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Yocca A, Akinyuwa M, Bailey N, Cliver B, Estes H, Guillemette A, Hasannin O, Hutchison J, Jenkins W, Kaur I, Khanna RR, Loftin M, Lopes L, Moore-Pollard E, Olofintila O, Oyebode GO, Patel J, Thapa P, Waldinger M, Zhang J, Zhang Q, Goertzen L, Carey SB, Hargarten H, Mattheis J, Zhang H, Jones T, Boston L, Grimwood J, Ficklin S, Honaas L, Harkess A. A chromosome-scale assembly for 'd'Anjou' pear. G3 (BETHESDA, MD.) 2024; 14:jkae003. [PMID: 38190814 PMCID: PMC10917493 DOI: 10.1093/g3journal/jkae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 07/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024]
Abstract
Cultivated pear consists of several Pyrus species with Pyrus communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully phased chromosome-scale genome assembly of P. communis 'd'Anjou.' Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totaling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other and to the Malus domestica 'Honeycrisp' apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d'Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.
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Affiliation(s)
- Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mary Akinyuwa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Nick Bailey
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Brannan Cliver
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Harrison Estes
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | | | - Omar Hasannin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer Hutchison
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wren Jenkins
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ishveen Kaur
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | | | - Madelene Loftin
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Lauren Lopes
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Erika Moore-Pollard
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152-3530, USA
| | | | | | - Jinesh Patel
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Parbati Thapa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Martin Waldinger
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jie Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qiong Zhang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Leslie Goertzen
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Heidi Hargarten
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - James Mattheis
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Huiting Zhang
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Teresa Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - LoriBeth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Loren Honaas
- Physiology and Pathology of Tree Fruits Research Laboratory, USDA ARS, Wenatchee, WA 98801, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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2
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Chen S, Sun M, Xu S, Xue C, Wei S, Zheng P, Gu K, Qiao Z, Liu Z, Zhang M, Wu J. The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp. BMC PLANT BIOLOGY 2023; 23:430. [PMID: 37710163 PMCID: PMC10503127 DOI: 10.1186/s12870-023-04406-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data. DESCRIPTION Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services. CONCLUSIONS The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.
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Affiliation(s)
- Shulin Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Manyi Sun
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaozhuo Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Cheng Xue
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Shuwei Wei
- Shandong Institute of Pomology, Tai'an, 271000, China
| | - Pengfei Zheng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Kaidi Gu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiwen Qiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiying Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Mingyue Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Jun Wu
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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3
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Waite JM, Kelly EA, Zhang H, Hargarten HL, Waliullah S, Altman NS, dePamphilis CW, Honaas LA, Kalcsits L. Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit. G3 (BETHESDA, MD.) 2023; 13:jkad120. [PMID: 37259608 PMCID: PMC10411604 DOI: 10.1093/g3journal/jkad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 12/20/2022] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course-24, 48, and 72 h following a heat stimulus-to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA-GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.
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Affiliation(s)
- Jessica M Waite
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Elizabeth A Kelly
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, 101 Huck Life Sciences Building, University Park, PA, 16802, USA
| | - Huiting Zhang
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
- Department of Horticulture, Washington State University, 251 Clark Hall, Pullman, WA, 99164, USA
| | - Heidi L Hargarten
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Sumyya Waliullah
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
- Department of Plant Pathology, University of Georgia, 2360 Rainwater Rd, Tifton, GA, 31798, USA
| | - Naomi S Altman
- Department of Statistics, The Huck Institutes of the Life Sciences, Pennsylvania State University, 312 Thomas Building, University Park, PA, 16802, USA
| | - Claude W dePamphilis
- Department of Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, 101 Huck Life Sciences Building, University Park, PA, 16802, USA
| | - Loren A Honaas
- USDA Agricultural Research Service, Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA, 98801, USA
| | - Lee Kalcsits
- Tree Fruit Research and Extension Center, Department of Horticulture, Washington State University, 1100 N. Western Ave., Wenatchee, WA, 98801, USA
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4
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Wafula EK, Zhang H, Von Kuster G, Leebens-Mack JH, Honaas LA, dePamphilis CW. PlantTribes2: Tools for comparative gene family analysis in plant genomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1011199. [PMID: 36798801 PMCID: PMC9928214 DOI: 10.3389/fpls.2022.1011199] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/02/2022] [Indexed: 05/12/2023]
Abstract
Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range of genome assembly and annotation qualities across plant genomes due to their varying sizes, complexity, and the technology used for the assembly and annotation. To effectively work across genomes, researchers increasingly rely on comparative genomic approaches that integrate across plant community resources and data types. Such efforts have aided the genome annotation process and yielded novel insights into the evolutionary history of genomes and gene families, including complex non-model organisms. The essential tools to achieve these insights rely on gene family analysis at a genome-scale, but they are not well integrated for rapid analysis of new data, and the learning curve can be steep. Here we present PlantTribes2, a scalable, easily accessible, highly customizable, and broadly applicable gene family analysis framework with multiple entry points including user provided data. It uses objective classifications of annotated protein sequences from existing, high-quality plant genomes for comparative and evolutionary studies. PlantTribes2 can improve transcript models and then sort them, either genome-scale annotations or individual gene coding sequences, into pre-computed orthologous gene family clusters with rich functional annotation information. Then, for gene families of interest, PlantTribes2 performs downstream analyses and customizable visualizations including, (1) multiple sequence alignment, (2) gene family phylogeny, (3) estimation of synonymous and non-synonymous substitution rates among homologous sequences, and (4) inference of large-scale duplication events. We give examples of PlantTribes2 applications in functional genomic studies of economically important plant families, namely transcriptomics in the weedy Orobanchaceae and a core orthogroup analysis (CROG) in Rosaceae. PlantTribes2 is freely available for use within the main public Galaxy instance and can be downloaded from GitHub or Bioconda. Importantly, PlantTribes2 can be readily adapted for use with genomic and transcriptomic data from any kind of organism.
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Affiliation(s)
- Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Huiting Zhang
- Tree Fruit Research Laboratory, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Gregory Von Kuster
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | | | - Loren A Honaas
- Tree Fruit Research Laboratory, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Wenatchee, WA, United States
| | - Claude W dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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