1
|
Liu S, Zheng J, Li F, Chi M, Cheng S, Jiang W, Liu Y, Gu Z, Zhao J. Chromosome-scale assembly and quantitative trait locus mapping for major economic traits of the Culter alburnus genome using Illumina and PacBio sequencing with Hi-C mapping information. Front Genet 2023; 14:1072506. [PMID: 37303957 PMCID: PMC10248148 DOI: 10.3389/fgene.2023.1072506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Topmouth culter (Culter alburnus) is an economically important freshwater fish with high nutritional value. However, its potential genetic advantages have not been fully exploited. Therefore, we aimed to determine the genome sequence of C. alburnus and examine quantitative trait loci (QTLs) related to major economic traits. The results showed that 24 pseudochromosomes were anchored by 914.74 Mb of the C. alburnus genome sequence. De novo sequencing identified 31,279 protein-coding genes with an average length of 8507 bp and average coding sequ ence of 1115 bp. In addition, a high-density genetic linkage map consisting of 24 linkage groups was constructed based on 353,532 high-quality single nucleotide polymorphisms and 4,710 bin markers. A total of 28 QTLs corresponding to 11 genes, 26 QTLs corresponding to 11 genes, and 12 QTLs corresponding to 5 genes were identified for sex, intermuscular spine number and body weight traits, respectively. In this study, we assembled an accurate and nearly complete genome of C. alburnus by combining Illumina, PacBio, and high-throughput Chromosome conformation capture (Hi-C) technologies. In addition, we identified QTLs that explained variances in intermuscular spine number, body weight, and sex differences in C. alburnus. These genetic markers or candidate genes associated with growth traits provide a basis for marker-assisted selection in C. alburnus.
Collapse
Affiliation(s)
- Shili Liu
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Jianbo Zheng
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Fei Li
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Meili Chi
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shun Cheng
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Wenping Jiang
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Yinuo Liu
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Zhimin Gu
- Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Jinliang Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
2
|
Jia YY, Chi ML, Jiang WP, Liu SL, Cheng S, Zheng JB, Gu ZM. Identification of reproduction-related genes and pathways in the Culter alburnus H-P-G axis and characterization of their expression differences in malformed and normal gynogenetic ovaries. FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1-20. [PMID: 33156507 DOI: 10.1007/s10695-020-00859-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
This study applied RNA-seq technology to discover reproduction-related genes and pathways in female topmouth culter brain (including pituitary) and ovarian tissues. In functional analysis, 2479 and 2605 unigenes in the brain and ovary tissue were assigned to the "reproductive process" subcategory in addition to the 2660 and 2845 unigenes assigned to the "reproduction" subcategory. Twenty-three complete cDNA sequences were identified through the different gene expression (DGE) approach from five reproduction-related pathways (MAPK signaling pathway, neuroactive ligand-receptor interaction pathway, gonadotropin-releasing hormone signaling pathway, oocyte meiosis pathway, and steroid biosynthesis pathway). The expression levels of 16 candidate genes using qPCR in this study were in accordance with the results of transcriptome analysis. In addition, the expression levels of the FSH, 3β-HSD, PGR, and NPYR genes in malformed gynogenetic ovaries were considerably low, which was consistent with the progress of oocytogenesis in the ovaries of topmouth culter. The high expression of these four genes in the ovaries of normal topmouth culter suggested they might involve in the preparation for the shift of oogenesis to ovulation. Hence, our work identified a set of annotated gene products that are candidate factors affecting reproduction in the topmouth culter H-P-G axis. These results could be essential for further research in functional genomics and genetic editing for topmouth culter reproduction.
Collapse
Affiliation(s)
- Yong Y Jia
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Mei L Chi
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Wen P Jiang
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Shi L Liu
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Shun Cheng
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Jian B Zheng
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Zhi M Gu
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Freshwater Aquaculture Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China.
| |
Collapse
|
3
|
Tuo Y, Chu W, Zhang J, Cheng J, Chen L, Bao L, Xiao T. Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing. Front Genet 2020; 11:714. [PMID: 32793279 PMCID: PMC7393255 DOI: 10.3389/fgene.2020.00714] [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: 09/24/2019] [Accepted: 06/11/2020] [Indexed: 12/03/2022] Open
Abstract
Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.
Collapse
Affiliation(s)
- Yun Tuo
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China.,College of Life Science and Resources Environment, Yichun University, Yichun, China
| | - Wuying Chu
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jianshe Zhang
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jia Cheng
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lin Chen
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lingsheng Bao
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Tiaoyi Xiao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China
| |
Collapse
|
4
|
Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC PLANT BIOLOGY 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
Collapse
Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| |
Collapse
|
5
|
Tao M, Ji RL, Huang L, Fan SY, Liu T, Liu SJ, Tao YX. Regulation of Melanocortin-4 Receptor Pharmacology by Two Isoforms of Melanocortin Receptor Accessory Protein 2 in Topmouth Culter ( Culter alburnus). Front Endocrinol (Lausanne) 2020; 11:538. [PMID: 32922362 PMCID: PMC7456811 DOI: 10.3389/fendo.2020.00538] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/02/2020] [Indexed: 01/03/2023] Open
Abstract
Melanocortin-4 receptor (MC4R) plays important roles in regulation of multiple physiological processes, and interaction of MC4R and melanocortin receptor accessory protein 2 (MRAP2) is suggested to play pivotal role in energy balance of vertebrates. Topmouth culter (Culter alburnus) is an economically important freshwater fish in China. Herein we cloned culter mc4r, mrap2a, and mrap2b. Culter mc4r consisted of a 981 bp open reading frame encoding a protein of 326 amino acids. qRT-PCR revealed that mc4r, mrap2a, and mrap2b were primarily expressed in the central nervous system. In the periphery, mc4r and mrap2b were expressed more widely in the male, while mrap2a was expressed more widely in the female. Culter MC4R could bind to four peptide agonists and increase intracellular cAMP production dose dependently. Culter MC4R was constitutively active in both cAMP and ERK1/2 pathways, which was differentially regulated by culter MRAP2a and MRAP2b. Culter MRAP2a significantly increased Bmax and decreased agonist-stimulated cAMP, while MRAP2b increased cell surface and total expression but did not affect Bmax and agonist-stimulated cAMP. These results will aid the investigation of the potential physiological processes that MC4R might be involved in topmouth culter.
Collapse
Affiliation(s)
- Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Ren-Lei Ji
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Lu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Si-Yu Fan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ting Liu
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Shao-Jun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Shao-Jun Liu
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Ya-Xiong Tao
| |
Collapse
|
6
|
Shao L. DNA Damage Response Signals Transduce Stress From Rheumatoid Arthritis Risk Factors Into T Cell Dysfunction. Front Immunol 2018; 9:3055. [PMID: 30619377 PMCID: PMC6306440 DOI: 10.3389/fimmu.2018.03055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/10/2018] [Indexed: 12/18/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune-mediated disease that is associated with significant cartilage damage and immunosenescence. Despite decades of research, the major signal pathways that initiate RA are still unclear. The DNA damage response (DDR) is a specific and hierarchical network that includes cell cycle checkpoints, DNA repair, and DNA-damage tolerance pathways. Recent studies suggest that this condition is associated with deficits in telomere maintenance and overall genomic instability in the T cells of RA patients. Analysis of the underlying mechanisms has revealed defects in DDR pathways. Particularly, the DNA repair enzyme, ataxia telangiectasia mutated (ATM), is downregulated, which leaves the damaged DNA breaks in RA-associated T cells unrepaired and pushes them to apoptosis, exhausts the T cell pool, and promotes the arthritogenesis effector function of T cells. This review discusses recent advancements and illustrates that risk factors for RA, such as viral infections, environmental events, and genetic risk loci are combat with DDR signals, and the impaired DDR response of RA-associated T cells, in turn, triggers disease-related phenotypes. Therefore, DDR is the dominant signal that converts genetic and environmental stress to RA-related immune dysfunction. Understanding the orchestration of RA pathogenesis by DDR signals would further our current knowledge of RA and provide novel avenues in RA therapy.
Collapse
Affiliation(s)
- Lan Shao
- The Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
7
|
Hu Q, Wang Q, Meng Y, Tian H, Xiao H. Comparative transcriptome reveal the potential adaptive evolutionary genes in Andrias davidianus. Hereditas 2018; 155:18. [PMID: 29483849 PMCID: PMC5819198 DOI: 10.1186/s41065-018-0056-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 01/29/2018] [Indexed: 12/21/2022] Open
Abstract
To search the evidence of molecular evolution mechanism for aquatic and cave habitat in Andrias davidianus, the evolution analysis was carried out among several species transcriptome data. The transcriptome data of Notophthalmus viridescens, Xenopus tropicalis, Cynops pyrrhogaster, Hynobius chinensis and A. davidianus were obtained from the Genbank and reassembled except Xenopus tropicalis. The BLAST search of transcriptome data obtained 1244 single-copy orthologous genes among five species. A phylogenetic tree showed A. davidianus to have the closest relationship to H. chinensis. Fourteen positively selected genes were detected in A. davidianus and N. vridescens group and fifteen in A. davidianus and H. chinensis group. Five genes were shared in the both groups which involved in the immune system, suggesting that A. davidianus adaptation to an aquatic and cave environment required rapid evolution of the immune system compared to N. viridescens and H. chinensis.
Collapse
Affiliation(s)
- Qiaomu Hu
- 1Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223 China
| | - Quanhe Wang
- 1Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223 China.,2College of Life Science, Yangtze University, Jingzhou, 434025 China
| | - Yan Meng
- 1Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223 China
| | - Haifeng Tian
- 1Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223 China
| | - Hanbing Xiao
- 1Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223 China
| |
Collapse
|
8
|
Hawkins AK, Garza ER, Dietz VA, Hernandez OJ, Hawkins WD, Burrell AM, Pepper AE. Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biol Evol 2017; 9:3478-3494. [PMID: 29220486 PMCID: PMC5751042 DOI: 10.1093/gbe/evx259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 12/26/2022] Open
Abstract
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.
Collapse
|
9
|
Zhu C, Pan Z, Wang H, Chang G, Wu N, Ding H. De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis. PLoS One 2017; 12:e0171966. [PMID: 28196101 PMCID: PMC5308828 DOI: 10.1371/journal.pone.0171966] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/28/2017] [Indexed: 11/30/2022] Open
Abstract
The Chinese lake gudgeon Sarcocheilichthys sinensis is a small cyprinid fish with great aquaculture potential both for its edible and ornamental values. Nevertheless, available genomic and transcriptomic information for this fish is extremely deficient. In this study, a normalized cDNA library was constructed using 13 mixed tissues of an adult male S. sinensis, and was sequenced by the Illumina HiSeq2500 platform. De novo assembly was performed using 38,911,511 obtained clean reads, and a total of 147,282 unigenes with an average length of 900 bp were finally achieved. 96.2% of these unigenes were annotated in 9 public databases, and 16 segments of growth-related genes were identified for future studies. In addition, 28,493 unigenes were assigned to 61 subcategories of Gene Ontology (GO), and 10,483 unigenes were assigned to 25 categories of Cluster of Orthologous Group (COG). Moreover, 14,943 unigenes were classified into 225 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 30,666 microsatellites were detected from 17,627 unigenes with an average distribution density of 1:2405 bp. This transcriptome data set will be valuable for researches on discovery, expression and evolution on genes of interest. Meanwhile, the identified microsatellites would be useful tools for genetic and genomic studies in S. sinensis.
Collapse
Affiliation(s)
- Chuankun Zhu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
- * E-mail:
| | - Zhengjun Pan
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Hui Wang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Guoliang Chang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Nan Wu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Huaiyu Ding
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| |
Collapse
|
10
|
Ji R, Wang Y, Cheng Y, Zhang M, Zhang HB, Zhu L, Fang J, Zhu-Salzman K. Transcriptome Analysis of Green Peach Aphid ( Myzus persicae): Insight into Developmental Regulation and Inter-Species Divergence. FRONTIERS IN PLANT SCIENCE 2016; 7:1562. [PMID: 27812361 PMCID: PMC5072348 DOI: 10.3389/fpls.2016.01562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Green peach aphid (Myzus persicae) and pea aphid (Acyrthosiphon pisum) are two phylogenetically closely related agricultural pests. While pea aphid is restricted to Fabaceae, green peach aphid feeds on hundreds of plant species from more than 40 families. Transcriptome comparison could shed light on the genetic factors underlying the difference in host range between the two species. Furthermore, a large scale study contrasting gene expression between immature nymphs and fully developed adult aphids would fill a previous knowledge gap. Here, we obtained transcriptomic sequences of green peach aphid nymphs and adults, respectively, using Illumina sequencing technology. A total of 2244 genes were found to be differentially expressed between the two developmental stages, many of which were associated with detoxification, hormone production, cuticle formation, metabolism, food digestion, and absorption. When searched against publically available pea aphid mRNA sequences, 13,752 unigenes were found to have no homologous counterparts. Interestingly, many of these unigenes that could be annotated in other databases were involved in the "xenobiotics biodegradation and metabolism" pathway, suggesting the two aphids differ in their adaptation to secondary metabolites of host plants. Conversely, 3989 orthologous gene pairs between the two species were subjected to calculations of synonymous and nonsynonymous substitutions, and 148 of the genes potentially evolved in response to positive selection. Some of these genes were predicted to be associated with insect-plant interactions. Our study has revealed certain molecular events related to aphid development, and provided some insight into biological variations in two aphid species, possibly as a result of host plant adaptation.
Collapse
Affiliation(s)
- Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural SciencesNanjing, China
- Department of Entomology, Texas A&M UniversityCollege Station, TX, USA
| | - Yujun Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
| | - Yanbin Cheng
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jichao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M UniversityCollege Station, TX, USA
| |
Collapse
|
11
|
Zhao L, Tu J, Zhang Y, Wang J, Yang L, Wang W, Wu Z, Meng Q, Lin L. Transcriptomic analysis of the head kidney of Topmouth culter (Culter alburnus) infected with Flavobacterium columnare with an emphasis on phagosome pathway. FISH & SHELLFISH IMMUNOLOGY 2016; 57:413-418. [PMID: 27601296 DOI: 10.1016/j.fsi.2016.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/03/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
Flavobacterium columnare (FC) has caused worldwide fish columnaris disease with high mortality and great economic losses in cultured fish, including Topmouth culter (Culter alburnus). However, the knowledge about the host factors involved in FC infection is little known. In this study, the transcriptomic profiles of the head kidney from Topmouth culter with or without FC infection were obtained using HiSeq™ 2500 (Illumina). Totally 79,641 unigenes with high quality were obtained. Among them, 4037 differently expressed genes, including 1217 up-regulated and 2820 down-regulated genes, were identified and enriched using databases of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differently expressed genes were mainly associated with pathways such as immune response, carbohydrate metabolism, amino acid metabolism, and lipid metabolism. Since phagocytosis is a central mechanism of innate immune response by host cells to defense against infectious agents, genes related to the phagosome pathway were scrutinized and 9 differently expressed phagosome-related genes were identified including 3 up-regulated and 6 down-regulated genes. Five of them were further validated by quantitative real-time polymerase chain reaction (qRT-PCR). This transcriptomic analysis of host genes in response to FC infection provides data towards understanding the infection mechanisms and will shed a new light on the prevention of columnaris.
Collapse
Affiliation(s)
- Lijuan Zhao
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China; Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiagang Tu
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yulei Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jinfu Wang
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China
| | - Ling Yang
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China
| | - Weimin Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zaohe Wu
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China
| | - Qinglei Meng
- Shandong Freshwater Fisheries Research Institute, Shandong Provincial Key Laboratory of Freshwater Genetics and Breeding, Jinan, Shandong, 250013, China.
| | - Li Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, 510225, China.
| |
Collapse
|