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Wu F, Mai Y, Chen C, Xia R. SynGAP: a synteny-based toolkit for gene structure annotation polishing. Genome Biol 2024; 25:218. [PMID: 39138517 PMCID: PMC11323386 DOI: 10.1186/s13059-024-03359-8] [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: 12/03/2023] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Genome sequencing has become a routine task for biologists, but the challenge of gene structure annotation persists, impeding accurate genomic and genetic research. Here, we present a bioinformatics toolkit, SynGAP (Synteny-based Gene structure Annotation Polisher), which uses gene synteny information to accomplish precise and automated polishing of gene structure annotation of genomes. SynGAP offers exceptional capabilities in the improvement of gene structure annotation quality and the profiling of integrative gene synteny between species. Furthermore, an expression variation index is designed for comparative transcriptomics analysis to explore candidate genes responsible for the development of distinct traits observed in phylogenetically related species.
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Affiliation(s)
- Fengqi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China
| | - Yingxiao Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510640, Guangdong, China.
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Ochoa-Alejo N, Gómez-Jiménez MC, Martínez O. Editorial: Transcriptomics of fruit growth, development and ripening. FRONTIERS IN PLANT SCIENCE 2024; 15:1399376. [PMID: 38645390 PMCID: PMC11026863 DOI: 10.3389/fpls.2024.1399376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Affiliation(s)
- Neftali Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | | | - Octavio Martínez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
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Waite JM, Hollender CA, Eilers JR, Burchard E, Dardick C. Peach LAZY1 and DRO1 protein-protein interactions and co-expression with PRAF/RLD family support conserved gravity-related protein interactions across plants. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.000995. [PMID: 38287925 PMCID: PMC10823791 DOI: 10.17912/micropub.biology.000995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/12/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024]
Abstract
IGT/LAZY proteins play a central role in determining gravitropic set point angle and orientation of lateral organs across plant species. Recent work in model systems has demonstrated that interactions between IGT/LAZY proteins and BREVIS RADIX (BRX)-domain containing proteins, such as PH, RCC1, AND FYVE/RCC1-LIKE DOMAIN (PRAF/RLD), and BREVIS RADIX LIKE (BRXL) family members, are mechanistically important for setting gravitropic set point angle. Here, we identified peach PRAF/RLD proteins as interactors of the peach IGT/LAZY proteins PpeLAZY1 and DEEPER ROOTING 1 (PpeDRO1) from a yeast-two-hybrid screen. We also show that the BRX domains of these interacting proteins have high sequence similarity with PRAF/RLD and BRX family proteins from rice and Arabidopsis. Further, PpeLAZY1 and the peach PRAF/RLD interactors are all expressed at relatively high levels in leaf, meristem, and shoot tip tissues. Together, this evidence supports the importance and conservation of IGT/LAZY-BRX-domain interactions, which underlie setting gravitropic set point angle across angiosperms.
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Affiliation(s)
| | | | - Jon R. Eilers
- USDA ARS Tree Fruit Research Laboratory, Wenatchee, WA
| | - Erik Burchard
- USDA ARS Appalachian Fruit Research Station, Kearneysville, WV
| | - Chris Dardick
- USDA ARS Appalachian Fruit Research Station, Kearneysville, WV
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Li M, Mount SM, Liu Z. Rosaceae fruit transcriptome database (ROFT)-a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry. HORTICULTURE RESEARCH 2023; 10:uhad240. [PMID: 38162465 PMCID: PMC10756754 DOI: 10.1093/hr/uhad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Rosaceae is a large plant family consisting of many economically important fruit crops including peach, apple, pear, strawberry, raspberry, plum, and others. Investigations into their growth and development will promote both basic understanding and progress toward increasing fruit yield and quality. With the ever-increasing high-throughput sequencing data of Rosaceae, comparative studies are hindered by inconsistency of sample collection with regard to tissue, stage, growth conditions, and by vastly different handling of the data. Therefore, databases that enable easy access and effective utilization of directly comparable transcript data are highly desirable. Here, we describe a database for comparative analysis, ROsaceae Fruit Transcriptome database (ROFT), based on RNA-seq data generated from the same laboratory using similarly dissected and staged fruit tissues of four important Rosaceae fruit crops: apple, peach, strawberry, and red raspberry. Hence, the database is unique in allowing easy and robust comparisons among fruit gene expression across the four species. ROFT enables researchers to query orthologous genes and their expression patterns during different fruit developmental stages in the four species, identify tissue-specific and tissue-/stage-specific genes, visualize and compare ortholog expression in different fruit types, explore consensus co-expression networks, and download different data types. The database provides users access to vast amounts of RNA-seq data across the four economically important fruits, enables investigations of fruit type specification and evolution, and facilitates the selection of genes with critical roles in fruit development for further studies.
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Affiliation(s)
- Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Zhou J, Li M, Li Y, Xiao Y, Luo X, Gao S, Ma Z, Sadowski N, Timp W, Dardick C, Callahan A, Mount SM, Liu Z. Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification. PLANT PHYSIOLOGY 2023; 193:1016-1035. [PMID: 37440715 DOI: 10.1093/plphys/kiad409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/31/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023]
Abstract
Belonging to Rosaceae, red raspberry (Rubus idaeus) and wild strawberry (Fragaria vesca) are closely related species with distinct fruit types. While the numerous ovaries become the juicy drupelet fruits in raspberry, their strawberry counterparts become dry and tasteless achenes. In contrast, while the strawberry receptacle, the stem tip, enlarges to become a red fruit, the raspberry receptacle shrinks and dries. The distinct fruit-forming ability of homologous organs in these 2 species allows us to investigate fruit type determination. We assembled and annotated the genome of red raspberry (R. idaeus) and characterized its fruit development morphologically and physiologically. Subsequently, transcriptomes of dissected and staged raspberry fruit tissues were compared to those of strawberry from a prior study. Class B MADS box gene expression was negatively associated with fruit-forming ability, which suggested a conserved inhibitory role of class B heterodimers, PISTILLATA/TM6 or PISTILLATA/APETALA3, for fruit formation. Additionally, the inability of strawberry ovaries to develop into fruit flesh was associated with highly expressed lignification genes and extensive lignification of the ovary pericarp. Finally, coexpressed gene clusters preferentially expressed in the dry strawberry achenes were enriched in "cell wall biosynthesis" and "ABA signaling," while coexpressed clusters preferentially expressed in the fleshy raspberry drupelets were enriched in "protein translation." Our work provides extensive genomic resources as well as several potential mechanisms underlying fruit type specification. These findings provide the framework for understanding the evolution of different fruit types, a defining feature of angiosperms.
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Affiliation(s)
- Junhui Zhou
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences, Weifang, Shandong 2611325, China
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yongping Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yuwei Xiao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Xi Luo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Shenglan Gao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences, Weifang, Shandong 2611325, China
| | - Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences, Weifang, Shandong 2611325, China
| | - Norah Sadowski
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chris Dardick
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Ann Callahan
- USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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PpSAUR43, an Auxin-Responsive Gene, Is Involved in the Post-Ripening and Softening of Peaches. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Auxin’s role in the post-ripening of peaches is widely recognized as important. However, little is known about the processes by which auxin regulates fruit post-ripening. As one of the early auxin-responsive genes, it is critical to understand the role of small auxin-up RNA (SAUR) genes in fruit post-ripening and softening. Herein, we identified 72 PpSAUR auxin-responsive factors in the peach genome and divided them into eight subfamilies based on phylogenetic analysis. Subsequently, the members related to peach post-ripening in the PpSAUR gene family were screened, and we targeted PpSAUR43. The expression of PpSAUR43 was decreased with fruit post-ripening in melting flesh (MF) fruit and was high in non-melting flesh (NMF) fruit. The overexpression of PpSAUR43 showed a slower rate of firmness decline, reduced ethylene production, and a delayed fruit post-ripening process. The MADS-box gene family plays an important regulatory role in fruit ripening. In this study, we showed with yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BIFC) experiments that PpSAUR43 can interact with the MADS-box transcription factor PpCMB1(PpMADS2), which indicates that PpSAUR43 may inhibit fruit ripening by suppressing the function of the PpCMB1 protein. Together, these results indicate that PpSAUR43 acts as a negative regulator involved in the peach post-ripening process.
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