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Castanera R, de Tomás C, Ruggieri V, Vicient C, Eduardo I, Aranzana MJ, Arús P, Casacuberta JM. A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants. HORTICULTURE RESEARCH 2024; 11:uhae106. [PMID: 38883330 PMCID: PMC11179849 DOI: 10.1093/hr/uhae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 06/18/2024]
Abstract
The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here, we present a phased assembly of genome of the almond cv. Texas. This new assembly has 13% more assembled sequence than the previous version of the Texas genome and has an increased contiguity, in particular in repetitive regions such as the centromeres. Our analysis shows that the 'Texas' genome has a high degree of heterozygosity, both at SNPs, short indels, and structural variants level. Many of the SVs are the result of heterozygous transposable element insertions, and in many cases, they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes are often associated with allele-specific gene expression, which highlights the importance of heterozygous SVs in almond.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Carlos de Tomás
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Carlos Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
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2
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Feng L, Zhao G, An M, Wang C, Yin Y. Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species. BMC Genomics 2023; 24:739. [PMID: 38053028 DOI: 10.1186/s12864-023-09838-9] [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: 05/19/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Prunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast genome of P. cistena and compared it with related species of the genus Prunus based on the chloroplast genome. RESULTS The complete chloroplast genome of P. cistena is a 157,935 bp long typical tetrad structure, with an overall GC content of 36.72% and higher GC content in the in the inverted repeats (IR) regions than in the large single-copy (LSC) and small single-copy (SSC) regions. It contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes have two introns, with the longest intron in the trnK-UUU gene in the LSC region. Moreover, the genome has a total of 253SSRs, with the mononucleotide SSRs being the most abundant. The chloroplast sequences and gene arrangements of P. cistena are highly conserved, with the overall structure and gene order similar to other Prunus species. The atpE, ccsA, petA, rps8, and matK genes have undergone significant positive selection in Prunus species. P. cistena has a close evolutionary relationship with P. jamasakura. The coding and IR regions are more conserved than the noncoding regions, and the chloroplast DNA sequences are highly conserved throughout the genus Prunus. CONCLUSIONS The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of the genus Prunus.
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Affiliation(s)
- Lijuan Feng
- Shandong Institute of Pomology, Taian, 271000, Shandong, China
| | - Guopeng Zhao
- Yantai Testing Center for Food and Drug, Yantai, 264005, Shandong, China
| | - Mengmeng An
- Zibo Academy of Agricultural Sciences, Zibo, 255000, Shandong, China
| | - Chuanzeng Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.
| | - Yanlei Yin
- Shandong Institute of Pomology, Taian, 271000, Shandong, China.
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Fresnedo-Ramírez J, Anderson ES, D'Amico-Willman K, Gradziel TM. A review of plant epigenetics through the lens of almond. THE PLANT GENOME 2023; 16:e20367. [PMID: 37434488 DOI: 10.1002/tpg2.20367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023]
Abstract
While genomes were originally seen as static entities that stably held and organized genetic information, recent advances in sequencing have uncovered the dynamic nature of the genome. New conceptualizations of the genome include complex relationships between the environment and gene expression that must be maintained, regulated, and sometimes even transmitted over generations. The discovery of epigenetic mechanisms has allowed researchers to understand how traits like phenology, plasticity, and fitness can be altered without changing the underlying deoxyribonucleic acid sequence. While many discoveries were first made in animal systems, plants provide a particularly complex set of epigenetic mechanisms due to unique aspects of their biology and interactions with human selective breeding and cultivation. In the plant kingdom, annual plants have received the most attention; however, perennial plants endure and respond to their environment and human management in distinct ways. Perennials include crops such as almond, for which epigenetic effects have long been linked to phenomena and even considered relevant for breeding. Recent discoveries have elucidated epigenetic phenomena that influence traits such as dormancy and self-compatibility, as well as disorders like noninfectious bud failure, which are known to be triggered by the environment and influenced by inherent aspects of the plant. Thus, epigenetics represents fertile ground to further understand almond biology and production and optimize its breeding. Here, we provide our current understanding of epigenetic regulation in plants and use almond as an example of how advances in epigenetics research can be used to understand biological fitness and agricultural performance in crop plants.
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Affiliation(s)
| | - Elizabeth S Anderson
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, USA
| | | | - Thomas M Gradziel
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
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Lyu K, Xiao J, Lyu S, Liu R. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels. Int J Mol Sci 2023; 24:16935. [PMID: 38069258 PMCID: PMC10706760 DOI: 10.3390/ijms242316935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.
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Affiliation(s)
- Keliang Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jiajing Xiao
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shiheng Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (K.L.); (S.L.)
| | - Renyi Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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Wang Y, Li X, Feng Y, Wang J, Zhang J, Liu Z, Wang H, Chen T, He W, Wu Z, Lin Y, Zhang Y, Li M, Chen Q, Zhang Y, Luo Y, Tang H, Wang X. Autotetraploid Origin of Chinese Cherry Revealed by Chromosomal Karyotype and In Situ Hybridization of Seedling Progenies. PLANTS (BASEL, SWITZERLAND) 2023; 12:3116. [PMID: 37687365 PMCID: PMC10490022 DOI: 10.3390/plants12173116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Polyploidy is considered a driving force in plant evolution and diversification. Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], an economically important fruit crop native to China, has evolved at the tetraploid level, with a few pentaploid and hexaploid populations. However, its auto- or allo-polyploid origin remains unclear. To address this issue, we analyzed the ploidy levels and rDNA chromosomal distribution in self- and open-pollinated seedling progenies of tetraploid and hexaploid Chinese cherry. Genomic in situ hybridization (GISH) analysis was conducted to reveal the genomic relationships between Chinese cherry and diploid relatives from the genus Cerasus. Both self- and open-pollinated progenies of tetraploid Chinese cherry exhibited tetraploids, pentaploids, and hexaploids, with tetraploids being the most predominant. In the seedling progenies of hexaploid Chinese cherry, the majority of hexaploids and a few pentaploids were observed. A small number of aneuploids were also observed in the seedling progenies. Chromosome 1, characterized by distinct length characteristics, could be considered the representative chromosome of Chinese cherry. The basic Chinese cherry genome carried two 5S rDNA signals with similar intensity, and polyploids had the expected multiples of this copy number. The 5S rDNA sites were located at the per-centromeric regions of the short arm on chromosomes 4 and 5. Three 45S rDNA sites were detected on chr. 3, 4 and 7 in the haploid complement of Chinese cherry. Tetraploids exhibited 12 signals, while pentaploids and hexaploids showed fewer numbers than expected multiples. Based on the GISH signals, Chinese cherry demonstrated relatively close relationships with C. campanulata and C. conradinae, while being distantly related to another fruiting cherry, C. avium. In combination with the above results, our findings suggested that Chinese cherry likely originated from autotetraploidy.
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Affiliation(s)
- Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Xueou Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Rural Revitalization Service Center, Agricultural and Rural Bureau of Cuiping District Yibin City, Yibin 644000, China
| | - Juan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Tao Chen
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China;
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Zhiwei Wu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.W.); (X.L.); (Y.F.); (J.W.); (J.Z.); (Z.L.); (H.W.); (W.H.); (Z.W.); (Y.L.); (Y.Z.); (M.L.); (Q.C.); (Y.Z.); (Y.L.); (H.T.)
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu 611130, China
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Harun A, Liu H, Song S, Asghar S, Wen X, Fang Z, Chen C. Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2816. [PMID: 37570972 PMCID: PMC10420648 DOI: 10.3390/plants12152816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies.
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Affiliation(s)
- Arrashid Harun
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, China;
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Hui Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Shipeng Song
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Sumeera Asghar
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
| | - Zhongming Fang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, China;
| | - Chunli Chen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, China;
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
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7
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Nie C, Zhang Y, Zhang X, Xia W, Sun H, Zhang S, Li N, Ding Z, Lv Y, Wang N. Genome assembly, resequencing and genome-wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:519-533. [PMID: 36786729 DOI: 10.1111/tpj.16151] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 05/10/2023]
Abstract
Flowering cherry is a very popular species around the world. High-quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high-quality chromosome-scale genome of Prunus campanulata 'Plena' (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high-quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome-wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.
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Affiliation(s)
- Chaoren Nie
- School of Landscape Architecture, Beijing Forestry of University, Beijing, 100083, China
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Yingjie Zhang
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China
| | - Xiaoqin Zhang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Wensheng Xia
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Hongbing Sun
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Na Li
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Zhaoquan Ding
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Yingmin Lv
- School of Landscape Architecture, Beijing Forestry of University, Beijing, 100083, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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8
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Wang L, Feng Y, Wang Y, Zhang J, Chen Q, Liu Z, Liu C, He W, Wang H, Yang S, Zhang Y, Luo Y, Tang H, Wang X. Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH. Int J Mol Sci 2022; 23:ijms232113213. [PMID: 36361999 PMCID: PMC9653872 DOI: 10.3390/ijms232113213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
A precise, rapid and straightforward approach to chromosome identification is fundamental for cytogenetics studies. However, the identification of individual chromosomes was not previously possible for Chinese cherry or other Prunus species due to the small size and similar morphology of their chromosomes. To address this issue, we designed a pool of oligonucleotides distributed across specific pseudochromosome regions of Chinese cherry. This oligonucleotide pool was amplified through multiplex PCR with specific internal primers to produce probes that could recognize specific chromosomes. External primers modified with red and green fluorescence tags could produce unique signal barcoding patterns to identify each chromosome concomitantly. The same oligonucleotide pool could also discriminate all chromosomes in other Prunus species. Additionally, the 5S/45S rDNA probes and the oligo pool were applied in two sequential rounds of fluorescence in situ hybridization (FISH) localized to chromosomes and showed different distribution patterns among Prunus species. At the same time, comparative karyotype analysis revealed high conservation among P. pseudocerasus, P. avium, and P. persica. Together, these findings establish this oligonucleotide pool as the most effective tool for chromosome identification and the analysis of genome organization and evolution in the genus Prunus.
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Affiliation(s)
- Lei Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Congli Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 410100, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaofeng Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
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Zattera ML, Bruschi DP. Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells 2022; 11:3373. [PMID: 36359770 PMCID: PMC9659126 DOI: 10.3390/cells11213373] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 12/02/2022] Open
Abstract
The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host's gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.
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Affiliation(s)
- Michelle Louise Zattera
- Departamento de Genética, Programa de Pós-Graduação em Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Laboratorio de Citogenética Evolutiva e Conservação Animal, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
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