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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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2
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Tan WLA, Hudson NJ, Porto Neto LR, Reverter A, Afonso J, Fortes MRS. An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population. Anim Genet 2024; 55:495-510. [PMID: 38692842 DOI: 10.1111/age.13431] [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: 11/16/2023] [Revised: 02/26/2024] [Accepted: 04/01/2024] [Indexed: 05/03/2024]
Abstract
Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.
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Affiliation(s)
- Wei Liang Andre Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Nicholas James Hudson
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Queensland, Australia
| | | | | | - Juliana Afonso
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- Empresa Brasileira de Pesquisa Agropecuária, Pecuária Sudeste, São Carlos, São Paulo, Brazil
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3
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Chin HS, Ravi Varadharajulu N, Lin ZH, Chen WY, Zhang ZH, Arumugam S, Lai CY, Yu SSF. Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity. Front Microbiol 2024; 15:1415723. [PMID: 38983623 PMCID: PMC11231211 DOI: 10.3389/fmicb.2024.1415723] [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: 04/11/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024] Open
Abstract
The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.
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Affiliation(s)
- Hong Soon Chin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Narendrakumar Ravi Varadharajulu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Zhi-Han Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Yu Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Zong-Han Zhang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung City, Taiwan
| | | | - Ching-Yen Lai
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung City, Taiwan
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4
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Samanta D, Rauniyar S, Saxena P, Sani RK. From genome to evolution: investigating type II methylotrophs using a pangenomic analysis. mSystems 2024; 9:e0024824. [PMID: 38695578 PMCID: PMC11237726 DOI: 10.1128/msystems.00248-24] [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: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
A comprehensive pangenomic approach was employed to analyze the genomes of 75 type II methylotrophs spanning various genera. Our investigation revealed 256 exact core gene families shared by all 75 organisms, emphasizing their crucial role in the survival and adaptability of these organisms. Additionally, we predicted the functionality of 12 hypothetical proteins. The analysis unveiled a diverse array of genes associated with key metabolic pathways, including methane, serine, glyoxylate, and ethylmalonyl-CoA (EMC) metabolic pathways. While all selected organisms possessed essential genes for the serine pathway, Methylooceanibacter marginalis lacked serine hydroxymethyltransferase (SHMT), and Methylobacterium variabile exhibited both isozymes of SHMT, suggesting its potential to utilize a broader range of carbon sources. Notably, Methylobrevis sp. displayed a unique serine-glyoxylate transaminase isozyme not found in other organisms. Only nine organisms featured anaplerotic enzymes (isocitrate lyase and malate synthase) for the glyoxylate pathway, with the rest following the EMC pathway. Methylovirgula sp. 4MZ18 stood out by acquiring genes from both glyoxylate and EMC pathways, and Methylocapsa sp. S129 featured an A-form malate synthase, unlike the G-form found in the remaining organisms. Our findings also revealed distinct phylogenetic relationships and clustering patterns among type II methylotrophs, leading to the proposal of a separate genus for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129. This pangenomic study unveils remarkable metabolic diversity, unique gene characteristics, and distinct clustering patterns of type II methylotrophs, providing valuable insights for future carbon sequestration and biotechnological applications. IMPORTANCE Methylotrophs have played a significant role in methane-based product production for many years. However, a comprehensive investigation into the diverse genetic architectures across different genera of methylotrophs has been lacking. This study fills this knowledge gap by enhancing our understanding of core hypothetical proteins and unique enzymes involved in methane oxidation, serine, glyoxylate, and ethylmalonyl-CoA pathways. These findings provide a valuable reference for researchers working with other methylotrophic species. Furthermore, this study not only unveils distinctive gene characteristics and phylogenetic relationships but also suggests a reclassification for Methylovirgula sp. 4M-Z18 and Methylocapsa sp. S129 into separate genera due to their unique attributes within their respective genus. Leveraging the synergies among various methylotrophic organisms, the scientific community can potentially optimize metabolite production, increasing the yield of desired end products and overall productivity.
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Affiliation(s)
- Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA
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5
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Zavala B, Dineen L, Fisher KJ, Opulente DA, Harrison MC, Wolters JF, Shen XX, Zhou X, Groenewald M, Hittinger CT, Rokas A, LaBella AL. Genomic factors shaping codon usage across the Saccharomycotina subphylum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595506. [PMID: 38826271 PMCID: PMC11142207 DOI: 10.1101/2024.05.23.595506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. The biased use of synonymous codons has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. The Saccharomycotina, the fungal subphylum containing the yeasts Saccharomyces cerevisiae and Candida albicans , has been a model system for studying codon usage. We characterized codon usage across 1,154 strains from 1,051 species to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns across the subphylum. We found evidence of a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is also distinct between the 12 orders within the subphylum to such a degree that yeasts can be classified into orders with an accuracy greater than 90% using a machine learning algorithm trained on codon usage. We also characterized the degree to which codon usage bias is impacted by translational selection. Interestingly, the degree of translational selection was influenced by a combination of genome features and assembly metrics that included the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs. The order contains 24 species, and 23 are computationally predicted to lack tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that extreme avoidance of the CGN codons is associated with a decline in arginine tRNA function. Codon usage bias within the Saccharomycotina is generally consistent with previous investigations in fungi, which show a role for both genomic features and GC bias in shaping codon usage. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.
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6
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Brindisi LJ, Mattera R, Mudiyala S, Honig J, Simon JE. Genetic linkage mapping and quantitative trait locus (QTL) analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles. PLoS One 2024; 19:e0299825. [PMID: 38593174 PMCID: PMC11003626 DOI: 10.1371/journal.pone.0299825] [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] [Received: 10/06/2023] [Accepted: 02/15/2024] [Indexed: 04/11/2024] Open
Abstract
Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTLs) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the Rutgers advanced breeding line that served as a chilling tolerant parent, 'CB15', the chilling sensitive parent, 'Rutgers Obsession DMR' and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotype data using a reference genome alignment. A genetic linkage map was constructed and five statistically significant QTLs were identified in response to chilling temperatures with possible interactions between QTLs. The QTL on LG24 (qCH24) demonstrated the largest effect for chilling response and was significant in all three replicates. No QTLs were identified for linalool, as the population did not segregate sufficiently to detect this trait. Two significant QTLs were identified for estragole (also known as methyl chavicol) with only qEST1 on LG1 being significant in the multiple-QTL model (MQM). QEUC26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole) on LG26. These QTLs may represent key mechanisms for chilling tolerance and aroma in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding.
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Affiliation(s)
- Lara J. Brindisi
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Robert Mattera
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Sonika Mudiyala
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - Joshua Honig
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
| | - James E. Simon
- New Use Agriculture and Natural Plant Products Program, Department of Plant Biology, Rutgers University, New Jersey, United States of America
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7
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Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. Genomics and conservation: Guidance from training to analyses and applications. Mol Ecol Resour 2024; 24:e13893. [PMID: 37966259 DOI: 10.1111/1755-0998.13893] [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: 06/10/2022] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.
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Affiliation(s)
- Lauren M Schiebelhut
- Life and Environmental Sciences, University of California, Merced, California, USA
| | - Annie S Guillaume
- Geospatial Molecular Epidemiology group (GEOME), Laboratory for Biological Geochemistry (LGB), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arianna Kuhn
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
- Virginia Museum of Natural History, Martinsville, Virginia, USA
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, Western Australia, Australia
| | - Ted Cosart
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Leif Howard
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Shawn R Narum
- Hagerman Genetics Lab, University of Idaho, Hagerman, Idaho, USA
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Helen R Taylor
- Royal Zoological Society of Scotland, Edinburgh, Scotland
| | - Gregg W C Thomas
- Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Maren Wellenreuther
- Plant and Food Research, Nelson, New Zealand
- University of Auckland, Auckland, New Zealand
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
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Rey E, Maughan PJ, Maumus F, Lewis D, Wilson L, Fuller J, Schmöckel SM, Jellen EN, Tester M, Jarvis DE. A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes. Commun Biol 2023; 6:1263. [PMID: 38092895 PMCID: PMC10719370 DOI: 10.1038/s42003-023-05613-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use it, together with the A-genome diploid C. pallidicaule, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.2%, 48.6%, and 57.9% of the quinoa, C. pallidicaule, and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.
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Affiliation(s)
- Elodie Rey
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Peter J Maughan
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Daniel Lewis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Leanne Wilson
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Juliana Fuller
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Sandra M Schmöckel
- University of Hohenheim, Institute of Crop Science, Department Physiology of Yield Stability, 70599, Stuttgart, Germany
| | - Eric N Jellen
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA
| | - Mark Tester
- 1King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - David E Jarvis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, UT, 84602, USA.
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Matthews AE, Boves TJ, Percy KL, Schelsky WM, Wijeratne AJ. Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host-Symbiont Coevolution. Life (Basel) 2023; 13:2054. [PMID: 37895435 PMCID: PMC10608719 DOI: 10.3390/life13102054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host-symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host-symbiont coevolution at multiple evolutionary scales.
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Affiliation(s)
- Alix E. Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, AR 72401, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
| | - Than J. Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
| | - Katie L. Percy
- Audubon Delta, National Audubon Society, Baton Rouge, LA 70808, USA;
- United States Department of Agriculture, Natural Resources Conservation Service, Addis, LA 70710, USA
| | - Wendy M. Schelsky
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, Champaign, IL 61801, USA;
- Prairie Research Institute, Illinois Natural History Survey, University of Illinois, Urbana-Champaign, Champaign, IL 61820, USA
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72401, USA; (T.J.B.); (A.J.W.)
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10
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Kliver S, Houck ML, Perelman PL, Totikov A, Tomarovsky A, Dudchenko O, Omer AD, Colaric Z, Weisz D, Aiden EL, Chan S, Hastie A, Komissarov A, Ryder OA, Graphodatsky A, Johnson WE, Maldonado JE, Pukazhenthi BS, Marinari PE, Wildt DE, Koepfli KP. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). J Hered 2023; 114:539-548. [PMID: 37249392 PMCID: PMC10848218 DOI: 10.1093/jhered/esad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/27/2023] [Indexed: 05/31/2023] Open
Abstract
The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.
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Affiliation(s)
- Sergei Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, Copenhagen, Denmark
| | - Marlys L Houck
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Polina L Perelman
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Azamat Totikov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Andrey Tomarovsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, United States
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Saki Chan
- Department of Research and Development, Bionano Genomics, San Diego, CA, United States
| | - Alex Hastie
- Department of Research and Development, Bionano Genomics, San Diego, CA, United States
| | - Aleksey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, Russia
| | - Oliver A Ryder
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Alexander Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Warren E Johnson
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, United States
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Loyola University Maryland, Baltimore, MD, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Paul E Marinari
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - David E Wildt
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, United States
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, United States
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11
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Noll N, Molari M, Shaw LP, Neher RA. PanGraph: scalable bacterial pan-genome graph construction. Microb Genom 2023; 9:mgen001034. [PMID: 37278719 PMCID: PMC10327495 DOI: 10.1099/mgen.0.001034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
Abstract
The genomic diversity of microbes is commonly parameterized as SNPs relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome, the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the widespread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. In addition to pangenomic approaches that focus on the variation in the sets of genes present in different genomes, complete assemblies allow investigations of the evolution of genome structure and gene order. This latter problem, however, is computationally demanding with few tools available that shed light on these dynamics. Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as a path along vertices, which in turn encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into several common formats for either downstream analysis or immediate visualization.
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Affiliation(s)
- Nicholas Noll
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA, USA
| | - Marco Molari
- Swiss Institute of Bioinformatics, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Liam P. Shaw
- Department of Biology, University of Oxford, Oxford, UK
| | - Richard A. Neher
- Swiss Institute of Bioinformatics, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
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12
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Benchmarking machine learning robustness in Covid-19 genome sequence classification. Sci Rep 2023; 13:4154. [PMID: 36914815 PMCID: PMC10010240 DOI: 10.1038/s41598-023-31368-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome-millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses, is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches with different perturbation budgets are more robust (and accurate) than others for specific embedding methods to certain noise simulations on the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics.
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13
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Zuccolo A, Mfarrej S, Celii M, Mussurova S, Rivera LF, Llaca V, Mohammed N, Pain A, Alrefaei AF, Alrefaei AF, Wing RA. The gyrfalcon (Falco rusticolus) genome. G3 (BETHESDA, MD.) 2023; 13:6972330. [PMID: 36611193 PMCID: PMC9997569 DOI: 10.1093/g3journal/jkad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023]
Abstract
High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.193 Gbp, including 8,064 complete Benchmarking Universal Single-Copy Orthologs (BUSCOs) of the total 8,338 BUSCO groups present in the library aves_odb10. Of these BUSCO genes, 96.7% were complete, 96.1% were present as a single copy, and 0.6% were duplicated. Furthermore, 0.8% of BUSCO genes were fragmented and 2.5% (210) were missing. A de novo search for transposable elements (TEs) identified 5,716 TEs that masked 7.61% of the F. rusticolus genome assembly when combined with publicly available TE collections. Long interspersed nuclear elements, in particular, the element Chicken-repeat 1 (CR1), were the most abundant TEs in the F. rusticolus genome. A de novo first-pass gene annotation was performed using 293,349 PacBio Iso-Seq transcripts and 496,195 transcripts derived from the assembly of 42,429,525 Illumina PE RNA-seq reads. In all, 19,602 putative genes, of which 59.31% were functionally characterized and associated with Gene Ontology terms, were annotated. A comparison of the gyrfalcon genome assembly with the publicly available assemblies of the domestic chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and hummingbird (Calypte anna) revealed several genome rearrangements. In particular, nine putative chromosome fusions were identified in the gyrfalcon genome assembly compared with those in the G. gallus genome assembly. This genome assembly, its annotation for TEs and genes, and the comparative analyses presented, complement and strength the base of high-quality genome assemblies and associated resources available for comparative studies focusing on the evolution, ecology, and conservation of Aves.
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Affiliation(s)
- Andrea Zuccolo
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Sara Mfarrej
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah 23955-6900, Saudi Arabia
| | - Mirko Celii
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Saule Mussurova
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luis F Rivera
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Victor Llaca
- Research and Development, Corteva Agriscience, Johnston, IA 50131, USA
| | - Nahed Mohammed
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Arnab Pain
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah 23955-6900, Saudi Arabia
| | | | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Rod A Wing
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,School of Plant Sciences, Arizona Genomics Institute, University of Arizona, 24 Tucson, Arizona 85721, USA
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14
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Manee MM, Alqahtani FH, Al-Shomrani BM, El-Shafie HAF, Dias GB. Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest. INSECTS 2023; 14:255. [PMID: 36975940 PMCID: PMC10054242 DOI: 10.3390/insects14030255] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.
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Affiliation(s)
- Manee M. Manee
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Institute of Advanced Agricultural and Food Technologies, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Fahad H. Alqahtani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Institute of Advanced Agricultural and Food Technologies, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Badr M. Al-Shomrani
- National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Institute of Advanced Agricultural and Food Technologies, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
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15
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Thia JA, Korhonen PK, Young ND, Gasser RB, Umina PA, Yang Q, Edwards O, Walsh T, Hoffmann AA. The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range. J Evol Biol 2023; 36:381-398. [PMID: 36573922 PMCID: PMC10107102 DOI: 10.1111/jeb.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/13/2022] [Accepted: 11/03/2022] [Indexed: 12/28/2022]
Abstract
Genomic data provide valuable insights into pest management issues such as resistance evolution, historical patterns of pest invasions and ongoing population dynamics. We assembled the first reference genome for the redlegged earth mite, Halotydeus destructor (Tucker, 1925), to investigate adaptation to pesticide pressures and demography in its invasive Australian range using whole-genome pool-seq data from regionally distributed populations. Our reference genome comprises 132 autosomal contigs, with a total length of 48.90 Mb. We observed a large complex of ace genes, which has presumably evolved from a long history of organophosphate selection in H. destructor and may contribute towards organophosphate resistance through copy number variation, target-site mutations and structural variants. In the putative ancestral H. destructor ace gene, we identified three target-site mutations (G119S, A201S and F331Y) segregating in organophosphate-resistant populations. Additionally, we identified two new para sodium channel gene mutations (L925I and F1020Y) that may contribute to pyrethroid resistance. Regional structuring observed in population genomic analyses indicates that gene flow in H. destructor does not homogenize populations across large geographic distances. However, our demographic analyses were equivocal on the magnitude of gene flow; the short invasion history of H. destructor makes it difficult to distinguish scenarios of complete isolation vs. ongoing migration. Nonetheless, we identified clear signatures of reduced genetic diversity and smaller inferred effective population sizes in eastern vs. western populations, which is consistent with the stepping-stone invasion pathway of this pest in Australia. These new insights will inform development of diagnostic genetic markers of resistance, further investigation into the multifaceted organophosphate resistance mechanism and predictive modelling of resistance evolution and spread.
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Affiliation(s)
- Joshua A Thia
- Bio21 Institute, School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Qiong Yang
- Bio21 Institute, School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Owain Edwards
- Land and Water, CSIRO, Floreat, Western Australia, Australia
| | - Tom Walsh
- CSIRO, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia.,Applied BioSciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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16
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Wang Y, Yu J, Jiang M, Lei W, Zhang X, Tang H. Sequencing and Assembly of Polyploid Genomes. Methods Mol Biol 2023; 2545:429-458. [PMID: 36720827 DOI: 10.1007/978-1-0716-2561-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations often result in highly complex genome structures, posing challenges to genome assembly and phasing. Recent advances in sequencing technologies and genome assembly algorithms have enabled high-quality, near-complete chromosome-level assemblies of polyploid genomes. Advances in novel sequencing technologies include highly accurate single-molecule sequencing with HiFi reads, chromosome conformation capture with Hi-C technique, and linked reads sequencing. Additionally, new computational approaches have also significantly improved the precision and reliability of polyploid genome assembly and phasing, such as HiCanu, hifiasm, ALLHiC, and PolyGembler. Herein, we review recently published polyploid genomes and compare the various sequencing, assembly, and phasing approaches that are utilized in these genome studies. Finally, we anticipate that accurate and telomere-to-telomere chromosome-level assembly of polyploid genomes could ultimately become a routine procedure in the near future.
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Affiliation(s)
- Yibin Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaxin Yu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengwei Jiang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenlong Lei
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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17
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Papa Y, Wellenreuther M, Morrison MA, Ritchie PA. Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus). G3 (BETHESDA, MD.) 2022; 13:6883520. [PMID: 36477875 PMCID: PMC9911067 DOI: 10.1093/g3journal/jkac315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022]
Abstract
Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management. Here, we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi [Nemadactylus macropterus (Forster, 1801)], a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq reads were obtained to assist in gene annotation. The final genome assembly was 568 Mb long with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared with the same values reported for other fishes. Iso-Seq analysis recovered 91,313 unique transcripts from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly and the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics and comparative eco-evolutionary studies in teleosts and related organisms.
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Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Maren Wellenreuther
- Seafood Production Group, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand,School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Mark A Morrison
- National Institute of Water and Atmospheric Research, Auckland 1010, New Zealand
| | - Peter A Ritchie
- Corresponding author: Te Toki A Rata, Gate 7, Kelburn Parade, Wellington 6012, New Zealand.
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18
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Nunes R, Storer C, Doleck T, Kawahara AY, Pierce NE, Lohman DJ. Predictors of sequence capture in a large-scale anchored phylogenomics project. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.943361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.
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19
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Sjodin BMF, Russello MA. Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika ( Ochotona princeps). G3 GENES|GENOMES|GENETICS 2022; 12:6695220. [PMID: 36087005 PMCID: PMC9635661 DOI: 10.1093/g3journal/jkac241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/07/2022] [Indexed: 11/30/2022]
Abstract
High-elevation environments have lower atmospheric oxygen content, reduced temperatures, and higher levels of UV radiation than found at lower elevations. As such, species living at high elevations must overcome these challenges to survive, grow, and reproduce. American pikas (Ochotona princeps) are alpine lagomorphs that are habitat specialists typically found at elevations >2,000 m. Previous research has shown putative evidence for high-elevation adaptation; however, investigations to date have been limited to a fraction of the genome. Here, we took a comparative genomics approach to identify putative regions under selection using a chromosomal reference genome assembly for the American pika relative to 8 other mammalian species targeted based on phylogenetic relatedness and (dis)similarity in ecology. We first identified orthologous gene groups across species and then extracted groups containing only American pika genes as well as unclustered pika genes to inform functional enrichment analyses; among these, we found 141 enriched terms with many related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. We identified 15 significantly expanded gene families within the American pika across all orthologous gene groups that displayed functionally enriched terms associated with hypoxia adaptation. We further detected 196 positively selected genes, 41 of which have been associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. In particular, OXNAD1, NRDC, and those genes critical in DNA repair represent important targets for future research to examine their functional implications in the American pika, especially as they may relate to adaptation to rapidly changing environments.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, University of British Columbia, Okanagan Campus , Kelowna, V1V 1V7 BC, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus , Kelowna, V1V 1V7 BC, Canada
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20
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Chen Y, Zhang T, Xian M, Zhang R, Yang W, Su B, Yang G, Sun L, Xu W, Xu S, Gao H, Xu L, Gao X, Li J. A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. Commun Biol 2022; 5:353. [PMID: 35418663 PMCID: PMC9008013 DOI: 10.1038/s42003-022-03298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.
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Affiliation(s)
- Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Ming Xian
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Rui Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Weifei Yang
- 1 Gene Co., Ltd, 310051, Hangzhou, P.R. China
- Annoroad Gene Technology (Beijing) Co., Ltd, 100176, Beijing, P.R. China
| | - Baqi Su
- Drung Cattle Conservation Farm in Jiudang Wood, Drung and Nu Minority Autonomous County, Gongshan, 673500, Kunming, Yunnan, P.R. China
| | - Guoqiang Yang
- Livestock and Poultry Breed Improvement Center, Nujiang Lisu Minority Autonomous Prefecture, 673199, Kunming, Yunnan, P.R. China
| | - Limin Sun
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Wenkun Xu
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Shangzhong Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
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21
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Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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22
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Narum S, News JK, Fountain-Jones N, Hooper Junior R, Ortiz-Barrientos D, O'Boyle B, Sibbett B. Editorial 2022. Mol Ecol Resour 2021; 22:1-8. [PMID: 34919782 DOI: 10.1111/1755-0998.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Friel J, Bombarely A, Fornell CD, Luque F, Fernández-Ocaña AM. Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112514. [PMID: 34834877 PMCID: PMC8622120 DOI: 10.3390/plants10112514] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 05/11/2023]
Abstract
Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediterranean basin. Thousands of cultivars have been described, of which around 1200 are conserved in the different olive germplasm banks. The genetic characterisation of these cultivars can be performed in different ways. Whole-genome sequencing (WGS) provides more information than the reduced representation methods such as genotype by sequencing (GBS), but at a much higher cost. This may change as the cost of sequencing continues to drop, but, currently, genotyping hundreds of cultivars using WGS is not a realistic goal for most research groups. Our aim is to systematically compare both methodologies applied to olive genotyping and summarise any possible recommendations for the geneticists and molecular breeders of the olive scientific community. In this work, we used a selection of 24 cultivars from an olive core collection from the World Olive Germplasm Collection of the Andalusian Institute of Agricultural and Fisheries Research and Training (WOGBC), which represent the most of the cultivars present in cultivated fields over the world. Our results show that both methodologies deliver similar results in the context of phylogenetic analysis and popular population genetic analysis methods such as clustering. Furthermore, WGS and GBS datasets from different experiments can be merged in a single dataset to perform these analytical methodologies with proper filtering. We also tested the influence of the different olive reference genomes in this type of analysis, finding that they have almost no effect when estimating genetic relationships. This work represents the first comparative study between both sequencing techniques in olive. Our results demonstrate that the use of GBS is a perfectly viable option for replacing WGS and reducing research costs when the goal of the experiment is to characterise the genetic relationship between different accessions. Besides this, we show that it is possible to combine variants from GBS and WGS datasets, allowing the reuse of publicly available data.
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Affiliation(s)
- James Friel
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20122 Milan, Italy; (J.F.); (A.B.)
| | - Aureliano Bombarely
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20122 Milan, Italy; (J.F.); (A.B.)
- Instituto de Biologıa Molecular y Celular de Plantas (IBMCP), CSIC, Universitat Politecnica de Valencia, 46011 Valencia, Spain
| | - Carmen Dorca Fornell
- Departamento de Didáctica de las Matemáticas y las Ciencias Experimentales, Facultad de Educación, Universidad Internacional de la Rioja (UNIR), 26006 Logroño, Spain;
| | - Francisco Luque
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO), Universidad de Jaén, 23071 Jaén, Spain;
| | - Ana Maria Fernández-Ocaña
- Departamento de Biología Animal, Biologia Vegetal y Ecología, Facultad de Ciencias Experimentales, Campus de Las Lagunillas s/n, Universidad de Jaén UJA, 23071 Jaén, Spain
- Correspondence:
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24
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Ferchaud AL, Mérot C, Normandeau E, Ragoussis J, Babin C, Djambazian H, Bérubé P, Audet C, Treble M, Walkusz W, Bernatchez L. Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides). G3-GENES GENOMES GENETICS 2021; 12:6428537. [PMID: 34791178 DOI: 10.1093/g3journal/jkab376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022]
Abstract
Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that, similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex-determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.
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Affiliation(s)
- Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Babin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Haig Djambazian
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Pierre Bérubé
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Margaret Treble
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Wocjciech Walkusz
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
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25
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Sjodin BMF, Galbreath KE, Lanier HC, Russello MA. Chromosome-Level Reference Genome Assembly for the American Pika (Ochotona princeps). J Hered 2021; 112:549-557. [PMID: 34036348 PMCID: PMC8558581 DOI: 10.1093/jhered/esab031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023] Open
Abstract
The American pika (Ochotona princeps) is an alpine lagomorph found throughout western North America. Primarily inhabiting talus slopes at higher elevations (>2000 m), American pikas are well adapted to cold, montane environments. Warming climates on both historical and contemporary scales have contributed to population declines in American pikas, positioning them as a focal mammalian species for investigating the ecological effects of climate change. To support and expand ongoing research efforts, here, we present a highly contiguous and annotated reference genome assembly for the American pika (OchPri4.0). This assembly was produced using Dovetail de novo proximity ligation methods and annotated through the NCBI Eukaryotic Genome Annotation pipeline. The resulting assembly was chromosome- scale, with a total length of 2.23 Gb across 9350 scaffolds and a scaffold N50 of 75.8 Mb. The vast majority (>97%) of the total assembly length was found within 36 large scaffolds; 33 of these scaffolds correlated to whole autosomes, while the X chromosome was covered by 3 large scaffolds. Additionally, we identified 17 enriched gene ontology terms among American pika-specific genes putatively related to adaptation to high-elevation environments. This high-quality genome assembly will serve as a springboard for exploring the evolutionary underpinnings of behavioral, ecological, and taxonomic diversification in pikas as well as broader-scale eco-evolutionary questions pertaining to cold-adapted species in general.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Hayley C Lanier
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, Canada
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26
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Pépin N, Hebert FO, Joly DL. Genome-Wide Characterization of the MLO Gene Family in Cannabis sativa Reveals Two Genes as Strong Candidates for Powdery Mildew Susceptibility. FRONTIERS IN PLANT SCIENCE 2021; 12:729261. [PMID: 34589104 PMCID: PMC8475652 DOI: 10.3389/fpls.2021.729261] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Cannabis sativa is increasingly being grown around the world for medicinal, industrial, and recreational purposes. As in all cultivated plants, cannabis is exposed to a wide range of pathogens, including powdery mildew (PM). This fungal disease stresses cannabis plants and reduces flower bud quality, resulting in significant economic losses for licensed producers. The Mildew Locus O (MLO) gene family encodes plant-specific proteins distributed among conserved clades, of which clades IV and V are known to be involved in susceptibility to PM in monocots and dicots, respectively. In several studies, the inactivation of those genes resulted in durable resistance to the disease. In this study, we identified and characterized the MLO gene family members in five different cannabis genomes. Fifteen Cannabis sativa MLO (CsMLO) genes were manually curated in cannabis, with numbers varying between 14, 17, 19, 18, and 18 for CBDRx, Jamaican Lion female, Jamaican Lion male, Purple Kush, and Finola, respectively (when considering paralogs and incomplete genes). Further analysis of the CsMLO genes and their deduced protein sequences revealed that many characteristics of the gene family, such as the presence of seven transmembrane domains, the MLO functional domain, and particular amino acid positions, were present and well conserved. Phylogenetic analysis of the MLO protein sequences from all five cannabis genomes and other plant species indicated seven distinct clades (I through VII), as reported in other crops. Expression analysis revealed that the CsMLOs from clade V, CsMLO1 and CsMLO4, were significantly upregulated following Golovinomyces ambrosiae infection, providing preliminary evidence that they could be involved in PM susceptibility. Finally, the examination of variation within CsMLO1 and CsMLO4 in 32 cannabis cultivars revealed several amino acid changes, which could affect their function. Altogether, cannabis MLO genes were identified and characterized, among which candidates potentially involved in PM susceptibility were noted. The results of this study will lay the foundation for further investigations, such as the functional characterization of clade V MLOs as well as the potential impact of the amino acid changes reported. Those will be useful for breeding purposes in order to develop resistant cultivars.
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Affiliation(s)
- Noémi Pépin
- Centre d’Innovation et de Recherche sur le Cannabis, Université de Moncton, Département de biologie, Moncton, NB, Canada
| | - Francois Olivier Hebert
- Centre d’Innovation et de Recherche sur le Cannabis, Université de Moncton, Département de biologie, Moncton, NB, Canada
- Institut National des Cannabinoïdes, Montréal, QC, Canada
| | - David L. Joly
- Centre d’Innovation et de Recherche sur le Cannabis, Université de Moncton, Département de biologie, Moncton, NB, Canada
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27
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Urban JM, Foulk MS, Bliss JE, Coleman CM, Lu N, Mazloom R, Brown SJ, Spradling AC, Gerbi SA. High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing. BMC Genomics 2021; 22:643. [PMID: 34488624 PMCID: PMC8419958 DOI: 10.1186/s12864-021-07926-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/08/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. RESULTS We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. CONCLUSIONS We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.
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Affiliation(s)
- John M Urban
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA.
| | - Michael S Foulk
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
- Present Address: Department of Biology, Mercyhurst University, Erie, PA, 16546, USA
| | - Jacob E Bliss
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
| | - C Michelle Coleman
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Nanyan Lu
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Reza Mazloom
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Susan J Brown
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Allan C Spradling
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
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28
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Wood ZT, Wiegardt AK, Barton KL, Clark JD, Homola JJ, Olsen BJ, King BL, Kovach AI, Kinnison MT. Meta-analysis: Congruence of genomic and phenotypic differentiation across diverse natural study systems. Evol Appl 2021; 14:2189-2205. [PMID: 34603492 PMCID: PMC8477602 DOI: 10.1111/eva.13264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/17/2023] Open
Abstract
Linking genotype to phenotype is a primary goal for understanding the genomic underpinnings of evolution. However, little work has explored whether patterns of linked genomic and phenotypic differentiation are congruent across natural study systems and traits. Here, we investigate such patterns with a meta-analysis of studies examining population-level differentiation at subsets of loci and traits putatively responding to divergent selection. We show that across the 31 studies (88 natural population-level comparisons) we examined, there was a moderate (R 2 = 0.39) relationship between genomic differentiation (F ST ) and phenotypic differentiation (P ST ) for loci and traits putatively under selection. This quantitative relationship between P ST and F ST for loci under selection in diverse taxa provides broad context and cross-system predictions for genomic and phenotypic adaptation by natural selection in natural populations. This context may eventually allow for more precise ideas of what constitutes "strong" differentiation, predictions about the effect size of loci, comparisons of taxa evolving in nonparallel ways, and more. On the other hand, links between P ST and F ST within studies were very weak, suggesting that much work remains in linking genomic differentiation to phenotypic differentiation at specific phenotypes. We suggest that linking genotypes to specific phenotypes can be improved by correlating genomic and phenotypic differentiation across a spectrum of diverging populations within a taxon and including wide coverage of both genomes and phenomes.
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Affiliation(s)
- Zachary T. Wood
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
| | - Andrew K. Wiegardt
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Kayla L. Barton
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Jonathan D. Clark
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Brian J. Olsen
- Maine Center for Genetics in the EnvironmentOronoMEUSA
- Department of Wildlife, Fisheries, and Conservation BiologyUniversity of MaineOronoMEUSA
| | - Benjamin L. King
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Michael T. Kinnison
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
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29
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Yamaguchi K, Kadota M, Nishimura O, Ohishi Y, Naito Y, Kuraku S. Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies. Mol Ecol 2021; 30:5923-5934. [PMID: 34432923 PMCID: PMC9292758 DOI: 10.1111/mec.16146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome‐scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi‐C, a method for genome‐wide chromosome conformation capture that was originally developed for investigating the long‐range interaction of chromatins. Performing genomic scaffolding using Hi‐C data is highly resource‐demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi‐C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi‐C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome‐scale genome assemblies using single‐copy reference orthologues.
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Affiliation(s)
- Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), Mishima, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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Smith SR, Normandeau E, Djambazian H, Nawarathna PM, Berube P, Muir AM, Ragoussis J, Penney CM, Scribner KT, Luikart G, Wilson CC, Bernatchez L. A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush). Mol Ecol Resour 2021; 22:679-694. [PMID: 34351050 PMCID: PMC9291852 DOI: 10.1111/1755-0998.13483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 01/23/2023]
Abstract
Here, we present an annotated, chromosome‐anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long‐read sequencing, paired‐end Illumina sequencing, proximity ligation (Hi‐C) sequencing, and a previously published linkage map to produce a highly contiguous assembly composed of 7378 contigs (contig N50 = 1.8 Mb) assigned to 4120 scaffolds (scaffold N50 = 44.975 Mb). Long read sequencing data were generated using DNA from a female double haploid individual. 84.7% of the genome was assigned to 42 chromosome‐sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologues were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k‐mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitochondrial genome assembly was also produced. Self‐versus‐self synteny analysis allowed us to identify homeologs resulting from the salmonid specific autotetraploid event (Ss4R) as well as regions exhibiting delayed rediploidization. Alignment with three other salmonid genomes and the Northern Pike (Esox lucius) genome also allowed us to identify homologous chromosomes in related taxa. We also generated multiple resources useful for future genomic research on Lake Trout, including a repeat library and a sex‐averaged recombination map. A novel RNA sequencing data set for liver tissue was also generated in order to produce a publicly available set of annotations for 49,668 genes and pseudogenes. Potential applications of these resources to population genetics and the conservation of native populations are discussed.
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Affiliation(s)
- Seth R Smith
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Haig Djambazian
- McGill Genome Centre, Department of Human Genetics, Montreal, QC, Canada
| | - Pubudu M Nawarathna
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G, McGill University, Montréal, QC, Canada
| | - Pierre Berube
- McGill Genome Centre, Department of Human Genetics, Montreal, QC, Canada
| | | | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, Montreal, QC, Canada
| | - Chantelle M Penney
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Kim T Scribner
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Gordon Luikart
- Fish and Wildlife Genomics Group, University of Montana, Missoula, MT, USA.,Flathead Lake Biological Station, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Chris C Wilson
- Aquatic Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
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