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Kim G, Cho H, Kim S. Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:118. [PMID: 38709404 DOI: 10.1007/s00122-024-04626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE Through a map-based cloning approach, a gene coding for an R2R3-MYB transcription factor was identified as a causal gene for the I locus controlling the dominant white bulb color in onion. White bulb colors in onion (Allium cepa L.) are determined by either the C or I loci. The causal gene for the C locus was previously isolated, but the gene responsible for the I locus has not been identified yet. To identify candidate genes for the I locus, an approximately 7-Mb genomic DNA region harboring the I locus was obtained from onion and bunching onion (A. fistulosum) whole genome sequences using two tightly linked molecular markers. Within this interval, the AcMYB1 gene, known as a positive regulator of anthocyanin production, was identified. No polymorphic sequences were found between white and red AcMYB1 alleles in the 4,860-bp full-length genomic DNA sequences. However, a 4,838-bp LTR-retrotransposon was identified in the white allele, in the 79-bp upstream coding region from the stop codon. The insertion of this LTR-retrotransposon created a premature stop codon, resulting in the replacement of 26 amino acids with seven different residues. A molecular marker was developed based on the insertion of this LTR-retrotransposon to genotype the I locus. A perfect linkage between bulb color phenotypes and marker genotypes was observed among 5,303 individuals of segregating populations. The transcription of AcMYB1 appeared to be normal in both red and white onions, but the transcription of CHS-A, which encodes chalcone synthase and is involved in the first step of the anthocyanin biosynthesis pathway, was inactivated in the white onions. Taken together, an aberrant AcMYB1 protein produced from the mutant allele might be responsible for the dominant white bulb color in onions.
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Affiliation(s)
- Geonjoong Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Heejung Cho
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea.
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You C, Jiang S, Ding Y, Ye S, Zou X, Zhang H, Li Z, Chen F, Li Y, Ge X, Guo X. RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages. Virol Sin 2024; 39:156-168. [PMID: 38253258 PMCID: PMC10877444 DOI: 10.1016/j.virs.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.
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Affiliation(s)
- Changqiao You
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yunyun Ding
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shunxing Ye
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha, 410082, China
| | - Hongming Zhang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Zeqi Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xingyi Ge
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
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Li Y, Huo Y, Yang Y, Wang Z, Sun Y, Liu B, Wu X. Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion. FRONTIERS IN PLANT SCIENCE 2023; 14:1100691. [PMID: 36818885 PMCID: PMC9928573 DOI: 10.3389/fpls.2023.1100691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. RESULTS Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. DISCUSSION Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding.
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Affiliation(s)
| | | | | | | | | | | | - Xiong Wu
- *Correspondence: Bingjiang Liu, ; Xiong Wu,
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Ermolaev A, Kudryavtseva N, Pivovarov A, Kirov I, Karlov G, Khrustaleva L. Integrating Genetic and Chromosome Maps of Allium cepa: From Markers Visualization to Genome Assembly Verification. Int J Mol Sci 2022; 23:10486. [PMID: 36142398 PMCID: PMC9504663 DOI: 10.3390/ijms231810486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
The ability to directly look into genome sequences has opened great opportunities in plant breeding. Yet, the assembly of full-length chromosomes remains one of the most difficult problems in modern genomics. Genetic maps are commonly used in de novo genome assembly and are constructed on the basis of a statistical analysis of the number of recombinations. This may affect the accuracy of the ordering and orientation of scaffolds within the chromosome, especially in the region of recombination suppression. Moreover, it is impossible to assign contigs lacking DNA markers. Here, we report the use of Tyr-FISH to determine the position of the short DNA sequence of markers and non-mapped unique copy sequence on the physical chromosomes of a large-genome onion (Allium cepa L.). In order to minimize potential background masking of the target signal, we improved our earlier developed pipeline for probe design. A total of 23 markers were located on physical chromosomes 2 and 6. The order of markers was corrected by the integration of genetic, pseudochromosome maps and cytogenetic maps. Additionally, the position of the mlh1 gene, which was not on the genetic map, was defined on physical chromosome 2. Tyr-FISH mapping showed that the order of 23.1% (chromosome 2) and 27.3% (chromosome 6) of the tested genes differed between physical chromosomes and pseudochromosomes. The results can be used for the improvement of pseudochromosome 2 and 6 assembly. The present study aims to demonstrate the value of the in situ visualization of DNA sequences in chromosome-scaffold genome assembly.
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Affiliation(s)
- Aleksey Ermolaev
- Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
| | - Natalia Kudryavtseva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
| | - Anton Pivovarov
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
| | - Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
- Department of Botany, Breeding and Seed Production of Garden Plants, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskay 49 Str., 127550 Moscow, Russia
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Sekine D, Oku S, Nunome T, Hirakawa H, Tsujimura M, Terachi T, Toyoda A, Shigyo M, Sato S, Tsukazaki H. Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping. DNA Res 2022; 29:6675293. [PMID: 36007888 PMCID: PMC9410872 DOI: 10.1093/dnares/dsac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.
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Affiliation(s)
- Daisuke Sekine
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) , Tsu, Mie 514-2392, Japan
| | - Satoshi Oku
- Tohoku Agricultural Research Center, NARO , Morioka, Iwate 020-0198, Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) , Tsu, Mie 514-2392, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | - Mai Tsujimura
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University , Otsu, Shiga 520-2194, Japan
- Plant Organelle Genome Research Center, Kyoto Sangyo University , Kyoto 603-8555, Japan
| | - Toru Terachi
- Plant Organelle Genome Research Center, Kyoto Sangyo University , Kyoto 603-8555, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University , Yamaguchi City, Yamaguchi 753-8515, Japan
| | - Shusei Sato
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
| | - Hikaru Tsukazaki
- Tohoku Agricultural Research Center, NARO , Morioka, Iwate 020-0198, Japan
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Oku S, Ueno K, Sawazaki Y, Maeda T, Jitsuyama Y, Suzuki T, Onodera S, Fujino K, Shimura H. Functional characterization and vacuolar localization of fructan exohydrolase derived from onion (Allium cepa). JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4908-4922. [PMID: 35552692 DOI: 10.1093/jxb/erac197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Fructans such as inulin and levan accumulate in certain taxonomic groups of plants and are a reserve carbohydrate alternative to starch. Onion (Allium cepa L.) is a typical plant species that accumulates fructans, and it synthesizes inulin-type and inulin neoseries-type fructans in the bulb. Although genes for fructan biosynthesis in onion have been identified so far, no genes for fructan degradation had been found. In this study, phylogenetic analysis predicted that we isolated a putative vacuolar invertase gene (AcpVI1), but our functional analyses demonstrated that it encoded a fructan 1-exohydrolase (1-FEH) instead. Assessments of recombinant proteins and purified native protein showed that the protein had 1-FEH activity, hydrolyzing the β-(2,1)-fructosyl linkage in inulin-type fructans. Interestingly, AcpVI1 had an amino acid sequence close to those of vacuolar invertases and fructosyltransferases, unlike all other FEHs previously found in plants. We showed that AcpVI1 was localized in the vacuole, as are onion fructosyltransferases Ac1-SST and Ac6G-FFT. These results indicate that fructan-synthesizing and -degrading enzymes are both localized in the vacuole. In contrast to previously reported FEHs, our data suggest that onion 1-FEH evolved from a vacuolar invertase and not from a cell wall invertase. This demonstrates that classic phylogenetic analysis on its own is insufficient to discriminate between invertases and FEHs, highlighting the importance of functional markers in the nearby active site residues.
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Affiliation(s)
- Satoshi Oku
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Keiji Ueno
- Graduate School of Dairy Science, Rakuno Gakuen University, Ebetsu, 069-8501, Japan
| | - Yukiko Sawazaki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Tomoo Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, 036-8561, Japan
| | - Yutaka Jitsuyama
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Takashi Suzuki
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Shuichi Onodera
- Graduate School of Dairy Science, Rakuno Gakuen University, Ebetsu, 069-8501, Japan
| | - Kaien Fujino
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hanako Shimura
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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Jeon S, Han J, Kim CW, Kim JG, Moon JH, Kim S. Identification of a candidate gene responsible for the G locus determining chartreuse bulb color in onion (Allium cepa L.) using bulked segregant RNA-Seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1025-1036. [PMID: 35034161 DOI: 10.1007/s00122-021-04016-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
A gene encoding a laccase responsible for chartreuse onion bulb color was identified. Markers tagging this gene showed perfect linkage with bulb colors among diverse germplasm. To identify a casual gene for the G locus determining chartreuse bulb color in onion (Allium cepa L.), bulked segregant RNA-Seq (BSR-Seq) was performed using yellow and chartreuse individuals of a segregating population. Through single nucleotide polymorphism (SNP) and differentially expressed gene (DEG) screening processes, 163 and 143 transcripts were selected, respectively. One transcript encoding a laccase-like protein was commonly identified from SNP and DEG screening. This transcript contained four highly conserved copper-binding domains known to be signature sequences of laccases. This gene was designated AcLAC12 since it showed high homology with Arabidopsis AtLAC12. A 4-bp deletion creating a premature stop codon was identified in exon 5 of the chartreuse allele. Another mutant allele in which an intact LTR-retrotransposon was transposed in exon 5 was identified from other chartreuse breeding lines. Genotypes of molecular markers tagging AcLAC12 were perfectly matched with bulb color phenotypes in segregating populations and diverse breeding lines. All chartreuse breeding lines contained inactive alleles of DFR-A gene determining red bulb color, indicating that chartreuse color appeared when both DFR-A and AcLAC12 genes were inactivated. Linkage maps showed that AcLAC12 was positioned at the end of chromosome 7. Transcription levels of structural genes encoding enzymes in anthocyanin biosynthesis pathway were generally reduced in chartreuse bulk compared with yellow bulk. Concentrations of total quercetins were also reduced in chartreuse onion. However, significant amounts of quercetins were detected in chartreuse onion, implying that AcLAC12 might be involved in modification of quercetin derivatives in onion.
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Affiliation(s)
- SeongChan Jeon
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - JiWon Han
- National Institute of Horticultural and Herbal Science, RDA, Muan, 58545, Republic of Korea
| | - Cheol-Woo Kim
- National Institute of Horticultural and Herbal Science, RDA, Muan, 58545, Republic of Korea
| | - Ju-Gyeong Kim
- Department of Food Science and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jae-Hak Moon
- Department of Food Science and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Finkers R, van Kaauwen M, Ament K, Burger-Meijer K, Egging R, Huits H, Kodde L, Kroon L, Shigyo M, Sato S, Vosman B, van Workum W, Scholten O. Insights from the first genome assembly of Onion (Allium cepa). G3 (BETHESDA, MD.) 2021; 11. [PMID: 34544132 DOI: 10.1101/2021.03.05.434149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/06/2021] [Indexed: 05/18/2023]
Abstract
Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
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Affiliation(s)
- Richard Finkers
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Kai Ament
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Karin Burger-Meijer
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Henk Huits
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Linda Kodde
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Laurens Kroon
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University Yamaguchi City, Yamaguchi 753-8515, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Ben Vosman
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Olga Scholten
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
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9
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Finkers R, van Kaauwen M, Ament K, Burger-Meijer K, Egging R, Huits H, Kodde L, Kroon L, Shigyo M, Sato S, Vosman B, van Workum W, Scholten O. Insights from the first genome assembly of Onion (Allium cepa). G3 (BETHESDA, MD.) 2021; 11:jkab243. [PMID: 34544132 PMCID: PMC8496297 DOI: 10.1093/g3journal/jkab243] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022]
Abstract
Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
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Affiliation(s)
- Richard Finkers
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Kai Ament
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Karin Burger-Meijer
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Henk Huits
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Linda Kodde
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | - Laurens Kroon
- Bejo Zaden B.V., 1749 CZ Warmerhuizen, The Netherlands
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University Yamaguchi City, Yamaguchi 753-8515, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Ben Vosman
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
| | | | - Olga Scholten
- Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands
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