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An Y, Ban Q, Liu L, Zhang F, Yu S, Jing T, Zhao S. PPGV: a comprehensive database of peach population genome variation. BMC PLANT BIOLOGY 2024; 24:701. [PMID: 39048957 PMCID: PMC11267775 DOI: 10.1186/s12870-024-05437-2] [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: 01/28/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Peach tree is one of the most important fruit trees in the world, and it has been cultivated for more than 7,500 years. In recent years, the genome and population resequencing of peach trees have been published continuously, which has effectively promoted the research of peach tree genetics and breeding. In order to promote the further mining and utilization of these data, we integrated and constructed a comprehensive peach genome and variation database (PPGV, http://peachtree.work/home ). The PPGV contains 10 sets of published peach tree genome data, as well as genomic variation information for 1,378 peach tree samples (the resequencing data of 1,378 samples were aligned with the high-quality genomes of Lovell, CN14 and Chinesecling, respectively, for mutation detection). A variety of useful and flexible tools, such as BLAST, Gene ID Convert, KEGG/GO Enrichment, Primer Design and Gene function, were also specially designed for searching data and assisting in breeding.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Qiuyan Ban
- College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Li Liu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Shirui Yu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China.
| | - Shiqi Zhao
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China.
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An Y, Xia X, Zheng H, Yu S, Jing T, Zhang F. Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding. BMC Genom Data 2023; 24:62. [PMID: 37924022 PMCID: PMC10625204 DOI: 10.1186/s12863-023-01165-y] [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: 02/23/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND As an important food and cash crop, identification of DNA molecular markers is of great significance for molecular marker-assisted breeding of Sorghum (Sorghum bicolor (L.) moench). Although some sorghum-related mutation databases have been published, the special SSR and SV databases still need to be constructed and updated. RESULTS In this study, the quality of 18 different sorghum genomes was evaluated, and two genomes were assembled at chromosome level. Through the identification and comparative analysis of SSR loci in these genomes, the distribution characteristics of SSR in the above sorghum genomes were initially revealed. At the same time, five representative reference genomes were selected to identify the structural variation of sorghum. Finally, a convenient SSR/SV database of sorghum was constructed by integrating the above results ( http://www.sorghum.top:8079/ ; http://43.154.129.150:8079/ ; http://47.106.184.91:8079/ ). Users can query the information of related sites and primer pairs. CONCLUSIONS Anyway, our research provides convenience for sorghum researchers and will play an active role in sorghum molecular marker-assisted breeding.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Xiaobo Xia
- College of Plant Protection , Nanjing Agricultural University, Nanjing, 210095, China
| | - Huayan Zheng
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Shirui Yu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China.
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China.
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Patra AK, Ho PT, Jun S, Lee SJ, Kim Y, Won YJ. Genome assembly of the Korean intertidal mud-creeper Batillaria attramentaria. Sci Data 2023; 10:498. [PMID: 37507420 PMCID: PMC10382545 DOI: 10.1038/s41597-023-02403-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Batillaridae is a common gastropod family that occurs abundantly in the shallow coastal zone of the intertidal mudflats of the northwest Pacific Ocean, Australasia, and North America. In this family, Batillaria attramentaria is known for its biological invasion and colonization in estuarine and intertidal zones. It can endure and adapt the harsh intertidal conditions such as frequent temperature alteration, salinity, and air exposure. Therefore, we sequenced and assembled this Korean batillariid genome to get insight into its intertidal adaptive features. Approximately 53 Gb of DNA sequences were generated, and 863 scaffolds were assembled into a draft genome of 0.715 Gb with 97.1% BUSCO completeness value. A total of 40,596 genes were predicted. We estimated that B. attramentaria and Conus consors diverged about 230 million years ago (MYA) based on the phylogenetic analysis of closely related gastropod species. This genome study sets the footstep for genomics studies among native and introduced Batillaria populations and the Batillaridae family members.
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Affiliation(s)
- Ajit Kumar Patra
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | - Phuong-Thao Ho
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea
- Laboratory of Ecology and Environmental Management, Science and Technology Advanced Institute, Van Lang University, Ho Chi Minh City, Vietnam
- Department of International Program, US Vietnam Talent International School, Ho Chi Minh city, Viet Nam
| | - Siyeong Jun
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | | | - Yuseob Kim
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea.
| | - Yong-Jin Won
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea.
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Zhao SY, Muchuku JK, Liang HY, Wang QF. A complete chloroplast genome of a traditional Chinese medicine herb, Rubia podantha, and phylogenomics of Rubiaceae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:843-853. [PMID: 37520807 PMCID: PMC10382452 DOI: 10.1007/s12298-023-01302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 08/01/2023]
Abstract
Rubia podantha Diels is endemic to southwestern China and belongs to the family Rubiaceae. It is used in traditional Chinese medicines. To enrich the genetic data and resolve Rubiaceae's phylogeny, we assembled a complete chloroplast (cp) genome of R. podantha using Illumina HiSeq reads. The whole length of the cp genome was 154,866 bp. Annotation using PGA software found 113 genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The large single-copy region was 84,717 bp, the inverted repeat B (IRa) region was 26,516 bp, the small single copy was 17,117 bp, and the inverted repeats B (IRb) region was 26,516 bp. Moreover, 64 SSRs were identified. Phylogenomic analysis using cp genomes of 109 Rubiaceae species found that R. podantha is closely related to R. cordifola. Rubiaceae was separated into three subfamilies: Ixoroideae, Cinchonoideae, and Rubiodeae. The genus Saprosma was not imbedded within the Spermacoceae alliance as reported in previous studies. Instead, it was imbedded within the Psychotrieae alliance. Divergence time estimation indicated that R. podantha split from its relative R. cordifolia around 1.25 million years ago. The assembled chloroplast genome in this study provided useful molecular information about the evolution of R. podantha and was a basis for phylogenetic analyses of Rubiaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01302-y.
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Affiliation(s)
- Shu-Ying Zhao
- School of Environment and Ecology, Jiangsu Open University, Nanjing, 210036 China
| | - John K. Muchuku
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200 Kenya
| | - Hai-Ying Liang
- School of Environment and Ecology, Jiangsu Open University, Nanjing, 210036 China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
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Hou S, Wu F, Wang Z, Yan N, Chen H, Li H, Yang P, Zhang Y, Li C, Lin Y, Ma J, Huang L, Liu Y. Mapping Stripe Rust Resistance QTL in 'N2496', a Synthetic Hexaploid Wheat Derivative. PLANT DISEASE 2023; 107:443-449. [PMID: 35802018 DOI: 10.1094/pdis-07-22-1518-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stripe rust is a destructive disease that affects plant growth and substantially reduces wheat yields globally. An economically and environmentally friendly way to control this disease is to use resistant cultivars. 'N2496' is a synthetic hexaploid wheat derivative that exhibits high resistance and could serve as a source of resistance for breeding programs. We developed three recombinant inbred lines (RILs) populations by crossing 'N2496' with common wheat cultivars 'CN16', 'CM107', and 'MM37'. Stripe rust responses were evaluated in all three populations using a mixture of current predominant Chinese Puccinia striiformis f. sp. tritici races. A stripe rust resistance quantitative trait locus (QTL) in the 'N2496'/'CN16' RIL population was mapped on chromosome arm 6BL at 519.35 to 526.55 Mb using bulked segregant RNA sequencing. The population was genotyped using simple sequence repeats and kompetitive allele-specific polymerase (KASP) markers. The QTL QYr.sicau-6B was localized to a 1.19-cM interval flanked by markers KASP-TXK-10 and KASP-TXK-6. The genetic effect of QYr.sicau-6B was validated in the 'N2496' × 'CM107' and 'N2496' × 'MM37' RILs populations and explained up to 63.16% of the phenotypic variation. RNA sequencing and quantitative real-time polymerase chain reaction identified two differentially expressed candidate genes in the physical interval of QYr.sicau-6B.
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Affiliation(s)
- Shuai Hou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Fangkun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Zhiqiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Ning Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Hao Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Haojie Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Peiyu Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Ying Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Caixia Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, China
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An Y, Zhang X, Jiang S, Zhao J, Zhang F. TeaPVs: a comprehensive genomic variation database for tea plant (Camellia sinensis). BMC PLANT BIOLOGY 2022; 22:513. [PMID: 36324064 PMCID: PMC9632082 DOI: 10.1186/s12870-022-03901-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Genome variation not only plays an important role in plant phenotypic modeling and adaptive evolution, but also enhances population genetic diversity and regulates gene expression. The tea tree (Camellia sinensis) has a large genome (~ 3.0 Gb), making the identification of genome-wide variants time-consuming and expensive. With the continuous publication of a large number of different types of population sequencing data, there is a lack of an open platform to integrate these data and identify variants in the tea plant genome.To integrate the genetic variation confidence in the tea plant population genome, 238 whole-genome resequencing, 213 transcriptome sequencing, and 96 hybrid F1 individuals with a total of more than 20 Tb were collected for mutation site identification. Based on these variations information, we constructed the first tea tree variation web service database TeaPVs ( http://47.106.184.91:8025/ and http://liushang.top:8025/ ). It supports users to search all SNP, Indel, SV mutations and SSR/Polymorphic SSR sequences by location or gene ID. Furthermore, the website also provides the functions of gene expression search of different transcriptome, sequence blast, sequence extraction of CDS and mutation loci, etc.The features of the TeaPVs database make it a comprehensive tea plant genetic variation bioinformatics platform for researchers, and will also be helpful for revealing new functional mutations in the tea plant genome and molecular marker-assisted breeding.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, People's Republic of China
| | - Xiaoqin Zhang
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, People's Republic of China
| | - Sixia Jiang
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, People's Republic of China
| | - Jingjing Zhao
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, People's Republic of China
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Luban Street, Renhuai, 564502, Guizhou, People's Republic of China.
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Duan B, Mu S, Guan Y, Liu W, Kang T, Cheng Y, Li Z, Tian Y, Kang X. Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus). Front Genet 2022; 13:932173. [PMID: 35923702 PMCID: PMC9340201 DOI: 10.3389/fgene.2022.932173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/16/2022] [Indexed: 12/02/2022] Open
Abstract
P. trituberculatus is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of P. trituberculatus. Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which “general function prediction only” was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 P. trituberculatus individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise FST values were between 0.001 and 0.04 with an average of 0.0205 (p < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of P. trituberculatus in the future.
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Affiliation(s)
- Baohua Duan
- College of Life Sciences, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China
| | - Yueqiang Guan
- College of Life Sciences, Hebei University, Baoding, China
| | - Weibiao Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Tongxu Kang
- College of Life Sciences, Hebei University, Baoding, China
| | - Yana Cheng
- College of Life Sciences, Hebei University, Baoding, China
| | - Zejian Li
- Bureau of Agricultural and Rural Affairs of Huanghua City, Huanghua, China
| | - Yang Tian
- Hebei Fishery Technology Extension Station, Shijiazhuang, China
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China
- Institute of Life Science and Green Development, Hebei University, Baoding, China
- Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
- *Correspondence: Xianjiang Kang,
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Wang Z, Wu F, Chen X, Zhou W, Shi H, Lin Y, Hou S, Yu S, Zhou H, Li C, Liu Y. Fine mapping of the tiller inhibition gene TIN4 contributing to ideal plant architecture in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:527-535. [PMID: 34716761 DOI: 10.1007/s00122-021-03981-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 05/26/2023]
Abstract
A tiller inhibition gene, TIN4, was mapped to an approximately 311 kb genomic interval on chromosome arm 2DL of wheat. The tiller is one of the key components of plant morphological architecture and a central agronomic trait affecting spike number in wheat. Low tiller number has been proposed as a major component of crop ideotypes for high yield potential. In this study, we characterized the development of tillering in near-isogenic lines (NIL7A and NIL7B), indicating that the TIN4 gene inhibited the growth of tillering buds and negatively regulated tiller number. Low-tillering was controlled by a single gene (TIN4) located on chromosome 2DL by genetic analysis and bulked segregant RNA-seq analysis. A total of 17 new polymorphic markers were developed in this study, and 61 recombinants were identified in the secondary F2 population containing 4,266 individuals. TIN4 was finally mapped on a 0.35 cM interval, co-segregated with molecular marker M380, within a 311 kb genomic interval of the wheat cultivar Chinese Spring reference genome sequence that contained twelve predicted genes. Yield experiments showed that the yield of low-tillering lines was higher than that of high-tillering lines at a higher density. Overall, this study provides a foundation for the construction of a low-tillering ideotype for improving wheat yield and further cloning TIN4 by map-based cloning approach.
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Affiliation(s)
- Zhiqiang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Fangkun Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xudong Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Wanlin Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Haoran Shi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shuai Hou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shifan Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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Finding and Characterizing Repeats in Plant Genomes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2443:327-385. [PMID: 35037215 DOI: 10.1007/978-1-0716-2067-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of the available software that can help biologists to scan automatically for these repeats in sequence data or check hypothetical models intended to characterize their structures. Since transposable elements (TEs) are a major source of repeats in plants, many methods have been used or developed for this broad class of sequences. They are representative of the range of tools available for other classes of repeats and we have provided two sections on this topic (for the analysis of genomes or directly of sequenced reads), as well as a selection of the main existing software. It may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of an efficient search for repeats and more complex patterns. We first introduce the key concepts of the art of indexing and mapping or querying sequences. We end the chapter with the more prospective issue of building models of repeat families. We present the Machine Learning approach first, seeking to build predictors automatically for some families of ET, from a set of sequences known to belong to this family. A second approach, the linguistic (or syntactic) approach, allows biologists to describe themselves and check the validity of models of their favorite repeat family.
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Makarenko MS, Omelchenko DO, Usatov AV, Gavrilova VA. The Insights into Mitochondrial Genomes of Sunflowers. PLANTS (BASEL, SWITZERLAND) 2021; 10:1774. [PMID: 34579307 PMCID: PMC8466785 DOI: 10.3390/plants10091774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022]
Abstract
The significant difference in the mtDNA size and structure with simultaneous slow evolving genes makes the mitochondrial genome paradoxical among all three DNA carriers in the plant cell. Such features make mitochondrial genome investigations of particular interest. The genus Helianthus is a diverse taxonomic group, including at least two economically valuable species-common sunflower (H. annuus) and Jerusalem artichoke (H. tuberosus). The successful investigation of the sunflower nuclear genome provided insights into some genomics aspects and significantly intensified sunflower genetic studies. However, the investigations of organelles' genetic information in Helianthus, especially devoted to mitochondrial genomics, are presented by limited studies. Using NGS sequencing, we assembled the complete mitochondrial genomes for H. occidentalis (281,175 bp) and H. tuberosus (281,287 bp) in the current investigation. Besides the master circle chromosome, in the case of H. tuberosus, the 1361 bp circular plasmid was identified. The mitochondrial gene content was found to be identical for both sunflower species, counting 32 protein-coding genes, 3 rRNA, 23 tRNA genes, and 18 ORFs. The comparative analysis between perennial sunflowers revealed common and polymorphic SSR and SNPs. Comparison of perennial sunflowers with H. annuus allowed us to establish similar rearrangements in mitogenomes, which have possibly been inherited from a common ancestor after the divergence of annual and perennial sunflower species. It is notable that H. occidentalis and H. tuberosus mitogenomes are much more similar to H. strumosus than H. grosseserratus.
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Affiliation(s)
- Maksim S. Makarenko
- The Laboratory of Plant Genomics, The Institute for Information Transmission Problems, 127051 Moscow, Russia;
| | - Denis O. Omelchenko
- The Laboratory of Plant Genomics, The Institute for Information Transmission Problems, 127051 Moscow, Russia;
| | - Alexander V. Usatov
- The Department of Genetics, Southern Federal University, 344006 Rostov-on-Don, Russia;
| | - Vera A. Gavrilova
- Oil and Fiber Crops Genetic Resources Department, The N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190031 Saint Petersburg, Russia;
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