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Ding S, Wang S, He K, Jiang M, Li F. Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects. BMC Genomics 2017; 18:848. [PMID: 29110701 PMCID: PMC5674736 DOI: 10.1186/s12864-017-4234-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/23/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Simple sequence repeats (SSR), also called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. At present, the genomes of more than 100 insect species are available. However, the features of SSRs in most insect genomes remain largely unknown. RESULTS We identified 15.01 million SSRs across 136 insect genomes. The number of identified SSRs was positively associated with genome size in insects, but the frequency and density per megabase of genomes were not. Most insect SSRs (56.2-93.1%) were perfect (no mismatch). Imperfect (at least one mismatch) SSRs (average length 22-73 bp) were longer than perfect SSRs (16-30 bp). The most abundant insect SSRs were the di- and trinucleotide types, which accounted for 27.2% and 22.0% of all SSRs, respectively. On average, 59.1%, 36.8%, and 3.7% of insect SSRs were located in intergenic, intronic, and exonic regions, respectively. The percentages of various types of SSRs were similar among insects from the same family. However, they were dissimilar among insects from different families within orders. We carried out a phylogenetic analysis using the SSR frequencies. Species from the same family were generally clustered together in the evolutionary tree. However, insects from the same order but not in the same family did not cluster together. These results indicated that although SSRs undergo rapid expansions and contractions in different populations of the same species, the general genomic features of insect SSRs remain conserved at the family level. CONCLUSION Millions of insect SSRs were identified and their genome features were analyzed. Most insect SSRs were perfect and were located in intergenic regions. We presented evidence that the variance of insect SSRs accumulated after the differentiation of insect families.
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Affiliation(s)
- Simin Ding
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Shuping Wang
- Technical Centre for Animal Plant and Food Inspection and Quarantine, Shanghai Entry-exit Inspection and Quarantine Bureau, Shanghai, 200135 China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Mingxing Jiang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
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Li Z, Chen F, Huang C, Zheng W, Yu C, Cheng H, Zhou R. Genome-wide mapping and characterization of microsatellites in the swamp eel genome. Sci Rep 2017; 7:3157. [PMID: 28600492 PMCID: PMC5466649 DOI: 10.1038/s41598-017-03330-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.
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Affiliation(s)
- Zhigang Li
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Feng Chen
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chunhua Huang
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Weixin Zheng
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chunlai Yu
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China.
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Gerchen JF, Reichert SJ, Röhr JT, Dieterich C, Kloas W, Stöck M. A Single Transcriptome of a Green Toad (Bufo viridis) Yields Candidate Genes for Sex Determination and -Differentiation and Non-Anonymous Population Genetic Markers. PLoS One 2016; 11:e0156419. [PMID: 27232626 PMCID: PMC4883742 DOI: 10.1371/journal.pone.0156419] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/15/2016] [Indexed: 12/13/2022] Open
Abstract
Large genome size, including immense repetitive and non-coding fractions, still present challenges for capacity, bioinformatics and thus affordability of whole genome sequencing in most amphibians. Here, we test the performance of a single transcriptome to understand whether it can provide a cost-efficient resource for species with large unknown genomes. Using RNA from six different tissues from a single Palearctic green toad (Bufo viridis) specimen and Hiseq2000, we obtained 22,5 Mio reads and publish >100,000 unigene sequences. To evaluate efficacy and quality, we first use this data to identify green toad specific candidate genes, known from other vertebrates for their role in sex determination and differentiation. Of a list of 37 genes, the transcriptome yielded 32 (87%), many of which providing the first such data for this non-model anuran species. However, for many of these genes, only fragments could be retrieved. In order to allow also applications to population genetics, we further used the transcriptome for the targeted development of 21 non-anonymous microsatellites and tested them in genetic families and backcrosses. Eleven markers were specifically developed to be located on the B. viridis sex chromosomes; for eight markers we can indeed demonstrate sex-specific transmission in genetic families. Depending on phylogenetic distance, several markers, which are sex-linked in green toads, show high cross-amplification success across the anuran phylogeny, involving nine systematic anuran families. Our data support the view that single transcriptome sequencing (based on multiple tissues) provides a reliable genomic resource and cost-efficient method for non-model amphibian species with large genome size and, despite limitations, should be considered as long as genome sequencing remains unaffordable for most species.
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Affiliation(s)
- Jörn F Gerchen
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Samuel J Reichert
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Johannes T Röhr
- Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany.,Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Werner Kloas
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Matthias Stöck
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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Doyle JM, Hacking CC, Willoughby JR, Sundaram M, DeWoody JA. Mammalian genetic diversity as a function of habitat, body size, trophic class, and conservation status. J Mammal 2015. [DOI: 10.1093/jmammal/gyv061] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Doyle JM, Katzner TE, Bloom PH, Ji Y, Wijayawardena BK, DeWoody JA. The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos). PLoS One 2014; 9:e95599. [PMID: 24759626 PMCID: PMC3997482 DOI: 10.1371/journal.pone.0095599] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 03/28/2014] [Indexed: 12/05/2022] Open
Abstract
Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data to a depth of ∼40x coverage. The genome assembly includes 2,552 scaffolds >10 Kb and 415 scaffolds >1.2 Mb. We annotated 16,571 genes that are involved in myriad biological processes, including such disparate traits as beak formation and color vision. We also identified repetitive regions spanning 92 Mb (∼6% of the assembly), including LINES, SINES, LTR-RTs and DNA transposons. The mitochondrial genome encompasses 17,332 bp and is ∼91% identical to the Mountain Hawk-Eagle (Nisaetus nipalensis). Finally, the data reveal that several anonymous microsatellites commonly used for population studies are embedded within protein-coding genes and thus may not have evolved in a neutral fashion. Because the genome sequence includes ∼800,000 novel polymorphisms, markers can now be chosen based on their proximity to functional genes involved in migration, carnivory, and other biological processes.
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Affiliation(s)
- Jacqueline M. Doyle
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Todd E. Katzner
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, United States of America
- Northern Research Station, USDA Forest Service, Parsons, West Virginia, United States of America
| | - Peter H. Bloom
- Western Foundation of Vertebrate Zoology, Camarillo, California, United States of America
| | - Yanzhu Ji
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Bhagya K. Wijayawardena
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
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Polymorphic microsatellite loci for a neotropical leaf-litter frog (Craugastor bransfordii) characterized through Illumina sequencing. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0185-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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