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Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
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Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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Wang W, Huang J, Hu Y, Feng J, Gao D, Fang W, Xu M, Ma C, Fu Z, Chen Q, Liang X, Lu J. Seascapes Shaped the Local Adaptation and Population Structure of South China Coast Yellowfin Seabream (Acanthopagrus latus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:60-73. [PMID: 38147145 DOI: 10.1007/s10126-023-10277-6] [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: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023]
Abstract
Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.
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Affiliation(s)
- Wenhao Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yan Hu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianxiang Feng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Dong Gao
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Meng Xu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chunlei Ma
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zhenqiang Fu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Qinglong Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Xuanguang Liang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China.
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China.
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Marín I. Emergence of the Synucleins. BIOLOGY 2023; 12:1053. [PMID: 37626939 PMCID: PMC10451939 DOI: 10.3390/biology12081053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
This study establishes the origin and evolutionary history of the synuclein genes. A combination of phylogenetic analyses of the synucleins from twenty-two model species, characterization of local synteny similarities among humans, sharks and lampreys, and statistical comparisons among lamprey and human chromosomes, provides conclusive evidence for the current diversity of synuclein genes arising from the whole-genome duplications (WGDs) that occurred in vertebrates. An ancestral synuclein gene was duplicated in a first WGD, predating the diversification of all living vertebrates. The two resulting genes are still present in agnathan vertebrates. The second WGD, specific to the gnathostome lineage, led to the emergence of the three classical synuclein genes, SNCA, SNCB and SNCG, which are present in all jawed vertebrate lineages. Additional WGDs have added new genes in both agnathans and gnathostomes, while some gene losses have occurred in particular species. The emergence of synucleins through WGDs prevented these genes from experiencing dosage effects, thus avoiding the potential detrimental effects associated with individual duplications of genes that encode proteins prone to aggregation. Additional insights into the structural and functional features of synucleins are gained through the analysis of the highly divergent synuclein proteins present in chondrichthyans and agnathans.
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Affiliation(s)
- Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), 46010 Valencia, Spain
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