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Liu Q, Xiong G, Wang Z, Wu Y, Tu T, Schwarzacher T, Heslop-Harrison JS. Chromosome-level genome assembly of the diploid oat species Avena longiglumis. Sci Data 2024; 11:412. [PMID: 38649380 PMCID: PMC11035610 DOI: 10.1038/s41597-024-03248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Diploid wild oat Avena longiglumis has nutritional and adaptive traits which are valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies. Two recent whole-genome duplication events were characterized in genomes of diploid Avena species. These findings provide new knowledge for the genomic features of A. longiglumis, give information about the species diversity, and will accelerate the functional genomics and breeding studies in oat and related cereal crops.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, China.
| | - Gui Xiong
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziwei Wang
- School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Yongxing Wu
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Tieyao Tu
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, China
| | - Trude Schwarzacher
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, China
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester, UK
| | - John Seymour Heslop-Harrison
- State Key Laboratory of Plant Diversity and Specialty Crops / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, China.
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester, UK.
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Masters LE, Tomaszewska P, Schwarzacher T, Hackel J, Zuntini AR, Heslop-Harrison P, Vorontsova MS. Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa. Ann Bot 2024:mcae022. [PMID: 38365451 DOI: 10.1093/aob/mcae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND AND AIMS The grass genus Urochloa (Brachiaria) sensu lato includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America, and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis, and Megathyrsus maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems, and frequent polyploidy are widely shared within the genus. The combination of these traits likely favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. We aim to produce a phylogeny for Urochloa that includes all important forage species, and identify their closest wild relatives (crop wild relatives). Finally, we will use our phylogeny and available trait data to infer the ancestral states of important forage traits across Urochloa s.l. and model the evolution of forage syndromes across the genus. METHODS Using a target enrichment sequencing approach (Angiosperms353), we inferred a species level phylogeny for Urochloa s.l., encompassing 54 species (~40% of the genus) and outgroups. Phylogenies were inferred using a multispecies coalescent model and maximum likelihood method. We determined the phylogenetic placement of agriculturally important species and identified their closest wild relatives, or crop wild relatives, based on well-supported monophyly. Further, we mapped key traits associated with Urochloa forage crops to the species tree and estimated ancestral states for forage traits along branch lengths for continuous traits and at ancestral nodes in discrete traits. KEY RESULTS Agricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis, and large seeds) independently evolved in forage clades. CONCLUSIONS Urochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. All forage species and their crop wild relatives naturally occur on the African continent and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives needs to be better assessed both to develop conservation strategies, and exploit the diversity in the genus for improved sustainability in Urochloa cultivar production.
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Affiliation(s)
- Lizo E Masters
- Accelerated Taxonomy, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester LE1 7RH, UK
| | - Paulina Tomaszewska
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester LE1 7RH, UK
- Department of Genetics and Cell Physiology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Trude Schwarzacher
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | | | - Alexandre R Zuntini
- Accelerated Taxonomy, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Pat Heslop-Harrison
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Maria S Vorontsova
- Accelerated Taxonomy, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
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Liu Q, Ye L, Li M, Wang Z, Xiong G, Ye Y, Tu T, Schwarzacher T, Heslop-Harrison JSP. Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena. BMC Plant Biol 2023; 23:627. [PMID: 38062402 PMCID: PMC10704644 DOI: 10.1186/s12870-023-04644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural variation, and chromosomal rearrangements from rice and Brachypodium, to diploids in the tribe Aveneae (e.g., Avena longiglumis, 2n = 2x = 14; 3,961 Mb assembled to 3,850 Mb in chromosomes). RESULTS Most of the Avena chromosome arms show relatively uniform expansion over the 10-fold to 15-fold genome-size increase. Apart from non-coding sequence diversification and accumulation around the centromeres, blocks of genes are not interspersed with blocks of repeats, even in subterminal regions. As in the tribe Triticeae, blocks of conserved synteny are seen between the analyzed species with chromosome fusion, fission, and nesting (insertion) events showing deep evolutionary conservation of chromosome structure during genomic expansion. Unexpectedly, the terminal gene-rich chromosomal segments (representing about 50 Mb) show translocations between chromosomes during speciation, with homogenization of genome-specific repetitive elements within the tribe Aveneae. Newly-formed intergenomic translocations of similar extent are found in the hexaploid A. sativa. CONCLUSIONS The study provides insight into evolutionary mechanisms and speciation in the BOP clade, which is valuable for measurement of biodiversity, development of a clade-wide pangenome, and exploitation of genomic diversity through breeding programs in Poaceae.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Lyuhan Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingzhi Li
- Bio&Data Biotechnologies Co. Ltd, Guangzhou, 510663, China
| | - Ziwei Wang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Gui Xiong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yushi Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK.
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Alisawi O, Richert-Pöggeler KR, Heslop-Harrison J(P, Schwarzacher T. The nature and organization of satellite DNAs in Petunia hybrida, related, and ancestral genomes. Front Plant Sci 2023; 14:1232588. [PMID: 37868307 PMCID: PMC10587573 DOI: 10.3389/fpls.2023.1232588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023]
Abstract
Introduction The garden petunia, Petunia hybrida (Solanaceae) is a fertile, diploid, annual hybrid species (2n=14) originating from P. axillaris and P. inflata 200 years ago. To understand the recent evolution of the P. hybrida genome, we examined tandemly repeated or satellite sequences using bioinformatic and molecular cytogenetic analysis. Methods Raw reads from available genomic assemblies and survey sequences of P. axillaris N (PaxiN), P. inflata S6, (PinfS6), P. hybrida (PhybR27) and the here sequenced P. parodii S7 (PparS7) were used for graph and k-mer based cluster analysis of TAREAN and RepeatExplorer. Analysis of repeat specific monomer lengths and sequence heterogeneity of the major tandem repeat families with more than 0.01% genome proportion were complemented by fluorescent in situ hybridization (FISH) using consensus sequences as probes to chromosomes of all four species. Results Seven repeat families, PSAT1, PSAT3, PSAT4, PSAT5 PSAT6, PSAT7 and PSAT8, shared high consensus sequence similarity and organisation between the four genomes. Additionally, many degenerate copies were present. FISH in P. hybrida and in the three wild petunias confirmed the bioinformatics data and gave corresponding signals on all or some chromosomes. PSAT1 is located at the ends of all chromosomes except the 45S rDNA bearing short arms of chromosomes II and III, and we classify it as a telomere associated sequence (TAS). It is the most abundant satellite repeat with over 300,000 copies, 0.2% of the genomes. PSAT3 and the variant PSAT7 are located adjacent to the centromere or mid-arm of one to three chromosome pairs. PSAT5 has a strong signal at the end of the short arm of chromosome III in P. axillaris and P.inflata, while in P. hybrida additional interstitial sites were present. PSAT6 is located at the centromeres of chromosomes II and III. PSAT4 and PSAT8 were found with only short arrays. Discussion These results demonstrate that (i) repeat families occupy distinct niches within chromosomes, (ii) they differ in the copy number, cluster organization and homogenization events, and that (iii) the recent genome hybridization in breeding P. hybrida preserved the chromosomal position of repeats but affected the copy number of repetitive DNA.
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Affiliation(s)
- Osamah Alisawi
- Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
| | - Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - J.S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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White OW, Biswas MK, Abebe WM, Dussert Y, Kebede F, Nichols RA, Buggs RJA, Demissew S, Woldeyes F, Papadopulos AST, Schwarzacher T, Heslop-Harrison PJS, Wilkin P, Borrell JS. Maintenance and expansion of genetic and trait variation following domestication in a clonal crop. Mol Ecol 2023. [PMID: 37264989 DOI: 10.1111/mec.17033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/24/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterize the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and a principal starch staple for 20 million Ethiopians. Wild enset reproduction occurs strictly by sexual outcrossing, but for cultivation, it is propagated clonally and associated with diversification and specialization into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested an accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by the amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages, we found a significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. The development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.
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Affiliation(s)
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Yann Dussert
- CNRS, Université de Poitiers, EBI, Poitiers, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Firew Kebede
- Department of Biology, Hawassa University, Hawassa, Ethiopia
| | - Richard A Nichols
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Richard J A Buggs
- Royal Botanic Gardens Kew, Richmond, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sebsebe Demissew
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Pat J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Liu Q, Yuan H, Xu J, Cui D, Xiong G, Schwarzacher T, Heslop-Harrison JS. The mitochondrial genome of the diploid oat Avena longiglumis. BMC Plant Biol 2023; 23:218. [PMID: 37098475 PMCID: PMC10131481 DOI: 10.1186/s12870-023-04217-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Avena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species. RESULTS The complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100-31,235 bp) and medium (144-792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts. CONCLUSIONS Comparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Hongyu Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaxin Xu
- College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gui Xiong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK.
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Desjardins SD, Bailey JP, Zhang B, Zhao K, Schwarzacher T. New insights into the phylogenetic relationships of Japanese knotweed ( Reynoutriajaponica) and allied taxa in subtribe Reynoutriinae (Polygonaceae). PhytoKeys 2023; 220:83-108. [PMID: 37251615 PMCID: PMC10209619 DOI: 10.3897/phytokeys.220.96922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/13/2023] [Indexed: 05/31/2023]
Abstract
Japanese knotweed (Reynoutriajaponica) is native to East Asia, but has been introduced to the West where it is a noxious invasive weed. Taxonomically, Japanese knotweed is placed within subtribe Reynoutriinae (Polygonaceae), which also contains the austral genus Muehlenbeckia (incl. Homalocladium) and north temperate Fallopia. In the current study, we conducted a phylogenetic analysis using sequence data from six markers, two nuclear (LEAFYi2, ITS) and four plastid (matK, rbcL, rps16-trnK and trnL-trnF) to further resolve the evolutionary relationships within this group, using the widest sampling of in-group taxa to date. The results of this analysis confirmed that subtribe Reynoutriinae is a monophyletic group, characterised by the presence of extra-floral, nectariferous glands at the base of leaf petioles. Within the subtribe, four main clades were identified: Reynoutria, Fallopiasect.Parogonum, Fallopia s.s. (including Fallopia sects. Fallopia and Sarmentosae) and Muehlenbeckia. The Fallopia s.s. and Muehlenbeckia clades are sister to one another, while the Fallopiasect.Parogonum clade is immediately basal to them and Reynoutria basal to all three. Fallopia, as currently circumscribed, is paraphyletic as Muehlenbeckia is nested within it. To resolve this, we propose that species of Fallopiasect.Parogonum should be treated as a new genus, Parogonum (Haraldson) Desjardins & J.P.Bailey, gen. et stat. nov. Within Reynoutria, the allied specific and infraspecific taxa that fall under the name Japanese knotweed s.l. form a monophyletic group and their taxonomic status is discussed.
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Affiliation(s)
- Stuart D. Desjardins
- Department of Genetics and Genome Biology, University of Leicester, Leicester (Leicestershire), UKUniversity of LeicesterLeicesterUnited Kingdom
| | - John P. Bailey
- Department of Genetics and Genome Biology, University of Leicester, Leicester (Leicestershire), UKUniversity of LeicesterLeicesterUnited Kingdom
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei (Anhui), ChinaAnhui UniversityHefeiChina
| | - Kai Zhao
- The National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei (Anhui), ChinaAnhui Agricultural UniversityHefeiChina
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester (Leicestershire), UKUniversity of LeicesterLeicesterUnited Kingdom
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Tomaszewska P, Vorontsova MS, Renvoize SA, Ficinski SZ, Tohme J, Schwarzacher T, Castiblanco V, de Vega JJ, Mitchell RAC, Heslop-Harrison JS(P. Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species. Ann Bot 2023; 131:87-108. [PMID: 34874999 PMCID: PMC9904353 DOI: 10.1093/aob/mcab147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/06/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. METHODS Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. KEY RESULTS Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. CONCLUSIONS We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands.
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Affiliation(s)
| | | | | | | | - Joseph Tohme
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | | | | | - J S (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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9
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Zhang F, Chen F, Schwarzacher T, Heslop-Harrison JS, Teng N. The nature and genomic landscape of repetitive DNA classes in Chrysanthemum nankingense shows recent genomic changes. Ann Bot 2023; 131:215-228. [PMID: 35639931 PMCID: PMC9904347 DOI: 10.1093/aob/mcac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Tandemly repeated DNA and transposable elements represent most of the DNA in higher plant genomes. High-throughput sequencing allows a survey of the DNA in a genome, but whole-genome assembly can miss a substantial fraction of highly repeated sequence motifs. Chrysanthemum nankingense (2n = 2x = 18; genome size = 3.07 Gb; Asteraceae), a diploid reference for the many auto- and allopolyploids in the genus, was considered as an ancestral species and serves as an ornamental plant and high-value food. We aimed to characterize the major repetitive DNA motifs, understand their structure and identify key features that are shaped by genome and sequence evolution. METHODS Graph-based clustering with RepeatExplorer was used to identify and classify repetitive motifs in 2.14 millions of 250-bp paired-end Illumina reads from total genomic DNA of C. nankingense. Independently, the frequency of all canonical motifs k-bases long was counted in the raw read data and abundant k-mers (16, 21, 32, 64 and 128) were extracted and assembled to generate longer contigs for repetitive motif identification. For comparison, long terminal repeat retrotransposons were checked in the published C. nankingense reference genome. Fluorescent in situ hybridization was performed to show the chromosomal distribution of the main types of repetitive motifs. KEY RESULTS Apart from rDNA (0.86 % of the total genome), a few microsatellites (0.16 %), and telomeric sequences, no highly abundant tandem repeats were identified. There were many transposable elements: 40 % of the genome had sequences with recognizable domains related to transposable elements. Long terminal repeat retrotransposons showed widespread distribution over chromosomes, although different sequence families had characteristic features such as abundance at or exclusion from centromeric or subtelomeric regions. Another group of very abundant repetitive motifs, including those most identified as low-complexity sequences (9.07 %) in the genome, showed no similarity to known sequence motifs or tandemly repeated elements. CONCLUSIONS The Chrysanthemum genome has an unusual structure with a very low proportion of tandemly repeated sequences (~1.02 %) in the genome, and a high proportion of low-complexity sequences, most likely degenerated remains of transposable elements. Identifying the presence, nature and genomic organization of major genome fractions enables inference of the evolutionary history of sequences, including degeneration and loss, critical to understanding biodiversity and diversification processes in the genomes of diploid and polyploid Chrysanthemum, Asteraceae and plants more widely.
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Affiliation(s)
- Fengjiao Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Fadi Chen
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Heslop-Harrison JS(P, Schwarzacher T, Liu Q. Polyploidy: its consequences and enabling role in plant diversification and evolution. Ann Bot 2023; 131:1-10. [PMID: 36282971 PMCID: PMC9904344 DOI: 10.1093/aob/mcac132] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/24/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility. SCOPE World-wide interest in how green plants have evolved under different conditions - whether in small, isolated populations, or globally - suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids. CONCLUSION Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy - generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.
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Affiliation(s)
- J S (Pat) Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Schwarzacher T, Liu Q, Pat Heslop-Harrison JS. Plant Cytogenetics: From Chromosomes to Cytogenomics. Methods Mol Biol 2023; 2672:3-21. [PMID: 37335467 DOI: 10.1007/978-1-0716-3226-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Chromosomes have been studied since the late nineteenth century in the disciplines of cytology and cytogenetics. Analyzing their numbers, features, and dynamics has been tightly linked to the technical development of preparation methods, microscopes, and chemicals to stain them, with latest continuing developments described in this volume. At the end of the twentieth and beginning of the twenty-first centuries, DNA technology, genome sequencing, and bioinformatics have revolutionized how we see, use, and analyze chromosomes. The advent of in situ hybridization has shaped our understanding of genome organization and behavior by linking molecular sequence information with the physical location along chromosomes and genomes. Microscopy is the best technique to accurately determine chromosome number. Many features of chromosomes in interphase nuclei or pairing and disjunction at meiosis, involving physical movement of chromosomes, can only be studied by microscopy. In situ hybridization is the method of choice to characterize the abundance and chromosomal distribution of repetitive sequences that make up the majority of most plant genomes. These most variable components of a genome are found to be species- and occasionally chromosome-specific and give information about evolution and phylogeny. Multicolor fluorescence hybridization and large pools of BAC or synthetic probes can paint chromosomes and we can follow them through evolution involving hybridization, polyploidization, and rearrangements, important at a time when structural variations in the genome are being increasingly recognized. This volume discusses many of the most recent developments in the field of plant cytogenetics and gives carefully compiled protocols and useful resources.
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Affiliation(s)
- Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
- South China National Botanical Garden, Guangzhou, China.
| | - Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - J S Pat Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
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Tomaszewska P, Schwarzacher T, Heslop-Harrison JS(P. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. Front Plant Sci 2022; 13:1026364. [PMID: 36483968 PMCID: PMC9725029 DOI: 10.3389/fpls.2022.1026364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.
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Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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13
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Higgins J, Tomaszewska P, Pellny TK, Castiblanco V, Arango J, Tohme J, Schwarzacher T, Mitchell RA, Heslop-Harrison JS, De Vega JJ. Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution. Ann Bot 2022; 130:657-669. [PMID: 36112370 PMCID: PMC9670755 DOI: 10.1093/aob/mcac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction. METHODS We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations. RESULTS We observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy: one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima. CONCLUSIONS Polyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual-apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas.
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Affiliation(s)
- J Higgins
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - P Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - T K Pellny
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - V Castiblanco
- International Center for Tropical Agriculture (CIAT), 6713 Cali, Colombia
| | - J Arango
- International Center for Tropical Agriculture (CIAT), 6713 Cali, Colombia
| | - J Tohme
- International Center for Tropical Agriculture (CIAT), 6713 Cali, Colombia
| | - T Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - R A Mitchell
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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14
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Rathore P, Schwarzacher T, Heslop-Harrison JS, Bhat V, Tomaszewska P. The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris. Front Plant Sci 2022; 13:952968. [PMID: 36186069 PMCID: PMC9521199 DOI: 10.3389/fpls.2022.952968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found, and here, we analyzed a 2n = 4x + 3 = 39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with a global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. Approximately one-third of Ty1-copia sites overlapped or spanned centromeric DAPI-positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methylcytosine signals, except for some Ty3-gypsy on the arms of chromosomes, which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. The probes developed from RepeatExplorer clusters gave strong in situ hybridization signals, mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris, likely having different repeat sequence variants amplified before the genomes came together in the tetraploid.
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Affiliation(s)
- Priyanka Rathore
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, India
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangzhou, China
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - J. S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangzhou, China
- Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Vishnu Bhat
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, India
| | - Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
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Taheri S, Teo CH, Heslop-Harrison JS, Schwarzacher T, Tan YS, Wee WY, Khalid N, Biswas MK, Mutha NVR, Mohd-Yusuf Y, Gan HM, Harikrishna JA. Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger ( Boesenbergia rotunda). Int J Mol Sci 2022; 23:7269. [PMID: 35806276 PMCID: PMC9266397 DOI: 10.3390/ijms23137269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/27/2023] Open
Abstract
Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.
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Affiliation(s)
- Sima Taheri
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
| | - Chee How Teo
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
| | - John S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yew Seong Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Wei Yee Wee
- School of Science, Monash University Malaysia, Subang Jaya 47500, Malaysia;
| | - Norzulaani Khalid
- Department of Biology, International University of Malaya-Wales, Kuala Lumpur 50603, Malaysia;
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (T.S.); (M.K.B.)
| | - Naresh V. R. Mutha
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | - Yusmin Mohd-Yusuf
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
- Biology Division, Centre for Foundation Studies in Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Han Ming Gan
- Department of Biological Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Malaysia;
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.T.); (C.H.T.); (Y.M.-Y.)
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
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Wang Z, Rouard M, Biswas MK, Droc G, Cui D, Roux N, Baurens FC, Ge XJ, Schwarzacher T, Heslop-Harrison P(JS, Liu Q. A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae. Gigascience 2022; 11:6576245. [PMID: 35488861 PMCID: PMC9055855 DOI: 10.1093/gigascience/giac027] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. FINDINGS Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11. CONCLUSIONS The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.
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Affiliation(s)
- Ziwei Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France,French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gaetan Droc
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France,CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Pat (J S) Heslop-Harrison
- Correspondence address. Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China E-mail:
| | - Qing Liu
- Correspondence address. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK. E-mail:
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Nuraga GW, Feyissa T, Tesfaye K, Biswas MK, Schwarzacher T, Borrell JS, Wilkin P, Demissew S, Tadele Z, Heslop-Harrison JS(P. The Genetic Diversity of Enset ( Ensete ventricosum) Landraces Used in Traditional Medicine Is Similar to the Diversity Found in Non-medicinal Landraces. Front Plant Sci 2022; 12:756182. [PMID: 35069618 PMCID: PMC8770334 DOI: 10.3389/fpls.2021.756182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/08/2021] [Indexed: 05/02/2023]
Abstract
Enset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed, and fiber. It has immense contributions to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. These landraces are vulnerable to various human-related activities and environmental constraints. The genetic diversity among the landraces is not verified to plan conservation strategy. Moreover, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity. We evaluated the genetic diversity of 51 enset landraces, of which 38 have reported medicinal value. A total of 38 alleles across the 15 simple sequence repeat (SSR) loci and a moderate level of genetic diversity (He = 0.47) were detected. Analysis of molecular variation (AMOVA) revealed that only 2.4% of the total genetic variation was contributed by variation among the medicinal and non-medicinal groups of landraces, with an FST of 0.024. A neighbor-joining tree showed four separate clusters with no correlation to the use-values of the landraces. Except for two, all "medicinal" landraces with distinct vernacular names were found to be genetically different, showing that vernacular names are a good indicator of genetic distinctiveness in these specific groups of landraces. The discriminant analysis of the principal components also confirmed the absence of distinct clustering between the two groups. We found that enset landraces were clustered irrespective of their use-value, showing no evidence for genetic differentiation between the enset grown for 'medicinal' uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, might have resulted from the interaction of genotype with the environment or management practice, or partly misreported. The study provides baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces.
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Affiliation(s)
- Gizachew Woldesenbet Nuraga
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Horticulture, Wolkite University, Wolkite, Ethiopia
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - James S. Borrell
- Natural Capital and Plant Health Department, Royal Botanic Gardens, Kew, London, United Kingdom
| | - Paul Wilkin
- Natural Capital and Plant Health Department, Royal Botanic Gardens, Kew, London, United Kingdom
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
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18
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Zaki NM, Schwarzacher T, Singh R, Madon M, Wischmeyer C, Hanim Mohd Nor N, Zulkifli MA, Heslop-Harrison JSP. Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species. Chromosome Res 2021; 29:373-390. [PMID: 34657216 DOI: 10.1007/s10577-021-09675-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/26/2022]
Abstract
Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.
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Affiliation(s)
- Noorhariza Mohd Zaki
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | | | - Rajinder Singh
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | | | - Nordiana Hanim Mohd Nor
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Muhammad Azwan Zulkifli
- MPOB Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
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Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). Ann Bot 2021; 128:281-299. [PMID: 33729490 PMCID: PMC8389469 DOI: 10.1093/aob/mcab042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. METHODS Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. KEY RESULTS Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. CONCLUSIONS Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kathrin M Seibt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Beatrice Weber
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, PR China
| | - Thomas Schmidt
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
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20
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Pasa R, Menegídio FB, Rodrigues-Oliveira IH, da Silva IB, de Campos MLCB, Rocha-Reis DA, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. Ten Complete Mitochondrial Genomes of Gymnocharacini (Stethaprioninae, Characiformes). Insights Into Evolutionary Relationships and a Repetitive Element in the Control Region (D-loop). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.650783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Tomaszewska P, Pellny TK, Hernández LM, Mitchell RAC, Castiblanco V, de Vega JJ, Schwarzacher T, Heslop-Harrison P(J. Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l. Genes (Basel) 2021; 12:957. [PMID: 34201593 PMCID: PMC8306847 DOI: 10.3390/genes12070957] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 01/31/2023] Open
Abstract
Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to determine ploidy of germplasm collection of this tropical forage grass group using dried leaf material, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Our methods enable robust identification of ploidy levels (coefficient of variation of G0/G1 peaks, CV, typically <5%). Ploidy of some 348 forage grass accessions (ploidy range from 2x to 9x), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes are used in the current breeding programs at CIAT and EMBRAPA: the 'brizantha' and 'humidicola' agamic complexes are variable, with multiple ploidy levels. Some U. brizantha accessions have odd level of ploidy (5x), and the relative differences in fluorescence values of the peak positions between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed aneuploidy.
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Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (T.S.); (P.H.-H.)
| | - Till K. Pellny
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (T.K.P.); (R.A.C.M.)
| | - Luis M. Hernández
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia; (L.M.H.); (V.C.)
| | | | - Valheria Castiblanco
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia; (L.M.H.); (V.C.)
| | - José J. de Vega
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK;
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (T.S.); (P.H.-H.)
| | - Pat (J.S.) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (T.S.); (P.H.-H.)
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22
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Richert-Pöggeler KR, Vijverberg K, Alisawi O, Chofong GN, Heslop-Harrison JS(P, Schwarzacher T. Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs). Front Plant Sci 2021; 12:689307. [PMID: 34234799 PMCID: PMC8256270 DOI: 10.3389/fpls.2021.689307] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/19/2021] [Indexed: 05/11/2023]
Abstract
Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration - leading to Endogenous ParaRetroViruses, EPRVs - by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21-24 nt and 18-30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs.
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Affiliation(s)
- Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- *Correspondence: Katja R. Richert-Pöggeler,
| | - Kitty Vijverberg
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Leiden, Netherlands
- Radboud University, Institute for Water and Wetland Research (IWWR), Nijmegen, Netherlands
| | - Osamah Alisawi
- Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq
| | - Gilbert N. Chofong
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Rocha-Reis DA, Pasa R, Menegidio FB, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. The Complete Mitochondrial Genome of Two Armored Catfish Populations of the Genus Hypostomus (Siluriformes, Loricariidae, Hypostominae). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.579965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Biswas MK, Darbar JN, Borrell JS, Bagchi M, Biswas D, Nuraga GW, Demissew S, Wilkin P, Schwarzacher T, Heslop-Harrison JS. The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Sci Rep 2020; 10:15312. [PMID: 32943659 PMCID: PMC7498607 DOI: 10.1038/s41598-020-71984-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/24/2020] [Indexed: 12/25/2022] Open
Abstract
Ensete ventricosum (Musaceae, enset) is an Ethiopian food security crop. To realize the potential of enset for rural livelihoods, further knowledge of enset diversity, genetics and genomics is required to support breeding programs and conservation. This study was conducted to explore the enset genome to develop molecular markers, genomics resources, and characterize enset landraces while giving insight into the organization of the genome. We identified 233 microsatellites (simple sequence repeats, SSRs) per Mbp in the enset genome, representing 0.28% of the genome. Mono- and di-nucleotide repeats motifs were found in a higher proportion than other classes of SSR-motifs. In total, 154,586 non-redundant enset microsatellite markers (EMM) were identified and 40 selected for primer development. Marker validation by PCR and low-cost agarose gel electrophoresis revealed that 92.5% were polymorphic, showing a high PIC (Polymorphism Information Content; 0.87) and expected heterozygosity (He = 0.79-0.82). In silico analysis of genomes of closely related species showed 46.86% of the markers were transferable among enset species and 1.90% were transferable to Musa. The SSRs are robust (with basic PCR methods and agarose gel electrophoresis), informative, and applicable in measuring enset diversity, genotyping, selection and potentially breeding. Enset SSRs are available in a web-based database at https://enset-project.org/EnMom@base.html (or https://enset.aau.edu.et/index.html , downloadable from Figshare).
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Affiliation(s)
- Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - Jaypal N Darbar
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Mita Bagchi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Gizachew Woldesenbet Nuraga
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK. .,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China.
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25
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Liu Q, Li X, Li M, Xu W, Schwarzacher T, Heslop-Harrison JS. Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny. BMC Plant Biol 2020; 20:406. [PMID: 32878602 PMCID: PMC7466839 DOI: 10.1186/s12870-020-02621-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 08/25/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species. RESULTS The chloroplast genomes of eleven Avena species (size range of 135,889-135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014-80,132 bp), a small single copy (SSC; 12,575-12,679 bp) and a pair of inverted repeats (IRs; 21,603-21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 (rps19) to 0.0093 (rpl32) for ten most polymorphic genes and from 0.0084 (psbH-petB) to 0.0240 (petG-trnW-CCA) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena. Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus. CONCLUSIONS Diversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Independent Researcher, Guangzhou, China
| | - Wenkui Xu
- Independent Researcher, Guangzhou, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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Sepsi A, Schwarzacher T. Chromosome-nuclear envelope tethering - a process that orchestrates homologue pairing during plant meiosis? J Cell Sci 2020; 133:133/15/jcs243667. [PMID: 32788229 PMCID: PMC7438012 DOI: 10.1242/jcs.243667] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During prophase I of meiosis, homologous chromosomes pair, synapse and exchange their genetic material through reciprocal homologous recombination, a phenomenon essential for faithful chromosome segregation. Partial sequence identity between non-homologous and heterologous chromosomes can also lead to recombination (ectopic recombination), a highly deleterious process that rapidly compromises genome integrity. To avoid ectopic exchange, homology recognition must be extended from the narrow position of a crossover-competent double-strand break to the entire chromosome. Here, we review advances on chromosome behaviour during meiotic prophase I in higher plants, by integrating centromere- and telomere dynamics driven by cytoskeletal motor proteins, into the processes of homologue pairing, synapsis and recombination. Centromere–centromere associations and the gathering of telomeres at the onset of meiosis at opposite nuclear poles create a spatially organised and restricted nuclear state in which homologous DNA interactions are favoured but ectopic interactions also occur. The release and dispersion of centromeres from the nuclear periphery increases the motility of chromosome arms, allowing meiosis-specific movements that disrupt ectopic interactions. Subsequent expansion of interstitial synapsis from numerous homologous interactions further corrects ectopic interactions. Movement and organisation of chromosomes, thus, evolved to facilitate the pairing process, and can be modulated by distinct stages of chromatin associations at the nuclear envelope and their collective release. Summary: We review plant meiosis, including chromosome tethering at the nuclear periphery that, we propose, defines chromosome dynamics-facilitating DNA sequence-based pairing of homologues
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Affiliation(s)
- Adél Sepsi
- Department of Plant Cell Biology, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary .,BME Budapest University of Technology and Economics, Department of Applied Biotechnology and Food Science (ABÉT), 1111, Budapest, Mu˝ egyetem rkp. 3-9., Hungary
| | - Trude Schwarzacher
- University of Leicester, Department of Genetics and Genome Biology, University Road, Leicester LE1 7RH, UK.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Liu Q, Li X, Zhou X, Li M, Zhang F, Schwarzacher T, Heslop-Harrison JS. The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. BMC Plant Biol 2019; 19:226. [PMID: 31146681 PMCID: PMC6543597 DOI: 10.1186/s12870-019-1769-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/09/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. RESULTS Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. CONCLUSIONS The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangying Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Genepioneer Biotechnologies Co. Ltd., Nanjing, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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Borrell JS, Biswas MK, Goodwin M, Blomme G, Schwarzacher T, Heslop-Harrison JS(P, Wendawek AM, Berhanu A, Kallow S, Janssens S, Molla EL, Davis AP, Woldeyes F, Willis K, Demissew S, Wilkin P. Enset in Ethiopia: a poorly characterized but resilient starch staple. Ann Bot 2019; 123:747-766. [PMID: 30715125 PMCID: PMC6526316 DOI: 10.1093/aob/mcy214] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/16/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. SCOPE Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. CONCLUSION Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop.
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Affiliation(s)
| | - Manosh K Biswas
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Mark Goodwin
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Guy Blomme
- Bioversity International, Addis Ababa, Ethiopia
| | | | | | | | - Admas Berhanu
- Department of Biology and Biotechnology, Wolkite University, Hawassa, Ethiopia
| | - Simon Kallow
- Conservation Science Department, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, UK
- Division of Crop Biotechnics, Katholieke Universiteit Leuven, Willem de Croylaan, Leuven, Belgium
| | - Steven Janssens
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, Katholieke Universiteit Leuven, Kasteelpark, Arenberg, Leuven, Belgium
| | - Ermias L Molla
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Kathy Willis
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Sebsebe Demissew
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Gullele Botanic Garden, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
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Mustafa SI, Schwarzacher T, Heslop-Harrison JS. Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1180-1193. [DOI: 10.1080/24701394.2018.1431226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sarbast Ihsan Mustafa
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Department of Animal Production, University of Duhok, Duhok, Iraq
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Sepsi A, Fábián A, Jäger K, Heslop-Harrison JS, Schwarzacher T. ImmunoFISH: Simultaneous Visualisation of Proteins and DNA Sequences Gives Insight Into Meiotic Processes in Nuclei of Grasses. Front Plant Sci 2018; 9:1193. [PMID: 30154816 PMCID: PMC6102387 DOI: 10.3389/fpls.2018.01193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/25/2018] [Indexed: 05/04/2023]
Abstract
ImmunoFISH is a method combining immunolabelling (IL) with fluorescent in situ hybridisation (FISH) to simultaneously detect the nuclear distribution of proteins and specific DNA sequences within chromosomes. This approach is particularly important when analysing meiotic cell division where morphogenesis of individual proteins follows stage-specific changes and is accompanied by a noticeable chromatin dynamism. The method presented here is simple and provides reliable results of high quality signal, low background staining and can be completed within 2 days following preparation. Conventional widefield epifluorescent or laser scanning microscopy can be used for high resolution and three-dimensional analysis. Fixation and preparation techniques were optimised to best preserve nuclear morphology and protein epitopes without the need for any antigen retrieval. Preparation of plant material involved short cross-linking fixation of meiotic tissues with paraformaldehyde (PFA) followed by enzyme digestion and slide-mounting. In order to avoid rapid sample degradation typical of shortly fixed plant materials, and to be able to perform IL later, slides were snap-frozen and stored at -80°C. Ultra-freezing produced a remarkable degree of structural preservation for up to 12 months, whereby sample quality was similar to that of fresh material. Harsh chemicals and sample dehydration were avoided throughout the procedure and permeability was ensured by a 0.1-0.3% detergent treatment. The ImmunoFISH method was developed specifically for studying meiosis in Triticeae, but should also be applicable to other grass and plant species.
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Affiliation(s)
- Adél Sepsi
- Department of Plant Cell Biology, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- *Correspondence: Adél Sepsi ;,
| | - Attila Fábián
- Department of Plant Cell Biology, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Katalin Jäger
- Department of Plant Cell Biology, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - J. S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Gouveia JG, Wolf IR, Vilas-Boas LA, Heslop-Harrison JS, Schwarzacher T, Dias AL. Repetitive DNA in the Catfish Genome: rDNA, Microsatellites, and Tc1-Mariner Transposon Sequences in Imparfinis Species (Siluriformes, Heptapteridae). J Hered 2017; 108:650-657. [PMID: 28821184 DOI: 10.1093/jhered/esx065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/15/2017] [Indexed: 11/13/2022] Open
Abstract
Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes. The physical mapping of Tc1/Mariner on chromosomes revealed dispersed signals in heterochromatin blocks with small accumulations in the terminal and interstitial regions of I. borodini and I. schubarti. Tc1/Mariner was coincident with rDNA chromosomes sites in both species, suggesting that this transposable element may have participated in the dispersion and evolution of these sequences in the fish genome. Our analysis suggests that different transposons and microsatellites have accumulated in the I. borodini and I. schubarti genomes and that the distribution patterns of these elements may be related to karyotype evolution within Imparfinis.
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Affiliation(s)
- Juceli Gonzalez Gouveia
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Ivan Rodrigo Wolf
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Laurival Antonio Vilas-Boas
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Trude Schwarzacher
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Ana Lúcia Dias
- Department of Biology, Biological Sciences, CCB, University Estadual de Londrina, P.O. Box 6001, Londrina, Paraná CEP 86051-970, Brazil ; Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
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Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS(P. Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. Ann Bot 2017; 120:183-194. [PMID: 28854567 PMCID: PMC5737848 DOI: 10.1093/aob/mcx079] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/31/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy. APPROACHES Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical. CONCLUSIONS The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.
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Affiliation(s)
- Karine Alix
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- For correspondence. E-mail
| | - Pierre R. Gérard
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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M. Salih RH, Majeský Ľ, Schwarzacher T, Gornall R, Heslop-Harrison P. Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies. PLoS One 2017; 12:e0168008. [PMID: 28182646 PMCID: PMC5300115 DOI: 10.1371/journal.pone.0168008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/23/2016] [Indexed: 01/10/2023] Open
Abstract
Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.
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Affiliation(s)
- Rubar Hussein M. Salih
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- Field crops department, Faculty of Agricultural Sciences, University of Sulaimani, Sulaimani, Kurdistan Region, Iraq
| | - Ľuboš Majeský
- Department of Botany, Faculty of Science, Palacky University in Olomouc, Olomouc, Olomouc-Holice, Czech Republic
| | - Trude Schwarzacher
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Richard Gornall
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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Sepsi A, Higgins JD, Heslop-Harrison JSP, Schwarzacher T. CENH3 morphogenesis reveals dynamic centromere associations during synaptonemal complex formation and the progression through male meiosis in hexaploid wheat. Plant J 2017; 89:235-249. [PMID: 27624968 DOI: 10.1111/tpj.13379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/04/2016] [Accepted: 09/08/2016] [Indexed: 05/02/2023]
Abstract
During meiosis, centromeres in some species undergo a series of associations, but the processes and progression to homologous pairing is still a matter of debate. Here, we aimed to correlate meiotic centromere dynamics and early telomere behaviour to the progression of synaptonemal complex (SC) construction in hexaploid wheat (2n = 42) by triple immunolabelling of CENH3 protein marking functional centromeres, and SC proteins ASY1 (unpaired lateral elements) and ZYP1 (central elements in synapsed chromosomes). We show that single or multiple centromere associations formed in meiotic interphase undergo a progressive polarization (clustering) at the nuclear periphery in early leptotene, leading to formation of the telomere bouquet. Critically, immunolabelling shows the dynamics of these presynaptic centromere associations and a structural reorganization of the centromeric chromatin coinciding with key events of synapsis initiation from the subtelomeric regions. As short stretches of subtelomeric synapsis emerged at early zygotene, centromere clusters lost their strong polarization, gradually resolving as individual centromeres indicated by more than 21 CENH3 foci associated with unpaired lateral elements. Only following this centromere depolarization were homologous chromosome arms connected, as observed by the alignment and fusion of interstitial ZYP1 loci elongating at zygotene so synapsis at centromeres is a continuation of the interstitial synapsis. Our results thus reveal that centromere associations are a component of the timing and progression of chromosome synapsis, and the gradual release of the individual centromeres from the clusters correlates with the elongation of interstitial synapsis between the corresponding homologues.
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Affiliation(s)
- Adél Sepsi
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - James D Higgins
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | | | - Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
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Ali N, Heslop-Harrison JS(P, Ahmad H, Graybosch RA, Hein GL, Schwarzacher T. Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance. Heredity (Edinb) 2016; 117:114-23. [PMID: 27245423 PMCID: PMC4949730 DOI: 10.1038/hdy.2016.36] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/22/2016] [Accepted: 02/11/2016] [Indexed: 01/08/2023] Open
Abstract
Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridisation were applied to identify alien chromatin in four genetically diverse populations of wheat (Triticum aestivum) lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of 20 experimental lines, 10 carried Th. intermedium chromatin as T4DL*4Ai#2S translocations, while, unexpectedly, 7 lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin, transmitted from early in the pedigree, was associated with enhanced WSMV resistance. Under field conditions, the 1RS chromatin alone showed some resistance, while together with the Th. intermedium 4Ai#2S offered superior resistance to that demonstrated by the known resistant cultivar Mace. Most alien wheat lines carry whole chromosome arms, and it is notable that these lines showed intra-arm recombination within the 1BS arm. The translocation breakpoints between 1BS and alien chromatin fell in three categories: (i) at or near to the centromere, (ii) intercalary between markers UL-Thin5 and Xgwm1130 and (iii) towards the telomere between Xgwm0911 and Xbarc194. Labelled genomic Th. intermedium DNA hybridised to the rye 1RS chromatin under high stringency conditions, indicating the presence of shared tandem repeats among the cereals. The novel small alien fragments may explain the difficulty in developing well-adapted lines carrying Wsm1 despite improved tolerance to the virus. The results will facilitate directed chromosome engineering producing agronomically desirable WSMV-resistant germplasm.
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Affiliation(s)
- N Ali
- Department of Genetics, University of Leicester, Leicester, UK
- Hazara University, Mansehra, Pakistan
| | | | - H Ahmad
- Hazara University, Mansehra, Pakistan
| | - R A Graybosch
- USDA-ARS & Department of Agronomy & Horticulture, University of Nebraska, Lincoln, NE, USA
| | - G L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - T Schwarzacher
- Department of Genetics, University of Leicester, Leicester, UK
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Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nat Plants 2016; 2:16074. [PMID: 27255838 DOI: 10.1038/nplants.2016.74] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/22/2016] [Indexed: 05/21/2023]
Abstract
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.
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Affiliation(s)
- Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, 490 West Campus Dr., Blacksburg, Virginia 24061, USA
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Avichai Amrad
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manzhu Bao
- Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Laure Bapaume
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 6 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Mattijs Bliek
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Maaike R Boersma
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Lorenzo Borghi
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
| | - Marcel Bucher
- Cologne Biocenter, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zuelpicher Straße 47b, 50674 Cologne, Germany
| | - Nunzio D'Agostino
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per l'Orticoltura (CREA-ORT), via Cavalleggeri 25, 84098 Pontecagnano (Sa) Italy
| | - Kevin Davies
- Department of Breeding and Genomics, Plant and Food Research, Auckland, 120 Mt Albert Road, Mount Albert, Sandringham 1142, New Zealand
| | - Uwe Druege
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Marcos Egea-Cortines
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Noe Fernandez-Pozo
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Philipp Franken
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Laurie Grandont
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - J S Heslop-Harrison
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jennifer Hintzsche
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Mitrick Johns
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Ronald Koes
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Xiaodan Lv
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Diwa Malla
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Enrico Martinoia
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Neil S Mattson
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Patrice Morel
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Joëlle Muhlemann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Eva Nouri
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 4 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Valentina Passeri
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Qinzhou Qi
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 3 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Melanie Rich
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 5 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Tim P Robbins
- Department of Crop and Plant Sciences, University of Nottingham, Sutton Bonington, Leicestershire, UL LE12 5RD, UK
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robert C Schuurink
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kees Spelt
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Haibao Tang
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Susan L Urbanus
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Kitty Vijverberg
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Gonzalo H Villarino
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Ryan M Warner
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Julia Weiss
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Zhen Yue
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Jan Zethof
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Francesca Quattrocchio
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Thomas L Sims
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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Abstract
Good preparations are essential for informative analysis of both somatic and meiotic chromosomes, cytogenetics, and cell divisions. Fluorescent chromosome staining allows even small chromosomes to be visualized and counted, showing their morphology. Aneuploidies and polyploidies can be established for species, populations, or individuals while changes occurring in breeding lines during hybridization or tissue culture and transformation protocols can be assessed. The process of division can be followed during mitosis and meiosis including pairing and chiasma distribution, as well as DNA organization and structure during the evolution of chromosomes can be studied. This chapter presents protocols for pretreatment and fixation of material, including tips of how to grow plants to get good and healthy meristem with many divisions. The chromosome preparation technique is described using proteolytic enzymes, but acids can be used instead. Chromosome slide preparations are suitable for fluorochrome staining for fast screening (described in the chapter) or fluorescent in situ hybridization (see Schwarzacher and Heslop-Harrison, In situ hybridization. BIOS Scientific Publishers, Oxford, 2000).
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Affiliation(s)
- Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Sola-Campoy PJ, Robles F, Schwarzacher T, Ruiz Rejón C, de la Herrán R, Navajas-Pérez R. The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1. PLoS One 2015; 10:e0143861. [PMID: 26633808 PMCID: PMC4669136 DOI: 10.1371/journal.pone.0143861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/10/2015] [Indexed: 12/29/2022] Open
Abstract
This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176–178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree.
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Affiliation(s)
- Pedro J. Sola-Campoy
- Departamento de Genética, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
| | - Francisca Robles
- Departamento de Genética, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
| | - Trude Schwarzacher
- Department of Biology, University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom
| | - Carmelo Ruiz Rejón
- Departamento de Genética, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
| | - Roberto de la Herrán
- Departamento de Genética, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
| | - Rafael Navajas-Pérez
- Departamento de Genética, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
- * E-mail:
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Alsayied NF, Fernández JA, Schwarzacher T, Heslop-Harrison JS. Diversity and relationships of Crocus sativus and its relatives analysed by inter-retroelement amplified polymorphism (IRAP). Ann Bot 2015; 116:359-68. [PMID: 26138822 PMCID: PMC4549961 DOI: 10.1093/aob/mcv103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 04/08/2015] [Accepted: 05/27/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Saffron (Crocus sativus) is a sterile triploid (2n = 3x = 24) cultivated species, of unknown origin from other diploid and polyploid species in the genus Crocus (Iridaceae). Species in the genus have high morphological diversity, with no clear phylogenetic patterns below the level of section Crocus series Crocus. Using DNA markers, this study aimed to examine the diversity and relationships within and between species of Crocus series Crocus. METHODS Eleven inter-retroelement amplified polymorphism (IRAP) primers were used in 63 different combinations with 35 single-plant accessions of C. sativus and related Crocus species in order to determine genetic variability and to conduct phylogenetic analysis. KEY RESULTS A total of 4521 distinct polymorphic bands from 100 bp to approx. 4 kb were amplified; no fragment specific to all accessions of a single species was amplified. The polymorphic information content (PIC) values varied from approx. 0·37 to approx. 0·05 (mean 0·17 ± 0·1) and the major allele frequency had a mean of 0·87. High levels of polymorphism were identified between accessions of the six species of Crocus series Crocus related to C. sativus, with further variation between the species. In contrast, no polymorphisms were seen among 17 C. sativus accessions obtained in the region from Kashmir through Iran to Spain. CONCLUSIONS In contrast to the intraspecific variability seen in other Crocus species, C. sativus has minimal genetic variation, and it is concluded that the triploid hybrid species has most probably arisen only once. The data show that saffron is an allotriploid species, with the IRAP analysis indicating that the most likely ancestors are C. cartwrightianus and C. pallasii subsp. pallasii (or close relatives). The results may facilitate resynthesizing saffron with improved characteristics, and show the need for conservation and collection of wild Crocus.
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Affiliation(s)
| | - José Antonio Fernández
- Laboratorio de Biotecnología, Instituto de Desarrollo Regional, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Trude Schwarzacher
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK and
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Lau SE, Schwarzacher T, Othman RY, Harikrishna JA. dsRNA silencing of an R2R3-MYB transcription factor affects flower cell shape in a Dendrobium hybrid. BMC Plant Biol 2015; 15:194. [PMID: 26260631 PMCID: PMC4542095 DOI: 10.1186/s12870-015-0577-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/22/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND The R2R3-MYB genes regulate pigmentation and morphogenesis of flowers, including flower and cell shape, and therefore have importance in the development of new varieties of orchids. However, new variety development is limited by the long breeding time required in orchids. In this study, we identified a cDNA, DhMYB1, that is expressed during flower development in a hybrid orchid, Dendrobium hybrida (Dendrobium bobby messina X Dendrobium chao phraya) then used the direct application of dsRNA to observe the effect of gene silencing on flower phenotype and floral epidermal cell shape. RESULTS Flower bud development in the Dendrobium hybrid was characterised into seven stages and the time of meiosis was determined as between stages 3 to 5 when the bud is approximately half of the mature size. Scanning electron microscopy characterisation of adaxial epidermal cells of the flower perianth, showed that the petals and sepals each are divided into two distinct domains based on cell shape and size, while the labellum comprises seven domains. Thirty-two partial cDNA fragments representing R2R3-MYB gene sequences were isolated from D. hybrida. Phylogenetic analysis revealed that nine of the translated sequences were clustered with MYB sequences that are known to be involved in cell shape development and from these, DhMYB1 was selected for full length cDNA cloning and functional study. Direct application of a 430 bp dsRNA from the 3' region of DhMYB1 to emerging orchid flower buds reduced expression of DhMYB1 RNA compared with untreated control. Scanning electron microscopy of adaxial epidermal cells within domain one of the labellum of flowers treated with DhMYB1 dsRNA showed flattened epidermal cells whilst those of control flowers were conical. CONCLUSIONS DhMYB1 is expressed throughout flower bud development and is involved in the development of the conical cell shape of the epidermal cells of the Dendrobium hybrida flower labellum. The direct application of dsRNA changed the phenotype of floral cells, thus, this technique may have application in floriculture biotechnology.
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Affiliation(s)
- Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Trude Schwarzacher
- Department of Biology, University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom.
| | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Ottolini B, Hornsby MJ, Abujaber R, MacArthur JAL, Badge RM, Schwarzacher T, Albertson DG, Bevins CL, Solnick JV, Hollox EJ. Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene. Genome Biol Evol 2014; 6:3025-38. [PMID: 25349268 PMCID: PMC4255768 DOI: 10.1093/gbe/evu236] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
β-defensins are a family of important peptides of innate immunity, involved in host defense, immunomodulation, reproduction, and pigmentation. Genes encoding β-defensins show evidence of birth-and-death evolution, adaptation by amino acid sequence changes, and extensive copy number variation (CNV) within humans and other species. The role of CNV in the adaptation of β-defensins to new functions remains unclear, as does the adaptive role of CNV in general. Here, we fine-map CNV of a cluster of β-defensins in humans and rhesus macaques. Remarkably, we found that the structure of the CNV is different between primates, with distinct mutational origins and CNV boundaries defined by retroviral long terminal repeat elements. Although the human β-defensin CNV region is 322 kb and encompasses several genes, including β-defensins, a long noncoding RNA gene, and testes-specific zinc-finger transcription factors, the orthologous region in the rhesus macaque shows CNV of a 20-kb region, containing only a single gene, the ortholog of the human β-defensin-2 gene. Despite its independent origins, the range of gene copy numbers in the rhesus macaque is similar to humans. In addition, the rhesus macaque gene has been subject to divergent positive selection at the amino acid level following its initial duplication event between 3 and 9.5 Ma, suggesting adaptation of this gene as the macaque successfully colonized novel environments outside Africa. Therefore, the molecular phenotype of β-defensin-2 CNV has undergone convergent evolution, and this gene shows evidence of adaptation at the amino acid level in rhesus macaques.
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Affiliation(s)
| | - Michael J Hornsby
- Department of Microbiology and Immunology, University of California Davis School of Medicine
| | - Razan Abujaber
- Department of Genetics, University of Leicester, United Kingdom
| | - Jacqueline A L MacArthur
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco Present address: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Richard M Badge
- Department of Genetics, University of Leicester, United Kingdom
| | | | - Donna G Albertson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco Present address: Bluestone Center for Clinical Research, New York University College of Dentistry, New York, New York
| | - Charles L Bevins
- Department of Microbiology and Immunology, University of California Davis School of Medicine
| | - Jay V Solnick
- Department of Microbiology and Immunology, University of California Davis School of Medicine Department of Medicine, Center for Comparative Medicine, and the California National Primate Research Center, University of California
| | - Edward J Hollox
- Department of Genetics, University of Leicester, United Kingdom
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43
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Bertioli DJ, Vidigal B, Nielen S, Ratnaparkhe MB, Lee TH, Leal-Bertioli SCM, Kim C, Guimarães PM, Seijo G, Schwarzacher T, Paterson AH, Heslop-Harrison P, Araujo ACG. The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome. Ann Bot 2013; 112:545-59. [PMID: 23828319 PMCID: PMC3718217 DOI: 10.1093/aob/mct128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Peanut (Arachis hypogaea) is an allotetraploid (AABB-type genome) of recent origin, with a genome of about 2·8 Gb and a high repetitive content. This study reports an analysis of the repetitive component of the peanut A genome using bacterial artificial chromosome (BAC) clones from A. duranensis, the most probable A genome donor, and the probable consequences of the activity of these elements since the divergence of the peanut A and B genomes. METHODS The repetitive content of the A genome was analysed by using A. duranensis BAC clones as probes for fluorescence in situ hybridization (BAC-FISH), and by sequencing and characterization of 12 genomic regions. For the analysis of the evolutionary dynamics, two A genome regions are compared with their B genome homeologues. KEY RESULTS BAC-FISH using 27 A. duranensis BAC clones as probes gave dispersed and repetitive DNA characteristic signals, predominantly in interstitial regions of the peanut A chromosomes. The sequences of 14 BAC clones showed complete and truncated copies of ten abundant long terminal repeat (LTR) retrotransposons, characterized here. Almost all dateable transposition events occurred <3·5 million years ago, the estimated date of the divergence of A and B genomes. The most abundant retrotransposon is Feral, apparently parasitic on the retrotransposon FIDEL, followed by Pipa, also non-autonomous and probably parasitic on a retrotransposon we named Pipoka. The comparison of the A and B genome homeologous regions showed conserved segments of high sequence identity, punctuated by predominantly indel regions without significant similarity. CONCLUSIONS A substantial proportion of the highly repetitive component of the peanut A genome appears to be accounted for by relatively few LTR retrotransposons and their truncated copies or solo LTRs. The most abundant of the retrotransposons are non-autonomous. The activity of these retrotransposons has been a very significant driver of genome evolution since the evolutionary divergence of the A and B genomes.
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Affiliation(s)
- David J. Bertioli
- University of Brasilia, Department of Genetics, Campus Universitário, Brasília DF, Brazil
| | - Bruna Vidigal
- University of Brasilia, Department of Genetics, Campus Universitário, Brasília DF, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF, Brazil
| | - Stephan Nielen
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF, Brazil
| | | | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA 30605, USA
| | | | - Changsoo Kim
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA 30605, USA
| | | | - Guillermo Seijo
- Plant Cytogenetic and Evolution Laboratory, Instituto de Botánica del Nordeste and Faculty of Exact and Natural Sciences, National University of the Northeast, Corrientes, Argentina
| | | | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA 30605, USA
| | | | - Ana C. G. Araujo
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF, Brazil
- For correspondence. E-mail
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Abstract
The plant genome is organized into chromosomes that provide the structure for the genetic linkage groups and allow faithful replication, transcription and transmission of the hereditary information. Genome sizes in plants are remarkably diverse, with a 2350-fold range from 63 to 149,000 Mb, divided into n=2 to n= approximately 600 chromosomes. Despite this huge range, structural features of chromosomes like centromeres, telomeres and chromatin packaging are well-conserved. The smallest genomes consist of mostly coding and regulatory DNA sequences present in low copy, along with highly repeated rDNA (rRNA genes and intergenic spacers), centromeric and telomeric repetitive DNA and some transposable elements. The larger genomes have similar numbers of genes, with abundant tandemly repeated sequence motifs, and transposable elements alone represent more than half the DNA present. Chromosomes evolve by fission, fusion, duplication and insertion events, allowing evolution of chromosome size and chromosome number. A combination of sequence analysis, genetic mapping and molecular cytogenetic methods with comparative analysis, all only becoming widely available in the 21st century, is elucidating the exact nature of the chromosome evolution events at all timescales, from the base of the plant kingdom, to intraspecific or hybridization events associated with recent plant breeding. As well as being of fundamental interest, understanding and exploiting evolutionary mechanisms in plant genomes is likely to be a key to crop development for food production.
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Kuhn GCS, Schwarzacher T, Heslop-Harrison JS. The non-regular orbit: three satellite DNAs in Drosophila martensis (buzzatii complex, repleta group) followed three different evolutionary pathways. Mol Genet Genomics 2010; 284:251-62. [PMID: 20683615 DOI: 10.1007/s00438-010-0564-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 07/20/2010] [Indexed: 11/29/2022]
Abstract
The genome of species from the buzzatii cluster (buzzatii complex, repleta group) is hosted by a number of satellite DNAs (satDNAs) showing contrasting structural characteristics, genomic organization and evolution, such as pBuM-alpha (~190 bp repeats), pBuM-alpha/beta (~370 bp repeats) and the DBC-150 (~150 bp repeats). In the present study, we aimed to investigate the evolution of these three satDNAs by looking for homologous sequences in the genome of the closest outgroup species: Drosophila martensis (buzzatii complex). After PCR, we isolated and sequenced 9 alpha, 8 alpha/beta and 11 DBC-150 sequences from this species. The results were compared to all pBuM and DBC-150 sequences available in literature. After D. martensis split from the buzzatii cluster some 6 Mya, the three satDNAs evolved differently in the genome of D. martensis by: (1) maintenance of a collection of major types of ancestral repeats in the genome (alpha); (2) fixation for a single major type of ancestral repeats (alpha/beta) or (3) fixation for new divergent species-specific repeat types (DBC-150). Curiously, D. seriema and D. martensis, although belonging to different and allopatric clusters, became independently fixed for the same major type of alpha/beta ancestral repeats, illustrating a rare case of parallelism in satDNA evolution. The contrasting pictures illustrate the diversity of evolutionary pathways a satDNA can follow, defining a "non-regular orbit" with outcomes difficult to predict.
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Affiliation(s)
- Gustavo C S Kuhn
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luís, Km 235, São Carlos, SP 13565-905, Brazil.
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Navajas-Pérez R, Schwarzacher T, Ruiz Rejón M, Garrido-Ramos MA. Characterization of RUSI, a telomere-associated satellite DNA, in the genus Rumex (Polygonaceae). Cytogenet Genome Res 2009; 124:81-9. [PMID: 19372672 DOI: 10.1159/000200091] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2008] [Indexed: 11/19/2022] Open
Abstract
A satellite-DNA family (RUSI) has been isolated and characterized in Rumexinduratus Boiss and Reuter (Polygonaceae), an Iberian endemic polygamous sorrel. The RUSI repeats are 170 bp in length and approximately 68% AT-rich containing different variants of degenerate telomere motifs--(TT)(n)AN(GG)(n) -, a typical feature of subtelomeric DNA repeats adjacent to telomeres, which have been referred to as telomere-associated sequences or TASs. In fact, fluorescent in situhybridization showed that this satellite DNA is located in subtelomeric positions of most of the chromosomes of R. induratus, with some centromeric loci. PCR and Southern-blot hybridization assays for sequence conservation in the genus Rumex, indicated that the RUSI sequences are restricted to the genomes of R. induratus and R. scutatus, both species of the section Scutati, suggesting that they are recently evolved. Sequence variation within the two species is high (mean value of sequence differences between repeats of 15% for R. induratus and 7.5% for R. scutatus) and the degree of sequence differentiation between species is low with no species-specific variants, postulated to be due to slowed rates of spreading of sequence variants by molecular homogenizing mechanisms. Characteristics of RUSI sequences are discussed in the light of their chromosomal location and analyzed for their evolutionary and phylogenetic implications.
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Affiliation(s)
- R Navajas-Pérez
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA.
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47
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Abstract
Fluorescent chromosome analysis technologies have advanced our understanding of genome organization during the last 30 years and have enabled the investigation of DNA organization and structure as well as the evolution of chromosomes. Fluorescent chromosome staining allows even small chromosomes to be visualized, characterized by their composition and morphology, and counted. Aneuploidies and polyploidies can be established for species, breeding lines, and individuals, including changes occurring during hybridization or tissue culture and transformation protocols. Fluorescent in situ hybridization correlates molecular information of a DNA sequence with its physical location on chromosomes and genomes. It thus allows determination of the physical position of sequences and often is the only means to determine the abundance and distribution of DNA sequences that are difficult to map with any other molecular method or would require segregation analysis, in particular multicopy or repetitive DNA. Equally, it is often the best way to establish the incorporation of transgenes, their numbers, and physical organization along chromosomes. This chapter presents protocols for probe and chromosome preparation, fluorescent in situ hybridization, chromosome staining, and the analysis of results.
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Schwarzacher T. Chromosomes, recombination and proteins at meiosis--a tribute to Peter Moens (1931-2008). Chromosome Res 2008; 16:679-82. [PMID: 18668331 DOI: 10.1007/s10577-008-1251-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Moscone EA, Samuel R, Schwarzacher T, Schweizer D, Pedrosa-Harand A. Complex rearrangements are involved in Cephalanthera (Orchidaceae) chromosome evolution. Chromosome Res 2007; 15:931-43. [DOI: 10.1007/s10577-007-1174-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 08/08/2007] [Accepted: 08/08/2007] [Indexed: 10/22/2022]
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Heslop-Harrison JS, Schwarzacher T. Domestication, genomics and the future for banana. Ann Bot 2007; 100:1073-84. [PMID: 17766312 PMCID: PMC2759213 DOI: 10.1093/aob/mcm191] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 07/22/2007] [Accepted: 07/25/2007] [Indexed: 05/17/2023]
Abstract
BACKGROUND Cultivated bananas and plantains are giant herbaceous plants within the genus Musa. They are both sterile and parthenocarpic so the fruit develops without seed. The cultivated hybrids and species are mostly triploid (2n = 3x = 33; a few are diploid or tetraploid), and most have been propagated from mutants found in the wild. With a production of 100 million tons annually, banana is a staple food across the Asian, African and American tropics, with the 15 % that is exported being important to many economies. SCOPE There are well over a thousand domesticated Musa cultivars and their genetic diversity is high, indicating multiple origins from different wild hybrids between two principle ancestral species. However, the difficulty of genetics and sterility of the crop has meant that the development of new varieties through hybridization, mutation or transformation was not very successful in the 20th century. Knowledge of structural and functional genomics and genes, reproductive physiology, cytogenetics, and comparative genomics with rice, Arabidopsis and other model species has increased our understanding of Musa and its diversity enormously. CONCLUSIONS There are major challenges to banana production from virulent diseases, abiotic stresses and new demands for sustainability, quality, transport and yield. Within the genepool of cultivars and wild species there are genetic resistances to many stresses. Genomic approaches are now rapidly advancing in Musa and have the prospect of helping enable banana to maintain and increase its importance as a staple food and cash crop through integration of genetical, evolutionary and structural data, allowing targeted breeding, transformation and efficient use of Musa biodiversity in the future.
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