High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)

The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better exam...
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Gespeichert in:

Autor*in:	Liang Lu [verfasserIn] Jinliang Zhao [verfasserIn] Chenhong Li [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2020

Schlagwörter:	siniperca knerii chinese perch genome sequencing genome assembly 10x genomics

Übergeordnetes Werk:	In: G3: Genes, Genomes, Genetics - Oxford University Press, 2012, 10(2020), 3, Seite 877-880
Übergeordnetes Werk:	volume:10 ; year:2020 ; number:3 ; pages:877-880

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1534/g3.119.400930

Katalog-ID:	DOAJ005453496

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520			\|a The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions.
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allfields	10.1534/g3.119.400930 doi (DE-627)DOAJ005453496 (DE-599)DOAJ0bf7b70ead5c4b60aad53c2bca5be226 DE-627 ger DE-627 rakwb eng QH426-470 Liang Lu verfasserin aut High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii) 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions. siniperca knerii chinese perch genome sequencing genome assembly 10x genomics Genetics Jinliang Zhao verfasserin aut Chenhong Li verfasserin aut In G3: Genes, Genomes, Genetics Oxford University Press, 2012 10(2020), 3, Seite 877-880 (DE-627)668901071 (DE-600)2629978-1 21601836 nnns volume:10 year:2020 number:3 pages:877-880 https://doi.org/10.1534/g3.119.400930 kostenfrei https://doaj.org/article/0bf7b70ead5c4b60aad53c2bca5be226 kostenfrei http://g3journal.org/lookup/doi/10.1534/g3.119.400930 kostenfrei https://doaj.org/toc/2160-1836 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020 3 877-880
spelling	10.1534/g3.119.400930 doi (DE-627)DOAJ005453496 (DE-599)DOAJ0bf7b70ead5c4b60aad53c2bca5be226 DE-627 ger DE-627 rakwb eng QH426-470 Liang Lu verfasserin aut High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii) 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions. siniperca knerii chinese perch genome sequencing genome assembly 10x genomics Genetics Jinliang Zhao verfasserin aut Chenhong Li verfasserin aut In G3: Genes, Genomes, Genetics Oxford University Press, 2012 10(2020), 3, Seite 877-880 (DE-627)668901071 (DE-600)2629978-1 21601836 nnns volume:10 year:2020 number:3 pages:877-880 https://doi.org/10.1534/g3.119.400930 kostenfrei https://doaj.org/article/0bf7b70ead5c4b60aad53c2bca5be226 kostenfrei http://g3journal.org/lookup/doi/10.1534/g3.119.400930 kostenfrei https://doaj.org/toc/2160-1836 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020 3 877-880
allfields_unstemmed	10.1534/g3.119.400930 doi (DE-627)DOAJ005453496 (DE-599)DOAJ0bf7b70ead5c4b60aad53c2bca5be226 DE-627 ger DE-627 rakwb eng QH426-470 Liang Lu verfasserin aut High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii) 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions. siniperca knerii chinese perch genome sequencing genome assembly 10x genomics Genetics Jinliang Zhao verfasserin aut Chenhong Li verfasserin aut In G3: Genes, Genomes, Genetics Oxford University Press, 2012 10(2020), 3, Seite 877-880 (DE-627)668901071 (DE-600)2629978-1 21601836 nnns volume:10 year:2020 number:3 pages:877-880 https://doi.org/10.1534/g3.119.400930 kostenfrei https://doaj.org/article/0bf7b70ead5c4b60aad53c2bca5be226 kostenfrei http://g3journal.org/lookup/doi/10.1534/g3.119.400930 kostenfrei https://doaj.org/toc/2160-1836 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020 3 877-880
allfieldsGer	10.1534/g3.119.400930 doi (DE-627)DOAJ005453496 (DE-599)DOAJ0bf7b70ead5c4b60aad53c2bca5be226 DE-627 ger DE-627 rakwb eng QH426-470 Liang Lu verfasserin aut High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii) 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions. siniperca knerii chinese perch genome sequencing genome assembly 10x genomics Genetics Jinliang Zhao verfasserin aut Chenhong Li verfasserin aut In G3: Genes, Genomes, Genetics Oxford University Press, 2012 10(2020), 3, Seite 877-880 (DE-627)668901071 (DE-600)2629978-1 21601836 nnns volume:10 year:2020 number:3 pages:877-880 https://doi.org/10.1534/g3.119.400930 kostenfrei https://doaj.org/article/0bf7b70ead5c4b60aad53c2bca5be226 kostenfrei http://g3journal.org/lookup/doi/10.1534/g3.119.400930 kostenfrei https://doaj.org/toc/2160-1836 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020 3 877-880
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callnumber-first	Q - Science
author	Liang Lu
spellingShingle	Liang Lu misc QH426-470 misc siniperca knerii misc chinese perch misc genome sequencing misc genome assembly misc 10x genomics misc Genetics High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
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topic_title	QH426-470 High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii) siniperca knerii chinese perch genome sequencing genome assembly 10x genomics
topic	misc QH426-470 misc siniperca knerii misc chinese perch misc genome sequencing misc genome assembly misc 10x genomics misc Genetics
topic_unstemmed	misc QH426-470 misc siniperca knerii misc chinese perch misc genome sequencing misc genome assembly misc 10x genomics misc Genetics
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title	High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
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title_full	High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
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title_sort	high-quality genome assembly and annotation of the big-eye mandarin fish (siniperca knerii)
callnumber	QH426-470
title_auth	High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
abstract	The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions.
abstractGer	The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions.
abstract_unstemmed	The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions.
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title_short	High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)
url	https://doi.org/10.1534/g3.119.400930 https://doaj.org/article/0bf7b70ead5c4b60aad53c2bca5be226 http://g3journal.org/lookup/doi/10.1534/g3.119.400930 https://doaj.org/toc/2160-1836
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High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)

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