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Li H, Durbin R. Genome assembly in the telomere-to-telomere era. Nat Rev Genet 2024; 25:658-670. [PMID: 38649458 DOI: 10.1038/s41576-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly - the process of reconstructing the genome sequence of an organism from sequencing reads - has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome - also known as telomere-to-telomere assembly - for many organisms. Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes.
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Affiliation(s)
- Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Richard Durbin
- Department of Genetics, Cambridge University, Cambridge, UK.
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Zhai J, Gokaslan A, Schiff Y, Berthel A, Liu ZY, Lai WY, Miller ZR, Scheben A, Stitzer MC, Romay C, Buckler ES, Kuleshov V. Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.596709. [PMID: 38895432 PMCID: PMC11185591 DOI: 10.1101/2024.06.04.596709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pre-trained on large-scale biological sequences can learn evolutionary conservation and offer cross-species prediction better than supervised models through fine-tuning limited labeled data. We introduce PlantCaduceus, a plant DNA LM based on the Caduceus and Mamba architectures, pre-trained on a curated dataset of 16 Angiosperm genomes. Fine-tuning PlantCaduceus on limited labeled Arabidopsis data for four tasks, including predicting translation initiation/termination sites and splice donor and acceptor sites, demonstrated high transferability to 160 million year diverged maize, outperforming the best existing DNA LM by 1.45 to 7.23-fold. PlantCaduceus is competitive to state-of-the-art protein LMs in terms of deleterious mutation identification, and is threefold better than PhyloP. Additionally, PlantCaduceus successfully identifies well-known causal variants in both Arabidopsis and maize. Overall, PlantCaduceus is a versatile DNA LM that can accelerate plant genomics and crop breeding applications.
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Schreiber M, Jayakodi M, Stein N, Mascher M. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet 2024; 25:563-577. [PMID: 38378816 DOI: 10.1038/s41576-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 02/22/2024]
Abstract
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, Marburg, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Conover JL, Grover CE, Sharbrough J, Sloan DB, Peterson DG, Wendel JF. Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids. AMERICAN JOURNAL OF BOTANY 2024; 111:e16386. [PMID: 39107998 DOI: 10.1002/ajb2.16386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 08/24/2024]
Abstract
PREMISE A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events. METHODS Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid Gossypium species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange. RESULTS We found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best-supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species. CONCLUSIONS Overall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon in Gossypium, affecting between zero and 24 genes per subgenome (0.0-0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.
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Affiliation(s)
- Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, 50010, IA, USA
- Ecology and Evolutionary Biology Department, University of Arizona, Tucson, 85718, AZ, USA
- Molecular and Cellular Biology Department, University of Arizona, Tucson, 85718, AZ, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, 50010, IA, USA
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, 87801, NM, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, 80521, CO, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, 39762, MS, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, 50010, IA, USA
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Banović Đeri B, Nešić S, Vićić I, Samardžić J, Nikolić D. Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs. Front Microbiol 2024; 15:1401985. [PMID: 39101033 PMCID: PMC11294920 DOI: 10.3389/fmicb.2024.1401985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024] Open
Abstract
Advances in small RNAs (sRNAs)-related studies have posed a challenge for NGS-related bioinformatics, especially regarding the correct mapping of sRNAs. Depending on the algorithms and scoring matrices on which they are based, aligners are influenced by the characteristics of the dataset and the reference genome. These influences have been studied mainly in eukaryotes and to some extent in prokaryotes. However, in bacteria, the selection of aligners depending on sRNA-seq data associated with outer membrane vesicles (OMVs) and the features of the corresponding bacterial reference genome has not yet been investigated. We selected five aligners: BBmap, Bowtie2, BWA, Minimap2 and Segemehl, known for their generally good performance, to test them in mapping OMV-associated sRNAs from Aliivibrio fischeri to the bacterial reference genome. Significant differences in the performance of the five aligners were observed, resulting in differential recognition of OMV-associated sRNA biotypes in A. fischeri. Our results suggest that aligner(s) should not be arbitrarily selected for this task, which is often done, as this can be detrimental to the biological interpretation of NGS analysis results. Since each aligner has specific advantages and disadvantages, these need to be considered depending on the characteristics of the input OMV sRNAs dataset and the corresponding bacterial reference genome to improve the detection of existing, biologically important OMV sRNAs. Until we learn more about these dependencies, we recommend using at least two, preferably three, aligners that have good metrics for the given dataset/bacterial reference genome. The overlapping results should be considered trustworthy, yet their differences should not be dismissed lightly, but treated carefully in order not to overlook any biologically important OMV sRNA. This can be achieved by applying the intersect-then-combine approach. For the mapping of OMV-associated sRNAs of A. fischeri to the reference genome organized into two circular chromosomes and one circular plasmid, containing copies of sequences with rRNA- and tRNA-related features and no copies of sequences with protein-encoding features, if the aligners are used with their default parameters, we advise avoiding Segemehl, and recommend using the intersect-then-combine approach with BBmap, BWA and Minimap2 to improve the potential for discovery of biologically important OMV-associated sRNAs.
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Affiliation(s)
- Bojana Banović Đeri
- Group for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sofija Nešić
- Group for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Ivan Vićić
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Samardžić
- Group for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Dragana Nikolić
- Group for Plant Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Zhou H, Su X, Song B. ACMGA: a reference-free multiple-genome alignment pipeline for plant species. BMC Genomics 2024; 25:515. [PMID: 38796435 PMCID: PMC11127342 DOI: 10.1186/s12864-024-10430-y] [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: 01/17/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND The short-read whole-genome sequencing (WGS) approach has been widely applied to investigate the genomic variation in the natural populations of many plant species. With the rapid advancements in long-read sequencing and genome assembly technologies, high-quality genome sequences are available for a group of varieties for many plant species. These genome sequences are expected to help researchers comprehensively investigate any type of genomic variants that are missed by the WGS technology. However, multiple genome alignment (MGA) tools designed by the human genome research community might be unsuitable for plant genomes. RESULTS To fill this gap, we developed the AnchorWave-Cactus Multiple Genome Alignment (ACMGA) pipeline, which improved the alignment of repeat elements and could identify long (> 50 bp) deletions or insertions (INDELs). We conducted MGA using ACMGA and Cactus for 8 Arabidopsis (Arabidopsis thaliana) and 26 Maize (Zea mays) de novo assembled genome sequences and compared them with the previously published short-read variant calling results. MGA identified more single nucleotide variants (SNVs) and long INDELs than did previously published WGS variant callings. Additionally, ACMGA detected significantly more SNVs and long INDELs in repetitive regions and the whole genome than did Cactus. Compared with the results of Cactus, the results of ACMGA were more similar to the previously published variants called using short-read. These two MGA pipelines identified numerous multi-allelic variants that were missed by the WGS variant calling pipeline. CONCLUSIONS Aligning de novo assembled genome sequences could identify more SNVs and INDELs than mapping short-read. ACMGA combines the advantages of AnchorWave and Cactus and offers a practical solution for plant MGA by integrating global alignment, a 2-piece-affine-gap cost strategy, and the progressive MGA algorithm.
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Affiliation(s)
- Huafeng Zhou
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, 266071, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, 266071, China.
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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