Chromosome-level genome and characteristic analysis of <i>Platax teira</i>

OUYANG Yan; PAN Jinmin; XIAN Lin; LIU Baosuo; GUO Huayang; Zhu Tengfei; ZHANG Nan; ZHU Kecheng; ZHANG Dianchang

doi:10.12131/20240112

Volume 20 Issue 6

Dec. 2024

Turn off MathJax

Article Contents

Abstract

References

South China Fisheries Science > 2024 > 20(6): 31-42. > DOI: 10.12131/20240112

OUYANG Yan, PAN Jinmin, XIAN Lin, LIU Baosuo, GUO Huayang, Zhu Tengfei, ZHANG Nan, ZHU Kecheng, ZHANG Dianchang. Chromosome-level genome and characteristic analysis of Platax teira[J]. South China Fisheries Science, 2024, 20(6): 31-42. DOI: 10.12131/20240112

Citation:

PDF (1035 KB)

Chromosome-level genome and characteristic analysis of Platax teira

OUYANG Yan^{1, 2, 3,},
PAN Jinmin^{2, 3},
XIAN Lin^{2, 3, 4},
LIU Baosuo^{2, 3, 4},
GUO Huayang^{2, 3, 4},
Zhu Tengfei^{2, 3, 4},
ZHANG Nan^{2, 3, 4},
ZHU Kecheng^{2, 3, 4},
ZHANG Dianchang^{2, 3, 4, ,}

1.
College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
2.
Sanya Tropical Fisheries Research Institutes, Sanya 572000, China
3.
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
4.
Guangdong Key Laboratory of Fishery Ecological Environment, Guangzhou 510300, China

More Information

Received Date: May 22, 2024
Revised Date: May 27, 2024
Accepted Date: October 22, 2024
Available Online: October 28, 2024

Graphical Abstract

Abstract

Abstract

Platax teira has the characteristics of fast growth rate, delicious meat and high nutritional content, and its strange appearance, especially for young fish, makes it an ornamental fish, being one of the important potential fishes for the cage culture development in the South China Sea. Due to the lack of genomic information, most of the functional genes of P. teira have not been explored, which has become an important factor of restricting its genetic breeding. We utilized triple sequencing technology and assembly to obtain a high-quality genome map of P. teira on chromosome level, and obtained the basic biological information of P. teira genome sequence through genome annotation. The results show that the genome size of P. teira was 697.98 Mb, assembling into 24 chromosomes with an assembly rate of 99.26%. P. teira genome contained 177.79 Mb of repetitive sequences, accounting for 25.47% of the total genome and encoding 22 851 genes. Comparative genomic analysis with 11 other fish species reveals that P. teira shared the closest relationship with Cheilinus undulatus, and the differentiation time was about 82.89 Ma. Genes under positive selection in P. teira were enriched in pathways related to ion channels and cardiac function, while the expanded gene families were enriched in pathways related to olfactory transmission and nitrogen metabolism, which reveals its survival, adaptation basis and ecological adaptation strategies in specific environment.
- Platax teira,
- Chromosome,
- Genome,
- Comparative genomics,
- Ephippidae

FullText(HTML)

References (53)

References

[1]	BRAY R A, CRIBB T H. Lepocreadiidae (Digenea) from the batfish of the genus Platax Cuvier (Teleostei: Ephippidae) from the southern Great Barrier Reef, Queensland, Australia[J]. Syst Parasitol, 2003, 55(1): 1-9. doi: 10.1023/A:1023974022432
[2]	MARIMUTHU N, WILSON J J, KUMARAGURU A K. Teira batrish, Platax teira (Forsskal, 1775) in Pudhumadam coastal waters, drifted due to the tsunami of 26 December 2004[J]. Current Sci, 2005, 89(8): 1310-1312.
[3]	GOLANI D, SONIN O, EDELIST D. Second records of the Lessepsian fish migrants Priacanthus sagittarius and Platax teira and distribution extension of Tylerius spinosissimus in the Mediterranean[J]. Aquat Invasions, 2011, 6(S1): S7-S11.
[4]	刘明鉴, 郭华阳, 高杰, 等. 尖翅燕鱼早期胚胎发育及仔稚鱼形态观察[J]. 南方水产科学, 2022, 18(4): 103-111. doi: 10.12131/20210251
[5]	BILECENOGLU M, KAYA M. A new alien fish in the Mediterranean Sea-Platax teira (Forsskål, 1775) (Osteichthyes: Ephippidae)[J]. Aquat Invasions, 2006, 1(2): 80-83. doi: 10.3391/ai.2006.1.2.5
[6]	LEIS J M, HAY A C, HOWARTH G J. Ontogeny of in situ behaviours relevant to dispersal and population connectivity in larvae of coral-reef fishes[J]. Mar Ecol Prog Ser, 2009, 379: 163-179. doi: 10.3354/meps07904
[7]	LIU M J, GAO J, GUO H Y, et al. Transcriptomics reveal the effects of breeding temperature on growth and metabolism in the early developmental stage of Platax teira[J]. Biology, 2023, 12(9): 1161. doi: 10.3390/biology12091161
[8]	陈松林, 徐文腾, 刘洋. 鱼类基因组研究十年回顾与展望[J]. 水产学报, 2019, 43(1): 1-14.
[9]	APARICIO S, CHAPMAN J, STUPKA E, et al. Whole-genomeshotgun assembly and analysis of the genome of Fugu rubripes[J]. Science, 2002, 297(5585): 1301-1310.
[10]	LIU D, WANG X Y, GUO H Y, et al. Chromosome-level genome assembly of the endangered humphead wrasse Cheilinus undulatus: insight into the expansion of opsin genes in fishes[J]. Mol Ecol Resour, 2021, 21(7): 2388-2406.
[11]	ZHENG S Q, SHAO F, TAO W J, et al. Chromosome-level assembly of southern catfish (Silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles[J]. Mol Ecol Resour, 2021, 21(5): 1575-1592. doi: 10.1111/1755-0998.13338
[12]	廖静. 人工养殖尖翅燕鱼性价比高[J]. 海洋与渔业, 2018(11): 62-63.
[13]	LIU B, GUO H Y, ZHU K C, et al. Nutritional compositions in different parts of muscle in the longfin batfish, Platax teira (Forsskål, 1775)[J]. J Appl Anim Res, 2019, 47(1): 403-407. doi: 10.1080/09712119.2019.1649680
[14]	CHEN S F, ZHOU Y Q, CHEN Y R, et al. fastp: an ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics, 2018, 34(17): i884-i890. doi: 10.1093/bioinformatics/bty560
[15]	ROBERTS R J, CARNEIRO M O, SCHATZ M C. The advantages of SMRT sequencing[J]. Genome Biol, 2013, 14(7): 405. doi: 10.1186/gb-2013-14-6-405
[16]	HU J, WANG Z, SUN Z Y, et al. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads[J]. Genome Biol, 2024, 25(1): 107. doi: 10.1186/s13059-024-03252-4
[17]	HU J, FAN J P, SUN Z Y, et al. NextPolish: a fast and efficient genome polishing tool for long-read assembly[J]. Bioinformatics, 2020, 36(7): 2253-2255. doi: 10.1093/bioinformatics/btz891
[18]	SEPPEY M, MANNI M, ZDOBNOV E M. BUSCO: assessing genome assembly and annotation completeness[J]. Methods Mol Biol, 2019, 1962: 227-245.
[19]	FLYNN J M, HUBLEY R, GOUBERT C, et al. RepeatModeler2 for automated genomic discovery of transposable element families[J]. PNAS, 2020, 117(17): 9451-9457. doi: 10.1073/pnas.1921046117
[20]	HAAS B J, SALZBERG S L, ZHU W, et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments[J]. Genome Biol, 2008, 9(1): R7. doi: 10.1186/gb-2008-9-1-r7
[21]	BIRNEY E, CLAMP M, DURBIN R. GeneWise and Genomewise[J]. Genome Res, 2004, 14(5): 988-995. doi: 10.1101/gr.1865504
[22]	KIM D, LANGMEAD B, SALZBERG S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nat Methods, 2015, 12(4): 357-360. doi: 10.1038/nmeth.3317
[23]	PERTEA M, PERTEA G M, ANTONESCU C M, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads[J]. Nat Biotechnol, 2015, 33(3): 290-295. doi: 10.1038/nbt.3122
[24]	STANKE M, DIEKHANS M, BAERTSCH R, et al. Using native and syntenically mapped cDNA alignments to improve de novo gene finding[J]. Bioinformatics, 2008, 24(5): 637-644. doi: 10.1093/bioinformatics/btn013
[25]	EMMS D M, KELLY S. OrthoFinder: phylogenetic orthology inference for comparative genomics[J]. Genome Biol, 2019, 20(1): 238. doi: 10.1186/s13059-019-1832-y
[26]	KATOH K, STANDLEY D M. MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability[J]. Mol Biol Evol, 2013, 30(4): 772-780. doi: 10.1093/molbev/mst010
[27]	KUMAR S, SULESKI M, CRAIG J M, et al. TimeTree 5: an expanded resource for species divergence times[J]. Mol Biol Evol, 2022, 39(8): msac174. doi: 10.1093/molbev/msac174
[28]	YANG Z H. PAML 4: phylogenetic analysis by maximum likelihood[J]. Mol Biol Evol, 2007, 24(8): 1586-1591. doi: 10.1093/molbev/msm088
[29]	MENDES F K, VANDERPOOL D, FULTON B, et al. CAFE 5 models variation in evolutionary rates among gene families[J]. Bioinformatics, 2021, 36(22/23): 5516-5518.
[30]	EDDY S R. Accelerated profile HMM searches[J]. PLoS Comput Biol, 2011, 7(10): e1002195. doi: 10.1371/journal.pcbi.1002195
[31]	YU G C, WANG L G, HAN Y Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters[J]. OMICS, 2012, 16(5): 284-287. doi: 10.1089/omi.2011.0118
[32]	高杰, 郭华阳, 刘明鉴, 等. 尖翅燕鱼染色体核型分析[J]. 海洋渔业, 2022, 44(5): 535-542.
[33]	OSHIUMI H , TSUJITA T , SHIDA K, et al. Prediction of the prototype of the human Toll-like receptor gene family from the pufferfish, Fugu rubripes, genome[J]. Immunogenetics, 2003, 54: 791-800.
[34]	HU Y C, TAN R H, ZHU X, et al. Genome-wide identification, phylogeny and expressional profile of the Dmrt gene family in Chinese sturgeon (Acipenser sinensis)[J]. Sci Rep, 2024, 14(1): 4231. doi: 10.1038/s41598-024-54899-9
[35]	ZHU K C, ZHANG N, LIU B S, et al. A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus; Hottuyn, 1782) provides insights into its osmoregulation and sex reversal[J]. Genomics, 2021, 113(4): 1617-1627. doi: 10.1016/j.ygeno.2021.04.017
[36]	ZHANG D C, GUO L, GUO H Y, et al. Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae[J]. Sci Data, 2019, 6(1): 216. doi: 10.1038/s41597-019-0238-8
[37]	LIANG Y, XIAN L, PAN J M, et al. De Novo genome assembly of the whitespot parrotfish (Scarus forsteni): a valuable scaridae genomic resource[J]. Genes (Basel), 2024, 15(2): 249. doi: 10.3390/genes15020249
[38]	ZHOU Q, GUO X Y, HUANG Y, et al. De novo sequencing and chromosomal-scale genome assembly of leopard coral grouper, Plectropomus leopardus[J]. Mol Ecol Resour, 2020, 20(5): 1403-1413. doi: 10.1111/1755-0998.13207
[39]	CHEN X H, ZHONG L Q, BIAN C, et al. High-quality genome assembly of channel catfish, Ictalurus punctatus[J]. GigaScience, 2016, 5(1): 39. doi: 10.1186/s13742-016-0142-5
[40]	LI J, BIAN C, HU Y C, et al. A chromosome-level genome assembly of the Asian arowana, Scleropages formosus[J]. Sci Data, 2016, 3: 160105.
[41]	LI S S, XIE Z Z, CHEN P, et al. The complete mitochondrial genome of the Platax teira (Osteichthyes: Ephippidae)[J]. Mitochondrial DNA A DNA Mapp Seq Anal, 2016, 27(2): 796-797.
[42]	HUGHES L C, ORTÍ G, HUANG Y, et al. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data[J]. PNAS, 2018, 115(24): 6249-6254. doi: 10.1073/pnas.1719358115
[43]	HE S, LI L, LYU L Y, et al. Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding[J]. Commun Biol, 2020, 3(1): 361. doi: 10.1038/s42003-020-1094-y
[44]	MARSHALL H D, COULSON M W, CARR S M. Near neutrality, rate heterogeneity, and linkage govern mitochondrial genome evolution in Atlantic cod (Gadus morhua) and other gadine fish[J]. Mol Biol Evol, 2009, 26(3): 579-589.
[45]	TEREKHANOVA N V, LOGACHEVA M D, PENIN A A, et al. Fast evolution from precast bricks: genomics of young freshwater populations of threespine stickleback Gasterosteus aculeatus[J]. PLoS Genet, 2014, 10(10): e1004696. doi: 10.1371/journal.pgen.1004696
[46]	AO J Q, MU Y N, XIANG L X, et al. Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation[J]. PLoS Genet, 2015, 11(4): e1005118. doi: 10.1371/journal.pgen.1005118
[47]	NIEDERRITER A R, DAVIS E E, GOLZIO C, et al. In vivo modeling of the morbid human genome using Danio rerio[J]. J Vis Exp, 2013(78): e50338.
[48]	DAVIDSON W S, KOOP B F, JONES S J M, et al. Sequencing the genome of the Atlantic salmon (Salmo salar)[J]. Genome Biol, 2010, 11: 403. doi: 10.1186/gb-2010-11-9-403
[49]	LEVANTI M, RANDAZZO B, VIÑA E, et al. Acid-sensing ion channels and transient-receptor potential ion channels in zebrafish taste buds[J]. Ann Anat, 2016, 207: 32-37. doi: 10.1016/j.aanat.2016.06.006
[50]	MOHAMED N A, SAAD M F, SHUKRY M, et al. Physiological and ion changes of Nile tilapia (Oreochromis niloticus) under the effect of salinity stress[J]. Aquac Rep, 2021, 19: 100567. doi: 10.1016/j.aqrep.2020.100567
[51]	IP Y K, CHEW S F. Ammonia production, excretion, toxicity, and defense in fish: a review[J]. Front Physiol, 2010, 1: 134.
[52]	RANDALL D J, TSUI T K N. Ammonia toxicity in fish[J]. Mar Pollut Bull, 2002, 45(1/2/3/4/5/6/7/8/9/10/11/12): 17-23.
[53]	ARILLO A, MARGIOCCO C, MELODIA F, et al. Ammonia toxicity mechanism in fish: studies on rainbow trout (Salmo gairdneri Rich.)[J]. Ecotoxicol Environ Saf, 1981, 5(3): 316-328. doi: 10.1016/0147-6513(81)90006-3

[1]	MA Wenyu, YANG Wei, QIN Xiaoming, CAO Wenhong, LIN Haisheng. Ameliorative effect of oyster enzymatic products on glucocorticoid-induced osteoporosis in rats[J]. South China Fisheries Science. DOI: 10.12131/20240223
[2]	CHEN Zhizhao, ZHU Tao, LEI Caixia, JIANG Peng, DU Jinxing, ZHU Junjie, SONG Hongmei, LI Shengjie. Effects on growth and hepatic glucose metabolism of grass carp fed with high dietary carbohydrates[J]. South China Fisheries Science, 2023, 19(5): 75-85. DOI: 10.12131/20230020
[3]	JIA Puyuan, GUO Huayang, ZHU Kecheng, LIU Baosuo, GUO Liang, ZHANG Nan, JIANG Shigui, ZHANG Dianchang. Cryopreservation of sperm of Acanthopagrus latus[J]. South China Fisheries Science, 2021, 17(6): 58-65. DOI: 10.12131/20210083
[4]	HU Qiong, LI Shengzhong, CAO Jingcheng, CHU Hongwei. Effects of glucose, glycero and salt on spermatozoa motility of Schizothorax irregularis[J]. South China Fisheries Science, 2019, 15(2): 38-46. DOI: 10.12131/20180193
[5]	XU Xiaoxiao, LIU Wei, WEN Hua, JIANG Ming, WU Fan. Effect of high-carbohydrate diet on growth performance, feed utilization, glucose and lipid metabolism of GIFT Oreochromis niloticus[J]. South China Fisheries Science, 2017, 13(5): 94-102. DOI: 10.3969/j.issn.2095-0780.2017.05.013
[6]	QIU Ying, HUANG Guiju, LIU Baosuo, FAN Sigang, LI Youning, CHEN Mingqiang, YU Dahui. Cloning of GLUT1 gene from winged pearl oyster Pteria penguin and its expression in response to glucose challenge[J]. South China Fisheries Science, 2016, 12(5): 81-89. DOI: 10.3969/j.issn.2095-0780.2016.05.010
[7]	HU Jing, YE Le, WU Kaichang, WANG Yu. Effect of acute salinity stress on serum cortisol and activity of Na⁺ -K⁺ -ATPase of juvinile Amphiprion clarkii[J]. South China Fisheries Science, 2016, 12(2): 116-120. DOI: 10.3969/j.issn.2095-0780.2016.02.017
[8]	XIONG Hualong, YAO Junjie, AN Miao, WANG Jinna, JIANG Zuoyu. Effects of glucose and vitamin C on early development of Puan silve crucian carp (Carassius auratus gibelio)[J]. South China Fisheries Science, 2014, 10(6): 88-92. DOI: 10.3969/j.issn.2095-0780.2014.06.013
[9]	ZHANG Qin, XU Mingzhu, TONG Tong, DONG Lanfang. Effect of different carbohydrate sources on daily weight growth and digestive enzyme activities of larval peanut worm(Sipunculus nudus)[J]. South China Fisheries Science, 2014, 10(1): 21-26. DOI: 10.3969/j.issn.2095-0780.2014.01.004
[10]	HUANG Guangzhong, HU Hui, XIAO Keyu, LUO Shimin, XIE Peirong, OUYANG Juying. Effects of plant extract from grape seed and sweet wormwood on intestinal digestive enzyme activities and blood biochemical parameters of eel (Monopterus albus)[J]. South China Fisheries Science, 2013, 9(2): 70-75. DOI: 10.3969/j.issn.2095-0780.2013.02.012

Cited By

Get Citation

PDF

XML

Article views (424) PDF downloads (24)

Chromosome-level genome and characteristic analysis of Platax teira

Abstract

References

Related Articles

Catalog

Related

Chromosome-level genome and characteristic analysis of Platax teira

Abstract

References

Related Articles

Catalog

Related

Export File

Citation

Format

Content