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Blommaert J, Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper. Genomics 2024; 116:110929. [PMID: 39216708 DOI: 10.1016/j.ygeno.2024.110929] [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: 05/05/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.
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Affiliation(s)
- Julie Blommaert
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand.
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Xu M, Fang W, Lin G, Zhu X, Lu J. Transcriptomic Responses and Larval-Stage Growth of Protandrous Yellowfin Seabream (Acanthopagrus Latus) to Different Polyethylene Microplastics Exposure. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10334-8. [PMID: 38896300 DOI: 10.1007/s10126-024-10334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
Polyethylene microplastics (PE-MPs) were widespread in the marine environment; thus, their influences on marine hermaphroditic fish cannot be ignored. This study intends to evaluate the adverse biological effects of two different sources of PE, identified by Raman spectroscopy, on protandrous yellowfin seabream (Acanthopagrus latus) larvae. Growth retardation, brain lesions, head/body length ratio increase, and neuroendocrine system disorders were found, and growth and neuroendocrine regulation-related genes such as sstr2, ghrb, irs1, UGT2B15, UGT2C1, drd4a, esr2b, hsd3b7, and hsd17b2 were identified. PE microbeads (100 μm) showed more severe tissue damage on fish, while environmental PE fibers (500-2500 μm) showed more imperceptible adverse effects. There were 218 DEGs up-regulated and 147 DEGs down-regulated in the environmental PE group, while 1284 (up) and 1267 (down) DEGs were identified in the virgin PE group. PE-MP stress influenced physiological processes like growth and neuroendocrine regulation and cholesterol-steroid metabolism, and caused tissue damage in the fish larvae. The study highlights the effects of environmental PE exposure on hermaphroditic protandrous fish.
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Affiliation(s)
- Meng Xu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Genmei Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Xiaoshan Zhu
- School of Ecology and Environment, Hainan University, Haikou, 570228, People's Republic of China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China.
- Southern Marine Science and Engineering Guangdong Laboratory, 519080, Zhuhai, People's Republic of 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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Wu RX, Miao BB, Han FY, Niu SF, Liang YS, Liang ZB, Wang QH. Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala. Genes (Basel) 2023; 14:1268. [PMID: 37372448 DOI: 10.3390/genes14061268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes.
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Affiliation(s)
- Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan-Shan Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
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