1
|
Wang J, Xu Y, Peng Y, Wang Y, Kang Z, Zhao J. A fully haplotype-resolved and nearly gap-free genome assembly of wheat stripe rust fungus. Sci Data 2024; 11:508. [PMID: 38755209 PMCID: PMC11099153 DOI: 10.1038/s41597-024-03361-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Stripe rust fungus Puccinia striiformis f. sp. tritici (Pst) is a destructive pathogen of wheat worldwide. Pst has a macrocyclic-heteroecious lifecycle, in which one-celled urediniospores are dikaryotic, each nucleus containing one haploid genome. We successfully generated the first fully haplotype-resolved and nearly gap-free chromosome-scale genome assembly of Pst by combining PacBio HiFi sequencing and trio-binning strategy. The genome size of the two haploid assemblies was 75.59 Mb and 75.91 Mb with contig N50 of 4.17 Mb and 4.60 Mb, and both had 18 pseudochromosomes. The high consensus quality values of 55.57 and 59.02 for both haplotypes confirmed the correctness of the assembly. Of the total 18 chromosomes, 15 and 16 were gapless while there were only five and two gaps for the remaining chromosomes of the two haplotypes, respectively. In total, 15,046 and 15,050 protein-coding genes were predicted for the two haplotypes, and the complete BUSCO scores achieved 97.7% and 97.9%, respectively. The genome will lay the foundation for further research on genetic variations and the evolution of rust fungi.
Collapse
Affiliation(s)
- Jierong Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiwen Xu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuxi Peng
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiping Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jing Zhao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
2
|
Li C, Qiao L, Lu Y, Xing G, Wang X, Zhang G, Qian H, Shen Y, Zhang Y, Yao W, Cheng K, Ma Z, Liu N, Wang D, Zheng W. Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales. Microbiol Spectr 2023; 11:e0282822. [PMID: 36688678 PMCID: PMC9927501 DOI: 10.1128/spectrum.02828-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023] Open
Abstract
Chromosome evolution drives species evolution, speciation, and adaptive radiation. Accurate genome assembly is crucial to understanding chromosome evolution of species, such as dikaryotic fungi. Rust fungi (Pucciniales) in dikaryons represent the largest group of plant pathogens, but the evolutionary process of adaptive radiation in Pucciniales remains poorly understood. Here, we report a gapless genome for the wheat leaf rust fungus Puccinia triticina determined using PacBio high-fidelity (HiFi) sequencing. This gapless assembly contains two sets of chromosomes, showing that one contig represents one chromosome. Comparisons of homologous chromosomes between the phased haplotypes revealed that highly frequent small-scale sequence divergence shapes haplotypic variation. Genome analyses of Puccinia triticina along with other rusts revealed that recent transposable element bursts and extensive segmental gene duplications synergistically highlight the evolution of chromosome structures. Comparative analysis of chromosomes indicated that frequent chromosomal rearrangements may act as a major contributor to rapid radiation of Pucciniales. This study presents the first gapless, phased assembly for a dikaryotic rust fungus and provides insights into adaptive evolution and species radiation in Pucciniales. IMPORTANCE Rust fungi (Pucciniales) are the largest group of plant pathogens. Adaptive radiation is a predominant feature in Pucciniales evolution. Chromosome evolution plays an important role in adaptive evolution. Accurate chromosome-scale assembly is required to understand the role of chromosome evolution in Pucciniales. We took advantage of HiFi sequencing to construct a gapless, phased genome for Puccinia triticina. Further analyses revealed that the evolution of chromosome structures in rust lineage is shaped by the combination of transposable element bursts and segmental gene duplications. Chromosome comparisons of Puccinia triticina and other rusts suggested that frequent chromosomal arrangements may make remarkable contributions to high species diversity of rust fungi. Our results present the first gapless genome for Pucciniales and shed light on the feature of chromosome evolution in Pucciniales.
Collapse
Affiliation(s)
- Chuang Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Liuhui Qiao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Yanan Lu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Guozhen Xing
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | | | - Huimin Qian
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yilin Shen
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yibo Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Kun Cheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Na Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Wenming Zheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
3
|
de Almeida JR, Riaño Pachón DM, Franceschini LM, dos Santos IB, Ferrarezi JA, de Andrade PAM, Monteiro-Vitorello CB, Labate CA, Quecine MC. Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes. PLoS One 2021; 16:e0248054. [PMID: 33705433 PMCID: PMC7951889 DOI: 10.1371/journal.pone.0248054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.
Collapse
Affiliation(s)
- Jaqueline Raquel de Almeida
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Livia Maria Franceschini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Isaneli Batista dos Santos
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Jessica Aparecida Ferrarezi
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Pedro Avelino Maia de Andrade
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Carlos Alberto Labate
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| |
Collapse
|
4
|
Skowrońska R, Tomkowiak A, Nawracała J, Kwiatek MT. Molecular identification of slow rusting resistance Lr46/Yr29 gene locus in selected triticale (× Triticosecale Wittmack) cultivars. J Appl Genet 2020; 61:359-366. [PMID: 32424640 PMCID: PMC8651608 DOI: 10.1007/s13353-020-00562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/02/2022]
Abstract
Recently, leaf rust and yellow rust caused by the fungi Puccinia triticina Erikss. and P. striiformis Westend f. sp. tritici Eriks and Henn are diseases of increasing threat in triticale (× Triticosecale Wittmack, AABBRR, 2n = 6x = 42) growing areas. The use of genetic resistance is considered the most economical, effective and environmentally friendly method to control the disease and minimize the use of fungicides. Currently, breeding programs mainly relied on race-specific Lr and Yr genes (R), but new races of the rust fungi frequently defeat resistance. There is a small group of genes that causes partial type of resistance (PR) that are characterized by a slow epidemic build up despite a high infection type. In wheat slow rusting resistance genes displayed longer latent periods, low infection frequencies, smaller pustule size and less spore production. Slow rusting Lr46/Yr29 gene, located on chromosome 1B, is being exploited in many wheat breeding programs. So far, there is no information about slow rusting genes in triticale. This paper showed significant differences between the results of identification of wheat molecular markers Xwmc44 and csLV46G22 associated with Lr46/Yr29 in twenty triticale cultivars, which were characterized by high levels of field resistance to leaf and yellow rust. The csLV46G22res marker has been identified in the following cultivars: Kasyno, Mamut and Puzon. Belcanto and Kasyno showed the highest resistance levels in three-year (2016–2018), leaf and yellow rust severity tests under post-registration variety testing program (PDO). Leaf tip necrosis, a phenotypic trait associated with Lr34/Yr18 and Lr46/Yr29 was observed, among others, to Belcanto and Kasyno, which showed the highest resistance for leaf rust and yellow rust. Kasyno could be considered to have Lr46/Yr29 and can be used as a source of slow rust resistance in breeding and importantly as a component of gene pyramiding in triticale.
Collapse
Affiliation(s)
- Roksana Skowrońska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632, Poznań, Poland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632, Poznań, Poland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632, Poznań, Poland
| | - Michał T Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 11 Dojazd Str, 60-632, Poznań, Poland.
| |
Collapse
|
5
|
Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sørensen CK, Hovmøller MS, Rathjen JP, Justesen AF. Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. Genome Biol Evol 2020; 12:597-617. [PMID: 32271913 DOI: 10.1101/859728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 05/27/2023] Open
Abstract
Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
Collapse
Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Yan-Jun Chen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Richard Tien
- School of Dentistry, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Josef Korbinian Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Ramawatar Nagar
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, United Kingdom
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | | | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Annemarie Fejer Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| |
Collapse
|
6
|
Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sørensen CK, Hovmøller MS, Rathjen JP, Justesen AF. Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. Genome Biol Evol 2020; 12:597-617. [PMID: 32271913 PMCID: PMC7250506 DOI: 10.1093/gbe/evaa071] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
Collapse
Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Yan-Jun Chen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Richard Tien
- School of Dentistry, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Josef Korbinian Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Ramawatar Nagar
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, United Kingdom
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | | | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Annemarie Fejer Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| |
Collapse
|