PMID: 31872129 PMCID: PMC6909072 DOI: 10.1016/j.heliyon.2019.e02969] [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: 06/28/2019] [Revised: 11/04/2019] [Accepted: 11/28/2019] [Indexed: 11/26/2022] Open
Abstract
The subterranean termite Globitermus sulphureus is an important Southeast Asian pest with limited genomic resources that causes damages to agriculture crops and building structures. Therefore, the main goal of this study was to survey the G. sulphureus transcriptome composition. Here, we performed de novo transcriptome for G. sulphureus workers’ heads using Illumina HiSeq paired-end sequencing technology. A total of 88, 639, 408 clean reads were collected and assembled into 243, 057 transcripts and 193, 344 putative genes. The transcripts were annotated with the Trinotate pipeline. In total, 27, 061 transcripts were successfully annotated using BLASTX against the SwissProt database and 17, 816 genes were assigned to 47, 598 GO terms. We classified 14, 223 transcripts into COG classification, resulting in 25 groups of functional annotations. Next, a total of 12, 194 genes were matched in the KEGG pathway and 392 metabolic pathways were predicted based on the annotation. Moreover, we detected two endogenous cellulases in the sequences. The RT-qPCR analysis showed that there were significant differences in the expression levels of two genes β-glucosidase and endo-β-1,4-glucanase between worker and soldier heads of G. sulphureus. This is the first study to characterize the complete head transcriptome of a higher termite G. sulphureus using a high-throughput sequencing. Our study may provide an overview and comprehensive molecular resource for comparative studies of the transcriptomics and genomics of termites.
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Affiliation(s)
- Nurul Akmar Hussin
- Household and Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
| | - Abdul Hafiz Ab Majid
- Household and Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
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Gene Expression and Diet Breadth in Plant-Feeding Insects: Summarizing Trends. Trends Ecol Evol 2019; 35:259-277. [PMID: 31791830 DOI: 10.1016/j.tree.2019.10.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/18/2019] [Accepted: 10/29/2019] [Indexed: 11/20/2022]
Abstract
Transcriptomic studies lend insights into the role of transcriptional plasticity in adaptation and specialization. Recently, there has been growing interest in understanding the relationship between variation in herbivorous insect gene expression and the evolution of diet breadth. We review the studies that have emerged on insect gene expression and host plant use, and outline the questions and approaches in the field. Many candidate genes underlying herbivory and specialization have been identified, and a few key studies demonstrate increased transcriptional plasticity associated with generalist compared with specialist species. Addressing the roles that transcriptional variation plays in insect diet breadth will have important implications for our understanding of the evolution of specialization and the genetic and environmental factors that govern insect-plant interactions.
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Khattak AN, Wang T, Yu K, Yang R, Wan W, Ye B, Tian E. Exploring the basis of 2-propenyl and 3-butenyl glucosinolate synthesis by QTL mapping and RNA-sequencing in Brassica juncea. PLoS One 2019; 14:e0220597. [PMID: 31626668 PMCID: PMC6799926 DOI: 10.1371/journal.pone.0220597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/04/2019] [Indexed: 01/08/2023] Open
Abstract
Brassica juncea is used as a condiment, as vegetables and as an oilseed crop, especially in semiarid areas. In the present study, we constructed a genetic map using one recombinant inbred line (RIL) of B. juncea. A total of 304 ILP (intron length polymorphism) markers were mapped to 18 linkage groups designated LG01-LG18 in B. juncea. The constructed map covered a total genetic length of 1671.13 cM with an average marker interval of 5.50 cM. The QTLs for 2-propenyl glucosinolates (GSLs) colocalized with the QTLs for 3-butenyl GSLs between At1g26180 and BnapPIP1580 on LG08 in the field experiments of 2016 and 2017. These QTLs accounted for an average of 42.3% and 42.6% phenotypic variation for 2-propenyl and 3-butenyl GSLs, respectively. Furthermore, the Illumina RNA-sequencing technique was used to excavate the genes responsible for the synthesis of GSLs in the siliques of the parental lines of the RIL mapping population, because the bulk of the seed GSLs might originate from the siliques. Comparative analysis and annotation by gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) revealed that 324 genes were involved in GSL metabolism, among which only 24 transcripts were differentially expressed genes (DEGs). Among those DEGs, 15 genes were involved in the biosynthesis and transport of aliphatic GSLs, and their expression patterns were further validated by qRT-PCR analysis. Joint QTL mapping and RNA-sequencing analyses reveal one candidate gene of IIL1 (LOC106416451) for GSL metabolism in B. juncea. These results will be helpful for further fine mapping, gene cloning and genetic mechanisms of 2-propenyl and 3-butenyl GSLs in B. juncea.
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Affiliation(s)
- Aimal Nawaz Khattak
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Tianya Wang
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Kunjiang Yu
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Renqin Yang
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Wei Wan
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Botao Ye
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Entang Tian
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
- * E-mail:
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Zheng JC, Sun SL, Yue XR, Liu TX, Jing X. Phylogeny and evolution of the cholesterol transporter NPC1 in insects. JOURNAL OF INSECT PHYSIOLOGY 2018; 107:157-166. [PMID: 29649482 DOI: 10.1016/j.jinsphys.2018.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 04/08/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Sterols are essential nutrients for eukaryotes. Insects are obligate sterol auxotrophs and must acquire this key nutrient from their diets. The digestive tract is the organ for absorbing nutrients as well as sterols from food. In mice, the Niemann-Pick type C1 Like 1 (NPC1L1) gene is highly expressed in the intestine and is critical for cholesterol absorption. In contrast, the molecular mechanisms for the absorption of dietary sterols in insects have not been well studied. We annotated NPC1 genes in 39 insects from 10 orders using available genomic and transcriptomic information and inferred phylogenetic relationships. Insect NPC1 genes were grouped into two sister-clades, NPC1a and NPC1b, suggesting a likely duplication in the ancestor of insects. The former exhibited weaker gut-biased expression or a complete lack of tissue-biased expression, depending on the species, while the latter was highly enriched in the gut of three lepidopteran species. This result is similar to previous findings in Drosophila melanogaster. In insects, NPC1a accumulated non-synonymous substitutions at a lower rate than NPC1b. This pattern was consistent across orders, indicating that NPC1a evolved under stronger molecular constraint than NPC1b.
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Affiliation(s)
- Jin-Cheng Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shao-Lei Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiao-Rong Yue
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tong-Xian Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiangfeng Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Wu T, Dhami GK, Thompson GJ. Soldier‐biased gene expression in a subterranean termite implies functional specialization of the defensive caste. Evol Dev 2017; 20:3-16. [DOI: 10.1111/ede.12243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Tian Wu
- Biology DepartmentWestern UniversityLondonOntarioCanada
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Marynowska M, Goux X, Sillam-Dussès D, Rouland-Lefèvre C, Roisin Y, Delfosse P, Calusinska M. Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome. BMC Genomics 2017; 18:681. [PMID: 28863779 PMCID: PMC5580439 DOI: 10.1186/s12864-017-4076-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
Background Thanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. Especially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. Previous metatranscriptomic reports (high-throughput mRNA sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes. Nevertheless, several factors associated with the material sampling and library preparation steps make the metatranscriptomic studies of termite gut prokaryotic symbionts challenging. Methods In this study, we first examined the influence of the sampling strategy, including the whole termite gut and luminal fluid, on the diversity and the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. Secondly, we evaluated different commercially available kits combined in two library preparative pipelines for the best bacterial mRNA enrichment strategy. Results We showed that the sampling strategy did not significantly impact the generated results, both in terms of the representation of the microbes and their transcriptomic profiles. Nevertheless collecting luminal fluid reduces the co-amplification of unwanted RNA species of host origin. Furthermore, for the four studied higher termite species, the library preparative pipeline employing Ribo-Zero Gold rRNA Removal Kit “Epidemiology” in combination with Poly(A) Purist MAG kit resulted in a more efficient rRNA and poly-A-mRNAdepletion (up to 98.44% rRNA removed) than the pipeline utilizing MICROBExpress and MICROBEnrich kits. High correlation of both Ribo-Zero and MICROBExpresse depleted gene expression profiles with total non-depleted RNA-seq data has been shown for all studied samples, indicating no systematic skewing of the studied pipelines. Conclusions We have extensively evaluated the impact of the sampling strategy and library preparation steps on the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. The presented methodological approach has great potential to enhance metatranscriptomic studies of the higher termite intestinal flora and to unravel novel carbohydrate-active enzymes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4076-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martyna Marynowska
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Xavier Goux
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - David Sillam-Dussès
- Institute of Research for Development - Sorbonne Universités, Institute of Ecology and Environmental Sciences - Paris, U242, 32 avenue Henri Varagnat, F-93140, Bondy, France.,University Paris 13 - Sorbonne Paris Cité, Laboratory of Experimental and Comparative Ethology, EA4443, 99 avenue Jean-Baptiste Clément, F-93430, Villetaneuse, France
| | - Corinne Rouland-Lefèvre
- Institute of Research for Development - Sorbonne Universités, Institute of Ecology and Environmental Sciences - Paris, U242, 32 avenue Henri Varagnat, F-93140, Bondy, France
| | - Yves Roisin
- Université Libre de Bruxelles, 50 Avenue F.D. Roosevelt, B-1050, Brussels, Belgium
| | - Philippe Delfosse
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Magdalena Calusinska
- Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg.
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