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Liang Y, Carrillo-Baltodano AM, Martín-Durán JM. Emerging trends in the study of spiralian larvae. Evol Dev 2024; 26:e12459. [PMID: 37787615 DOI: 10.1111/ede.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
Many animals undergo indirect development, where their embryogenesis produces an intermediate life stage, or larva, that is often free-living and later metamorphoses into an adult. As their adult counterparts, larvae can have unique and diverse morphologies and occupy various ecological niches. Given their broad phylogenetic distribution, larvae have been central to hypotheses about animal evolution. However, the evolution of these intermediate forms and the developmental mechanisms diversifying animal life cycles are still debated. This review focuses on Spiralia, a large and diverse clade of bilaterally symmetrical animals with a fascinating array of larval forms, most notably the archetypical trochophore larva. We explore how classic research and modern advances have improved our understanding of spiralian larvae, their development, and evolution. Specifically, we examine three morphological features of spiralian larvae: the anterior neural system, the ciliary bands, and the posterior hyposphere. The combination of molecular and developmental evidence with modern high-throughput techniques, such as comparative genomics, single-cell transcriptomics, and epigenomics, is a promising strategy that will lead to new testable hypotheses about the mechanisms behind the evolution of larvae and life cycles in Spiralia and animals in general. We predict that the increasing number of available genomes for Spiralia and the optimization of genome-wide and single-cell approaches will unlock the study of many emerging spiralian taxa, transforming our views of the evolution of this animal group and their larvae.
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Affiliation(s)
- Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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2
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Zakas C. Streblospio benedicti: A genetic model for understanding the evolution of development and life-history. Curr Top Dev Biol 2022; 147:497-521. [PMID: 35337460 DOI: 10.1016/bs.ctdb.2021.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Investigating developmental evolution usually requires comparing differences across related species to infer how phenotypic change results from embryological modifications. However, when comparing organisms from different environments, ecologies, and evolutionary histories there can be many confounding factors to finding a genetic basis for developmental differences. In the marine annelid Streblospio benedicti, there are two distinct types of offspring with independent developmental pathways that converge on the same adult phenotype. To my knowledge, S. benedicti is the only known species that has heritable (additive) genetic variation in developmental traits that results in alternative life-history strategies. Females produce either hundreds of small, swimming and feeding larvae, or dozens of large, nonfeeding larvae. The larvae differ in their morphology, ecology, and dispersal potential. This developmental dimorphism makes S. benedicti a unique and useful model for understanding how genetic changes result in developmental modifications that ultimately lead to overall life-history differences. Because the offspring phenotypes of S. benedicti are heritable, we can use forward genetics within a single evolutionary lineage to disentangle how development evolves, and which genes and regulatory mechanisms are involved.
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Affiliation(s)
- Christina Zakas
- North Carolina State University, Raleigh, NC, United States.
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3
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SNP Development in Penaeus vannamei via Next-Generation Sequencing and DNA Pool Sequencing. FISHES 2021. [DOI: 10.3390/fishes6030036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing and pool sequencing have been widely used in SNP (single-nucleotide polymorphism) detection and population genetics research; however, there are few reports on SNPs related to the growth of Penaeus vannamei. The purpose of this study was to call SNPs from rapid-growing (RG) and slow-growing (SG) individuals’ transcriptomes and use DNA pool sequencing to assess the reliability of SNPs. Two parameters were applied to detect SNPs. One parameter was the p-values generated using Fisher’s exact test, which were used to calculate the significance of allele frequency differences between RG and SG. The other one was the AFI (minor allele frequency imbalance), which was defined to highlight the fold changes in MAF (minor allele frequency) values between RG and SG. There were 216,015 hypothetical SNPs, which were obtained based on the transcriptome data. Finally, 104 high-quality SNPs and 96,819 low-quality SNPs were predicted. Then, 18 high-quality SNPs and 17 low-quality SNPs were selected to assess the reliability of the detection process. Here, 72.22% (13/18) accuracy was achieved for high-quality SNPs, while only 52.94% (9/17) accuracy was achieved for low-quality SNPs. These SNPs enrich the data for population genetics studies of P. vannamei and may play a role in the development of SNP markers for future breeding studies.
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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.
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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
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Liao Z, Wan Q, Shang X, Su J. Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella. Sci Rep 2017; 7:1184. [PMID: 28446772 PMCID: PMC5430748 DOI: 10.1038/s41598-017-01338-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/28/2017] [Indexed: 02/02/2023] Open
Abstract
Grass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively. Comparative transcriptome analysis identified 413 and 832 grass carp reovirus (GCRV)-resistant-association SNPs as well as 1,381 and 1,606 GCRV-susceptible-association SNPs in individuals and cell lines, respectively. Integrated analysis indicated 22 genes with single SNP share common resistant/susceptible traits in two transcriptomes. Furthermore, we infected grass carp with GCRV, genotyping and association analyses were performed, and 9 in 22 SNPs were confirmed by PCR-RFLP. Meanwhile, mRNA expression profiles of 6 genes containing confirmed SNPs were examined by qRT-PCR. The results demonstrated that mRNA expressions were significant differences in resistant/susceptible individuals and cell lines. The present study develops an important strategy for high throughput screening of phenotype association genetic markers and the results will serve in grass carp breeding for GCRV resistance.
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Affiliation(s)
- Zhiwei Liao
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quanyuan Wan
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueying Shang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Su
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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6
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Crawford DL, Oleksiak MF. Ecological population genomics in the marine environment. Brief Funct Genomics 2016; 15:342-51. [DOI: 10.1093/bfgp/elw008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Riesgo A, Taboada S, Avila C. Evolutionary patterns in Antarctic marine invertebrates: an update on molecular studies. Mar Genomics 2015; 23:1-13. [PMID: 26228311 DOI: 10.1016/j.margen.2015.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Ana Riesgo
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Sergi Taboada
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain
| | - Conxita Avila
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain
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8
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Zakas C, Rockman MV. Gene-based polymorphisms reveal limited genomic divergence in a species with a heritable life-history dimorphism. Evol Dev 2015; 17:240-7. [DOI: 10.1111/ede.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liu H, Zheng H, Zhang H, Deng L, Liu W, Wang S, Meng F, Wang Y, Guo Z, Li S, Zhang G. A de novo transcriptome of the noble scallop, Chlamys nobilis, focusing on mining transcripts for carotenoid-based coloration. BMC Genomics 2015; 16:44. [PMID: 25651863 PMCID: PMC4342821 DOI: 10.1186/s12864-015-1241-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 01/13/2015] [Indexed: 12/03/2022] Open
Abstract
Background The noble scallop Chlamys nobilis Reeve displays polymorphism in shell and muscle colors. Previous research showed that the orange scallops with orange shell and muscle had a significantly higher carotenoid content than the brown ones with brown shell and white muscle. There is currently a need to identify candidate genes associated with carotenoid-based coloration. Results In the present study, 454 GS-FLX sequencing of noble scallop transcriptome yielded 1,181,060 clean sequence reads, which were assembled into 49,717 isotigs, leaving 110,158 reads as the singletons. Of the 159,875 unique sequences, 11.84% isotigs and 9.35% singletons were annotated. Moreover, 3,844 SSRs and over 120,000 high confidence variants (SNPs and INDELs) were identified. Especially, one class B scavenge receptor termed SRB-like-3 was discovered to express only in orange scallops and absent in brown ones, suggesting a significant association with high carotenoid content. Down-regulation of SRB-like-3 mRNA by RNA interference remarkably decreased blood carotenoid, providing compelling evidence that SRB-like-3 is an ideal candidate gene controlling carotenoid deposition and determining orange coloration. Conclusion Transcriptome analysis of noble scallop reveals a novel scavenger receptor significantly associated with orange scallop rich in carotenoid content. Our findings pave the way for further functional elucidation of this gene and molecular basis of carotenoid deposition in orange scallop. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1241-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helu Liu
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China. .,Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Science, Sanya, 572000, China.
| | - Huaiping Zheng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Hongkuan Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Longhui Deng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Wenhua Liu
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Shuqi Wang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Fang Meng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Yajun Wang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Zhicheng Guo
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Shengkang Li
- Key Laboratory of Marine Biotechnology of Guangdong Province, Shantou University, Shantou, 515063, China. .,Department of Education of Guangdong Province, Mariculture Research Center for Subtropical Shellfish & Algae, Shantou, 515063, China.
| | - Guofan Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
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Homogeneous nuclear background for mitochondrial cline in northern range of Notochthamalus scabrosus. G3-GENES GENOMES GENETICS 2014; 4:225-30. [PMID: 24347623 PMCID: PMC3931557 DOI: 10.1534/g3.113.008383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A mitochondrial cline along the Chilean coast in the barnacle Notochthamalus scabrosus suggests a species history of transient allopatry and secondary contact. However, previous studies of nuclear sequence divergence suggested population genetic homogeneity across northern and central Chile. Here, we collect single-nucleotide polymorphism data from pooled population samples sequenced with restriction site−associated DNA sequencing procedures, confirm these data with the use of a GoldenGate array, and identify a discordance between population genetic patterns in the nuclear and mitochondrial genomes. This discordance was noted in previous work on this species, but here it is confirmed that the nuclear genome exhibits only slight phylogeographic variation across 3000 km of coastline, in the presence of a strong and statistically significant mitochondrial cline. There are nevertheless markers (approximately 5% of nuclear single-nucleotide polymorphisms) exhibiting cytonuclear disequilibrium relative to mitotype. Although these data confirm our previous explorations of this species, it is likely that some of the nuclear genomic diversity of this species has yet to be explored, as comparison with other barnacle phylogeography studies suggest that a divergence of similar magnitude should be found in the nuclear genome somewhere else in the species range.
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11
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Yu Y, Wei J, Zhang X, Liu J, Liu C, Li F, Xiang J. SNP discovery in the transcriptome of white Pacific shrimp Litopenaeus vannamei by next generation sequencing. PLoS One 2014; 9:e87218. [PMID: 24498047 PMCID: PMC3907553 DOI: 10.1371/journal.pone.0087218] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/18/2013] [Indexed: 11/18/2022] Open
Abstract
The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP) discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei) generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp) and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies.
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Affiliation(s)
- Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiankai Wei
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jingwen Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengzhang Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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12
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Zhou ZC, Dong Y, Sun HJ, Yang AF, Chen Z, Gao S, Jiang JW, Guan XY, Jiang B, Wang B. Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers. Mol Ecol Resour 2013; 14:127-38. [PMID: 23855518 DOI: 10.1111/1755-0998.12147] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/23/2013] [Accepted: 06/25/2013] [Indexed: 11/30/2022]
Abstract
Sea cucumber (Apostichopus japonicus) is an ecologically and economically important species in East and South-East Asia. This project aimed to identify large numbers of gene-associated markers and differentially expressed genes (DEGs) after lipopolysaccharides (LPS) challenge in A. japonicus using high-throughput transcriptome sequencing. A total of 162 million high-quality reads of 174 million raw reads were obtained by deep sequencing using Illumina HiSeq™ 2000 platform. Assembly of these reads generated 94 704 unigenes, with read length ranging from 200 to 16 153 bp (average length of 810 bp). A total of 36 005 were identified as coding sequences (CDSs), 32 479 of which were successfully annotated. Based on the assembly transcriptome, we identified 142 511 high-quality single nucleotide polymorphisms (SNPs). Among them, 33 775, 63 120 and 45 616 were located in sequences without predicted CDS (non-CDSs), CDSs and untranslated regions (UTRs), respectively. These putative SNPs included 82 664 transitions and 59 847 transversions. Totally, 89 375 (59.1%) were distributed in 15 473 known genes. A total of 6417 microsatellites were detected in 5970 unigenes, 3216 of which were annotated and 2481 were successfully subjected for primer design. The numbers of simple sequence repeats (SSRs) identified in non-CDSs, CDSs and UTRs were 2367, 2316 and 1734. These potential SNPs and SSRs are expected to provide abundant resources for genetic, evolutionary and ecological studies in sea cucumber. Transcriptome comparison revealed 1330, 1347 and 1291 DEGs in the coelomocytes of A. japonicus at 4 h, 24 h and 72 h after LPS challenge, respectively. Approximately 58.4% (1802) of total DEGs have been successfully annotated.
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Affiliation(s)
- Z C Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, China
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Niu SH, Li ZX, Yuan HW, Chen XY, Li Y, Li W. Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny. BMC Genomics 2013; 14:263. [PMID: 23597112 PMCID: PMC3640921 DOI: 10.1186/1471-2164-14-263] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 04/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcriptome data were obtained using a next-generation sequencing platform to compensate for the lack of P. tabuliformis genomic information. RESULTS The increasing amount of transcriptome data on Pinus provides an excellent resource for multi-gene phylogenetic analysis and studies on how conserved genes and functions are maintained in the face of species divergence. The first P. tabuliformis transcriptome from a normalised cDNA library of multiple tissues and individuals was sequenced in a full 454 GS-FLX run, producing 911,302 sequencing reads. The high quality overlapping expressed sequence tags (ESTs) were assembled into 46,584 putative transcripts, and more than 700 SSRs and 92,000 SNPs/InDels were characterised. Comparative analysis of the transcriptome of six conifer species yielded 191 orthologues, from which we inferred a phylogenetic tree, evolutionary patterns and calculated rates of gene diversion. We also identified 938 fast evolving sequences that may be useful for identifying genes that perhaps evolved in response to positive selection and might be responsible for speciation in the Pinus lineage. CONCLUSIONS A large collection of high-quality ESTs was obtained, de novo assembled and characterised, which represents a dramatic expansion of the current transcript catalogues of P. tabuliformis and which will gradually be applied in breeding programs of P. tabuliformis. Furthermore, these data will facilitate future studies of the comparative genomics of P. tabuliformis and other related species.
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Affiliation(s)
- Shi-Hui Niu
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China
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Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis. G3-GENES GENOMES GENETICS 2013; 3:359-67. [PMID: 23390612 PMCID: PMC3564996 DOI: 10.1534/g3.112.003871] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 12/19/2012] [Indexed: 01/09/2023]
Abstract
Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.
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Zakas C, Wares JP. Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti. Mol Ecol 2012; 21:5447-60. [PMID: 23057973 PMCID: PMC4643657 DOI: 10.1111/mec.12040] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 08/06/2012] [Accepted: 08/15/2012] [Indexed: 11/29/2022]
Abstract
In many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects on the potential for local adaptation and on rates of speciation, extinction and molecular evolution. Here, we use the polychaete Streblospio benedicti to investigate the effects of dimorphic offspring type on gene flow and genetic structure in coastal populations. We use 84 single nucleotide polymorphism (SNP) markers for this species to assay populations on the East and West Coasts of the United States. Using these markers, we found that in their native East Coast distribution, populations of S. benedicti have high-population genetic structure, but this structure is associated primarily with geographic separation rather than developmental differences. Interestingly, very little genetic differentiation is recovered between individuals of different development types when they occur in the same or nearby populations, further supporting that this is a true case of poecilogony. In addition, we were able to demonstrate that the recently introduced (~100 ya) West Coast populations probably originated from a lecithotrophic population near Delaware.
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Affiliation(s)
- Christina Zakas
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Rockman MV. Patterns of nuclear genetic variation in the poecilogonous polychaete Streblospio benedicti. Integr Comp Biol 2012; 52:173-80. [PMID: 22659203 DOI: 10.1093/icb/ics083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The evolution of marine larvae is replete with transitions in trophic mode, but little is known about how, at the genetic level, these transitions are achieved. Basic parameters, including the number of underlying loci, their molecular characteristics, and the population-genetic processes that drive transitions remain unknown. Streblospio benedicti, an abundant benthic polychaete with heritable poecilogony, provides a unique genetically tractable system for addressing these issues. Individuals of S. benedicti vary in diverse aspects of development. Some females produce small, planktotrophic larvae, whereas others produce large, yolky larvae capable of settling without feeding. Here, I present estimates of basic features of nuclear genetic variation in S. benedicti to lay the foundations for subsequent efforts to understand the genetic basis of poecilogony. Sequence of ∼20 kb of random nuclear DNA indicates that the nucleotide composition, at 62.1% A + T, is typical of lophotrochozoan genomes. Population-genetic data, acquired by sequencing two loci (∼2500 bp) in multiple animals of each developmental morph, indicate that the morphs exhibit very little differentiation at random loci. Nucleotide heterozygosity (θπ) is ∼0.5-1% per site, and linkage disequilibrium decays within a few kilobases (ρ ∼ 3 × 10(-3) per site). These data suggest that genetic mapping by association will require a high density of markers, but linkage mapping and identification of regions of elevated inter-morph differentiation hold great promise.
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Affiliation(s)
- Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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