橈足類(節肢動物門：甲殼綱)為海洋裡最多的後生動物，種類約一萬三千種。橈足類在食物鏈中均扮演著重要角色，且由於體型小，富含高度的長鏈不飽和脂肪酸(如DHA與EPA)，為仔稚魚在早期生長階段重要的餌料生物。本研究以次世代定序與生物資訊學技術對台灣二種常見的餌料橈足類生物；短角異劍水蚤(Apocyclops royi)與雙葉紡錘水蚤(Acartia bilobata) 進行de-novo基因轉錄體定序與分析，同時探討二種橈足類蛋白質編碼基因的同義密碼子使用偏性模式，並由基因資料庫選取3種橈足類物種(Calanus rogercresseyi、 Lepeophtheirus salmonis、 Tigriopus japonicus)及外群Daphnia pulex進行橈足類多基因的親緣關係探討。利用Illumina HiSeqTM 2000對短角異劍水蚤及雙葉紡錘水蚤進行定序，產生53,363,934及55,433,040 reads序列，經組裝後分別產生35,363 unigene (mean size: 941 bp, N50 size: 1,547 bp)與35,442 unigene (mean size: 878 bp, N50 size: 1,6007 bp)。 KEGG pathway顯示，短角異劍水蚤可能有能力將linoleic acid (C18:3 n-3)經脂肪酸合成路徑轉換成EPA和DHA。鹽度是甲殼類生物存活的重要環境因子，本研究進一步分析與2種橈足類與鹽度適應有關的基因差異表現，共有Na+/K+-ATPase、H+-ATPase與ATP synthase等相關基因其表現量具有明顯的差異，A. bilobata從高鹽進入低鹽的鹽度差異大於A. royi，在滲透壓調節相關基因的表現量A. bilobata均大於A. royi，此現象符合甲殼類對滲透壓調節之研究。
在密碼子使用偏性分析結果顯示，雙葉紡錘水蚤的密碼子使用上則存有較大的偏性，但短角異劍水蚤在密碼子使用上並無太大的偏性，二種橈足類在基因間密碼子使用上存有的差異，這也意味著影響橈足類密碼子使用特徵因素的複雜性。本研究利用MEGA軟體建構5種橈足類的gene tree來探討橈足類物種多基因的親緣關係，共有31 gene產生20 gene tree模式，其中有14個gene tree呈現C. rogercressyi與L. salmonis親緣關係最為接近，佔gene tree 親緣模式的最大量，符合Caligus與Lepeophtheirus在分類上屬於同科物種(Caligidae)之親緣關係。以此進一步分析，{{{(Ca, Le), Ti}, Ap}, Ac}, Da 與 {{{(Ca, Le), Ap}, Ti}, Ac}, Da 共有7個gene tree，其親緣關係呈現 Siphonostomatoida、Calanoida、Cyclopoida與Harpactiocoida各為獨立系群之模式，5種橈足類的共祖時間約為454.3-457.4百萬年前。本研究的基因轉錄體資料，有助於對橈足類在基因層次上更進一步的認識與了解，並可提供橈足類未來科學研究上之參考依據。

SUMMARY

Copepods play an important role in the aquatic food web in marine and fresh water environments. Among the various species in copepods, Apocyclops royi and Acartia bilobata are very good live feed for fish larvae because of their small size and rich in long chain unsaturated fatty acid. In this study, we used the NGS approach to study the transcriptome of A. royi and A. bilobata, the codon usage bias was also analyzed, and another 3 copepods were selected (Calanus rogercresseyi, Lepeophtheirus salmonis and Tigriopus japonicus) to reconstruct the phylogeny of these species with outgroup of Daphnia pulex. Base on the results, we suggested that 1) A. royi may be able to synthesize DHA and EPA by using linoleic acid (C18:3 n-3) through fatty acid synthesizing pathway; 2) A. bilobata showed a higher expression of Na+/K+-ATPase, H+-ATPase and ATP synthase in diluted seawater; 3) In the codon usage bias pattern, genes of A. bilobata were biased, whereas A. royi was less biased, indicating that A. bilobata might be under compositional translational selection; 4) The estimated coalescence time for the five copepod species was about 454.3-457.4 myr (million years). Our data provided much important information for future copepod study.

INTRODUCTION

Copepods (Arthropoda: Crustacea) are among the most abundant metazoans in the oceans. They are a very ancient group and are considered to have diverged from other arthropod taxa about 388-522 million years ago. Ten orders comprise the subclass Copepoda, including Calanoida, Cyclopoida, and Harpacticoida, and a total of about 13,000 species are recognized. Copepods play an important role in the aquatic food web in marine and fresh water environments. They are also the best live feed for early stage of fish larvae because of their small size and rich in long chain unsaturated fatty acid, such as DHA and EPA. However, genome resources for copepods are only available for very few species. The information on genomic DNA sequences is increasingly important, especially for non-model organisms such as copepods. Recently, next generation sequencing (NGS) technology enables us to obtain extensive DNA or cDNA sequence information in a short period of time. In this study, we used an NGS approach to study the transcriptome for Apocyclops royi and Acartia bilobata, the codon usage bias was also analyzed, and another 3 copepods were selected (Calanus rogercresseyi, Lepeophtheirus salmonis and Tigriopus japonicus) to reconstruct the phylogeny of these species with outgroup of Daphnia pulex.

MATERIALS AND METHODS

A. royi and A. bilobata were collected from Tungkang Biotechnology Research Center of Fisheries Research Institute, Taiwan. The experiment was started with salinity acclimation of 20 psu and 30 psu for A. royi and A. bilobata, respectively, and transferred to 15 psu for 5 days. mRNAs were isolated from total RNA using oligo-dT and then converted to double-stranded cDNA. The samples were sequenced using Illumina HiSeqTM 2000. De-novo assembly of transcriptome was carried out using software Trinity. The GO, COG and KEGG annotations for the two copepod species were performed using the automatic annotation tool Blast2GO. The expression level of a transcript was quantified in read per kilobase of the transcript per million mapped reads (RPKM).

We analyzed the codon usage bias in A. royi and A. bilobata, the frequency of 59 codons code for 18 amino acids (exclude Met, Trp and termination codons) were determined for all the selected genes. Five codon usage indices, relative synonymous codon usage (RSCU), G+C content at the third position of synonymous codons (GC3s), effective number of codons (ENc), correspondence analysis (COA), and optimal codons, were used to analyze the codon usage in this study.

The sequences of A. royi and A. bilobata from annotated unigenes, as well as the sequences of C. rogercresseyi, L. salmonis, T. japonicus and D. pulex (outgroup) obtained from NCBI, were used in reconstructing phylogenetic trees with neighbor-joining method and maximum likelihood method in software MEGA 5.2. Maximum likelihood bootstrap analyses were conducted with 1000 replicates, while the values greater than 70% were shown on trees. The time to the most recent common ancestor (TMRCA) under an MCMC Bayesian approach was estimated with the BEAST 1.7.5. All simulations were performed using the HKY+G model and strict molecular clock with Fixed Rate Model.

RESULTS AND DISCUSSION

In this study, we obtained 53,363,934 and 55,433,040 NGS reads for A. royi and A. bilobata, respectively, generating 35,363 unigenes (mean size: 941 bp, N50 size: 1,547 bp) and 35,442 unigenes (mean size: 878 bp, N50 size: 1,600 bp) by de novo assembly. By mapping to databases, 20,062 and 17,214 unigenes could be annotated to NCBI Nr, 15,017 and 13,771 unigenes hadKEGG annotations, 8,317 and 8,219 had COG annotations, 4,064 and 3,327 had GO annotations. Some related enzymes involving in synthesizing long chain polyunsaturated fatty acids were identified, revealing that A. royi may be able to synthesize DHA and EPA through fatty acid synthesizing pathway. Since salinity is an important environmental factor for crustacean survival, we further analyzed the genes (Na+/K+-ATPase, H+-ATPase and ATP synthase) related to osmoregulation and found significant differences in gene expression between the two species. A. bilobata showed a higher expression of Na+/K+-ATPase, H+-ATPase and ATP synthase in diluted seawater.

Analysis of codon usage bias indicated some biases occurred at the genes of A. bilobata, whereas genes of A. royi was less biased, suggesting a complex pattern in codon usage in copepods. The result implied that A. bilobata was under compositional translational selection. The genealogical analysis of 31 orthologous genes displayed 20 tree topologies, 14 trees of which showed that C. rogercressyi and L. salmonis were most closely related. Furthermore, the estimated coalescence time for the five species was about 454.3-457.4 myr (million years) ago.

CONCLUSION

The A. royi and A. bilobata transcriptome analyzed using the next generation sequencing technique enhance our knowledge on the copepods genes, which will facilitate our understanding of the crustacean genome, and advances the studies on copepod.

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25: 3389-3402.
Andrew DR (2011) A new view of insectecrustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics. Arthropod Structure and Development, 40: 289-302.
Baranski M, Gopikrishna G, Robinson NA, Katneni VK, Shekhar MS, Shanmugakarthik J, Jothiveo S, Gopal C, Ravichandran P, Kent M et al. (2014) The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs. PLoS ONE, 9: e85413.
Barreto FS, Moy GW, Burton RS (2011) Interpopulation patterns of divergence and selection across the transcriptome of the copepod Tigriopus californicus. Molecular Ecology, 20: 560-572.
Beaugrand G, Brander K, Lindley J, Souissi S, Reid P (2003) Plankton effect on cod recruitment in the North Sea. Nature, 426: 661-664.
Belli NM, Faleiros RO, Firmino KCS, Masui DC, Leone FA, McNamara JC, Furriel RPM (2009) Na,K-ATPase activity and epithelial interfaces in gills of the freshwater shrimp Macrobrachium amazonicum (Decapoda, Palaemonidae). Comparative Biochemistry and Physiology, Part A 152: 431-439.
Benzécri JP (1973) L’Analyse des Donn´ees, Tome 2: L’Analyse des Correspondences. Dunod. Paris, p.619.
Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE et al. (2009) De novo transcriptome assembly with ABySS. Bioinformatics, 25: 2872-2877.
Birzele F, Schaub J, Rust W, Clemens C, Baum P, Kaufmann H, Weith A, Schulz TW, Hildebrandt T (2010) Into the unknown: Expression profiling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Research, 38: 3999-4010.
Blow NS, Salomon RN, Garrity K, Reveillaud I, Kopin A, Jackson FR, Watnick PI (2005) Vibrio cholerae infection of Drosophila melanogaster mimics the human disease cholera. PLOS Pathogens, 1: e8.
Broughton RE, Betancur RR, Li C, Arratia G, Ortí G (2013) Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLOS Currents , 16: 5.
Bucklin A, Frost BW, Kocher TD (1995) Molecular systematics of six Calanus and three Metridia species (Calanodia: Copepoda). Marine Biology, 1124: 655-664.
Bucklin A, Smolenack SB, Benley AM, Wiebe PH (1997) Gene flow patterns of the euphausid (Meganyctiphanes norvegica) in the NW Atlantic based on mtDNA sequences for cytochrome b and cytochrome oxidase I. Journal of plankton Research, 19: 1 793-1781.
Burton RS, Byrne RJ, Rawson PD (2007) Three divergent mitochondrial denomes from Calofornia populations of the Tigriopus californicus. Gene, 403: 53-59.
Castro-Longoria E (2001) Comparative observations on the external morphology of subitaneous and diapause eggs of Acartia species from Southampton water. Crustaceana, 74: 225-236.
Chang WB, Lei CH (1993) Development and energy content of a brackish water copepod, Apocyclops royi (Lindberg) reared in a laboratory. Bulletin of the Institute of Zoology Academia Sinica, 32: 62-81.
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK (2011) The ecoresponsive genome of Daphnia pulex. Science, 331: 555-561.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21: 3674-3676.
Davies PCW, Lineweaver CH (2011) Cancer tumors as metazoa 1.0: Tapping genes of ancient ancestors. Physical Biology, 8: p.015001.
Desvilettes C, Bourdier G, Breton J (1997) On the occurrence of a possible bioconversion of linolenic acid into docosahexaenoic acid by the copepod Eucyclops serrulatus fed on microalgae. Journal of Plankton Research, 19: 273-278.
Diez M, Zimmermann B, Borsch M, Konig M, Schweinberger E, Steigmiller S, Reuter R, Felekyan S, Kudryavtsev V, Seidel CA, Graber P (2004) Proton-powered subunit rotation in single membrane-bound F0F1-ATP synthase. Nature Stuctural and Molecular Biology, 11: 135-141.
Donaghay PL, Small LF (1979) Food selection capabilities of the estuarine copepod Acartia clause. Marine Biology, 52, p137-146.
Drillet G, Jorgensen NOG, Sorensen TF, Ramlov H, Hansen BW (2006) Biochemical and technical observations supporting the use of copepods as live feed organisms in marine larviculture. Aquaculture Research, 37: 756-772.
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7: 214.
Duret L (2000) tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly espressed genes. Trends in Genetics, 16: 287-289.
Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of United States of American, 96: 4482-4487.
Eichner R, Frost P, Dysvik B, Jonassen I, Kristiansen B, Nilsen F (2008) Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis. BMC Genomics, 9: 126.
Eyun SI, Lee YH, Suh HL, Kim S and Soh HY (2007) Genetic Identification and Molecular Phylogeny of Pseudodiaptomus Species (Calanoida, Pseudodiaptomidae) in Korean Waters. Zoological Science, 24: 265-271.
Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics, 12: 317.
Francino HP, Ochman H (1999) Isochores result from mutation not selection. Nature, 400: 30-31.
Frangoulis C, Christou E, Hecq J (2005) Comparison of marine copepod outfluxes: Nature, rate, fate and role in the carbon and nitrogen cycles. Advances in Marine Biology, 47: 253-309.
Furriel RPM (2000) Characterization of (Na+, K+)-ATPase in gill microsomes of the freshwater shrimp Macrobrachium olfersii. Comparative Biochemistry and Physiology, Part B 126: 303- 315.
Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Research, 18: 53-63
GO-EBI, EMBL-EBI (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Research, 34:322-326.
Gouy M, Gautier C (1982) Codon usage in bacteria correlation with gene expressivity. Nucleic Acids Research, 10: 7055-7074.
Gouzy J, Carrere S, Schiex T (2009) FrameDP: Sensitive peptide detection on noisy matured sequences. Bioinformatics, 25: 670-671.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29: 644-652.
Grantham R, Gautier C, Giuy M (1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Research, 8: 1893-1912.
Grasiela L, Pinho L, Bianchini A (2010) Acute copper toxicity in the euryhaline copepod Acartia tonsa: implications for the development of an estuarine and marine biotic ligand model. Environmental Toxicology and Chemistry, 29: 1834-1840.
Gronkjaer P, Jorgensen SB, Fredricksen M, St John M, Clemmensen C, Stottrup JG (1995) The influence of essential fatty acid composition on growth of larval cod (Gadus morhua L.). Preliminary observations, 19, 14. Baltic Fish Committee. ICES J.
Guo H, Ye CX, Wang AL, Xian JA, Liao SA, Miao YT, Zhang DP (2013) Trascriptome analysis of the Pacific White Shrimp Litopenaeus vannamei exposed to nitrite by RNA-Seq. Fish and Shellfish Immunology, 35: 2008-2016.
Gupta SK, Ghosh TC (2001) Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene, 273: 63-70.
Hill RS, Allen LD, Bucklin A (2001) Multiplexed species-specific PCR protocol to discriminate four N. Atlantic Calanus species, with an mtCOI gene tree for ten Calanus species. Marine Biology, 139: 279-287.
Holm L (1986) Codon usage and gene expression. Nucleic Acids Research, 14: 3075-3087.
Hsiao YY, Lin CH, Liu JK, Wong TY, Kuo J (2010) Analysis of codon usage patterns in toxic dinoflagellate Alexandrium tamarense through expressed sequence tag data. Comparative and Functional Genomics, 2010: 1-9.
Huang Y, Zhu L, Liu G (2006) The effects of bis (tributyltin) oxide on the development, reproduction and sex ratio of calanoid copepod Pseudodiaptomus marinus. Estuarine, coastal and shelf science, 69: 147-152.
Huq AE, Small PA, West MI, Huq R, Rahman R, Colwell R R (1983) Ecological relationships between Vibrio cholerae and planktonic crustacean copepods. Applied and Environment Microbiology, 45: 275-283.
Iannacone R, Grieco PD, Cellini (1997) Specific sequence modifications of a cry3B endotoxin gene result in high levels of expressionand insect resistance. Plant Molecular Biology, 34: 485-496.
Jayasundara N, Towle DW, Weihrauch D, Spanings-Pierrot C (2007) Gill-specific transcriptional regulation of Na+/K+-ATPase α-subunit in the euryhaline shore crab Pachygrapsus marmoratus: sequence variants and promoter structure. The Journal of Experimental Biology, 210: 2070-2081.
Jean CT, Wu CY, Tsai KC, Wang WK, Hsu YY, Chang YM, Lin HD (2014) Population genetic structure in the endemic cyprinid fish Microphysogobio alticorpus in Taiwan: Evidence for a new phylogeographical area. Biochemical Systematics and Ecology, 57: 108-116.
Jiang P, Sun X, Lu Z (2007) Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms. Journal of Genetics and Genomics, 34: 275-284.
Johnson CL, Runge JA, Curtis KA, Durbin EG, Hare JA, Incze LS, Link LS, Melvin GD, O’Brien TD, Van Gueipen L (2011) Biodiversity and ecosystem function in the Gulf of Maine: Pattern and role of zooplankton and pelagic nekton. Plos One, 6: e16491.
Jonasdottir SH (1994) Effects of food quality on the reproductive success of Acartia tonsaand and Acartia hudsonica: laboratory observations. Marine Biology, 121: 67-81.
Junga SO, Leea YM, Parka TJ, Parkb HG, Hagiwarac A, Leungd KMY, Dahmse HU, Leef W, Leea JS (2006) The complete mitochondrial genome of the intertidal copepod Tigriopus sp. (Copepoda, Harpactidae) from Korea and phylogenetic considerations. Journal of Experimental Marine Biology and Ecology, 333: 251-262.
Ju YM, Hsu CH, Fang LS, Lin HD, Wu JH, Han CC, Chen IS, Chiang TY (2013) Population structure and demographic history of Sicyopterus japonicus (Perciformes; Gobiidae) in Taiwan inferred from mitochondrial control region sequences. Genetics and Molecular Research, 12: 4046-4059.
Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of genes and genomes. Nucleic Acids Research, 28: 27-30.
Kawabe A, Miyashita NT (2003) Patterns of codon usage bias in three dicot and four monocot plant species. Genes and Genetic Systems, 78: 343-352.
Khatri P, Drăghici S (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics, 21: 3587-3595.
Ki JS, Park HG, Lee JS (2009) The complete mitochondrial genome of the cyclopoid copepod Paracyclopina nana: A highly divergent genome with novel gene order and atypical gene numbers. Gene, 435: 13-22.
Kidokoro K, Iwata K, Fujiwara Y, Takeda M (2006) Effects of juvenile hormone analogs and 20-hydroxyecdysone on diapause termination in eggs of Locusta migratoria and Oxya yezoensis. Journal of Insect Physiology, 52: 473-479.
Kim S, Lim BJ, Min GS, Choi HG (2013) The complete mitochondrial genome of Arctic Calanus hyperboreus (Copepoda, Calanoida) reveals characteristic patterns in calanoid mitochondrial genome. Gene, 520: 61-72.
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16:111-120.
Klein-Breteler WCM, Schogt N, Bass M, Schouten S, Kraay GW (1999) Trophic upgrading of food quality by protozoans enhancing copepod growth: role of essential lipids. Marine Biology, 135: 191-198.
Lacoste A, Poulet SP, Cueff A, Kattner GK, Ianora A, Laabir M (2001) New evidence of the copepod maternal food effect on reproduction. Journal of Experimental Marine Biology and Ecology, 259: 85-107.
Leandro SM, Tiselius P, Queiroga H (2013) Spatial and temporal scales of environmental forcing of Acartia populations (Copepoda: Calanoida) in the Canal de Mira (Ria de Aveiro, Portugal). International Council for the Exploration of the Sea. Published by Oxford University, fst008.
Lee JS, Rhee JS, Kim RO, Hwang DS, Han J, Choi BS, Park GS, Kim IC, Park HG, Lee YM (2010) The copepod Tigriopus japonicus genomic DNA information (574 Mb) and molecular anatomy. Marine Environmental Research, 69: S21-S23.
Lee KW, Park HG, Lee SM, Kang HK (2006) Effects of diets on the growth of the brackish water cyclopoid copepod Paracyclopina nana Smirnov. Aquaculture, 256: 346-353.
Lee RF, Hagen W, Kattner G (2006) Lipid storage in marine zooplankton. Marine Ecology Progress Series, 307: 273-306.
Lee YM, Kim IC, Jung SO, Lee JS (2005) Analysis of 686 expressed sequence tags (ESTs) from the intertidal harpacticoid copepod Tigriopus japonicus (Crustacea, Copepoda). Marine Pollution Bulletin, 51: 757–768.
Lee CE, Kiergaard M, Gelembiuk GW, Eads BD, Posavi M (2011) Pumping ions: rapid parallel evolution of ionic regulation following habitat invasions. Evolution 65: 2229-2244.
Lenz PH, Unal E, Hassett RP, Smith CM, Bucklin A, Christie AE, Towle DW (2012) Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray. Comparative Biochemistry and Physiology, Part D: Genomics and Proteomics, 7: 110-123.
Leonard AE, Pereira SL, Sprecher H, Huang Y (2004) Elongation of long-chain fatty acids. Progress in Lipid Research, 43: 36-54.
Lesnik T, Solomovici J, Deana A, Ehrlich R, Reiss C (2000) Ribosome traffic in E. coli and regulation of gene expression. Journal of Theoretical Biology, 202: 175-185.
Li C, Weng S, Chen Y, Yu X, Lu L, Zhang H, He J, Xu X (2012) Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique. PLoS One, 7: e47442.
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2：An improved ultrafast tool for short read alignment. Bioinformatics, 25: 1966-1967.
Li S, Zhang X, Sun Z, Li F, Xiang J (2013) Transcriptome analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV acute infection. PLoS One, 8:e58627.
Liu QP, Dou SJ, Ji ZJ, Xue QZ (2005) Synonymous codon usage and gene function are strongly related in Oryza sativa. BioSystems, 80: 123-131.
Liu QP, Xue QZ (2005) Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. Journal of Genetics, 84: 55-62.
Lovett DL, Colella T, Cannon AC, Lee DH, Evangelisto A, Muller EM, Towle DW (2006) Effect of salinity on osmoregulatory patch epithelia in gills of the blue crab Callinectes sapidus. The Biological Bulletin, 210: 132-139.
Lu TT, Lu GJ, Fan DL, Zhu CR, Li W, Zhao Q, Feng Q, Zhao Y, Guo YL, Li WJ, Huang XH, Han B (2010) Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Research, 20: 1238-1249.
Luizi FS, Gara B, Shields RJ, Bromage NR (1999) Further description of the development of the digestive organs in Atlantic halibut (Hippoglossus hippoglossus) larvae, with notes on differential absorption of copepod and Artemia prey. Aquaculture, 176: 101-116.
Luquet CM, Poste lU, Halperin J, Urcola MR, Marques R, Siebers D (2002) Transepithelial potential differences and Na+ flux in isolated perfused gills of the crab Chasmagnathus granulatus (Grapsidae) acclimated to hyper-and hypo-salinity. The Journal of Experimental Biology, 205: 71-77.
Luquet CM, Weihrauch D, Senek M, Towle DW (2005) Induction of branchial ion transporter mRNA expression during acclimation to salinity change in the euryhaline crab Chasmagnathus granulatus. The Journal of Experimental Biology, 208: 3627-3636.
Ma J, Zhang M, Ruan L, Shi H, Xu X (2010) Characterization of two novel ADP ribosylation factors from the shrimp Marsupenaeus japonicus. Fish and Shellfish Immunology, 29: 956-962.
Machida RJ, Miya MU, Nishida M, Nishida S (2002) Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Marine Biotechnology, 4: 406-417.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z et al. (2005) Genome sequencing in microfabricated high-density picolitrere actors. Nature, 437: 376-380.
Mckinnon AD, Duggan S, Nichols PD, Rimmer MA, Semmens G, Robino B (2003) The potential of tropical paracalanid copepods as live feeds in aquaculture. Aquaculture, 223: 89-106.
Milligan P, Stahl E, Schizas N, Turner J (2011) Phylogeography of the copepod Acartia hudsonica in estuaries of the northeastern United States. Hydrobiologia, 666: 155-165.
Minxiao W, Song S, Chaolun L, Xin S (2011) Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies. BMC Genomics, 12: 73.
Moriyama EN, Powell JR (1998) Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Research, 26: 3188-3193.
Musto H, Cruveiller S, D'Onofrio G, Romer H, Bernardi G (2001) Translational selection on codon usage in Xenopus laevis. Molecular Biology and Evolution, 18: 1703-1707.
Nagasawa S, Simidu U, Nemoto T (1985) Scanning electron microscopy investigation of bacterial colonization of the marine copepod Acartia clause. Marine Biology, 87: 61-66.
Nanton DA, Castell JD (1998) The effects of dietary fatty acids on the fatty acid composition of the harpacticoid copepod, Tisbe sp., for use as a live food for marine fish larvae. Aquaculture, 163: 251-261.
Nanton DA, Castell JD (1999) The effects of temperature and dietary fatty acids on the fatty acid composition of harpacticoid copepods, for use as a live food for marine fish larvae. Aquaculture, 175: 167-181.
Nesrine BB, Viviane B, Mireille CD, Evelyse G, Klaus, Guy C, Catherine LN (2014) Differential distribution of V-type H+-ATPase and Na+/K+-ATPase in the branchial chamber of the palaemonid shrimp Macrobrachium amazonicum. Cell Tissue Research, 357: 195-206.
Ning J, Wang M, Li C, Sun S (2013) Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX. PLoS One, 8: e63741.
Norsker NH, Støttrup JG (1994) The importance of dietary HUFAs for fecundity and HUFA content in the harpacticoid, Tisbe holothuriae Humes. Aquaculture, 125: 155-166.
Novoa E M, Ribas de Pouplana L (2012) Speeding with control: codon usage, tRNAs, and ribosomes. Trends in Genetics, 28: 574-581.
Øines Ø, Chram S (2008) Intra- or inter-specific difference in genotypes of Caligus elongatus Nordmann 1832?. Acta Parasitologica, 53: 93-105.
Palidwor GA, Perkins TJ, Xia X (2010) A general model of codon bias due to GC mutational bias. PLoS one, 5: e13431.
Pan A, Dutta C, Das J (1998) Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias. Gene, 215: 405-413.
Pan YJ, Souissi S, Souissi A, Wu CH, Cheng SH, Hwang JS (2014) Dietary effects on egg production, egg-hatching rate and female life span of the tropical calanoid copepod Acartia bilobata. Aquaculture Research, 45: 1659-1671.
Parrish CC, French VM, Whiticar M J (2012) Lipid class and fatty acid composition of copepods (Calanus finmarchicus, Calanus glacialis, Pseudocalanus sp., Tisbe furcata and Nitokra lacustris) fed various combinations of autotrophic and heterotrophic protists. Journal of Plankton Research, 34: 356-375.
Payne MF, Rippingale RJ, Cleary JJ (2001) Cultured copepods as food for West Australian dhufish Glaucosoma hebraicum and pink snapper Pagrus auratus larvae. Aquaculture, 194: 137-150.
Peden JF (1999) Analysis of codon usage. PhD thesis, University of Nottingham, UK.
Peden JF (1999) Analysis of Codon Usage. PhD thesis. Department Genetics, University of Nottingham UK, p.226.
Peixoto L, Zavala A, Romero H, Musto H (2003) The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium melioti. Gene, 320: 109-116.
Percudani R, Pavesi A, Ottonello S (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. Journal of Molecular Biology, 268: 322-330.
Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics, 14: 817-818.
Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proceedings of the National Academy of Sciences USA, 94: 7784-7790.
Qiu YL, Li L, Hendry T, Li R, Taylor DW, Issa MJ, Ronen AJ, Vekaria ML, White AM (2006) Reconstructing the basal angiosperm phylogeny: evaluating information content of the mitochondrial genes. Taxon 55: 837-856.
Raghavan R, Kelkar Y D, Ochman H (2012) A selective force favoring increased G+C content in bacterial genes. Proceedings of the National Academy of Sciences, 109: 14504-14507.
Regier J, Shultz J, Kambic R (2005) Pancrustacean phylogeny: Hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proceedings of the Royal Society of London, Biological Sciences, 272: 395-401.
Regier J, Shultz J, Zwick A, Hussey A, Ball B, Wetzer R, Martin J, Cunningham C (2010) Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature, 463: 1079-1083.
Richardson A (2008) In hot water: Zooplankton and climate change. ICES Journal of Marine Science and Technology, 65: 279-295.
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ et al. (2010) De novo assembly and analysis of RNA-seq data. Nature Methods, 7: 909-912.
Romano N, Zeng CS (2006) The effects of salinity on the survival, growth and haemolymph osmolality of early juvenile blue swimmer crabs, Portunus pelagicus. Aquaculture, 260: 151-162.
Romero H, Zavala A, Musto H, Bernardi G (2003) The influence of translational selection on codon usage in fishes from the family Cyprinidae. Gene, 317: 141-147.
Rouwendal GJA, Mendes O, Wolbert EJH, Douwe de Boer A (1997) Enhanced expression in tobacco of the gene encoding green fluorescent protein by modification of its codon usage. Plant Molecular Biology, 33: 989-999.
Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Phylogenetics and Evolution 4: 406-425.
Sang HM, Fotedar R (2004) Growth, survival, haemolymph osmolality and organosomatic indices of the western king prawn (Penaeus latisulcatus Kishinouye, 1896) reared at different salinities. Aquaculture, 234: 601-614.
Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: Robust de novo RNA-seq assembly across the dy¬namic range of expression levels. Bioinformatics, 28: 1086-1092.
Selden PA, Huys R, Stephenson MH, Heward AP, Taylor PN (2010) Crustaceans from bitumen clast in Carboniferous glacial diamictite extend fossil record of copepods. Natura Communications. 1:50.
Sharp PM, Cowe E, Higgins DG, Shield DC, Wolfe KH, Wright E (1988) Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Research, 16: 8207-8211.
Sharp PM, WH Li (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution, 24: 28-38.
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nature biotechnology, 26: 1135-1145.
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309: 1728-1732.
Shi SL, Jiang YR, Liu YQ, Xia RX, Qin Li (2013) Selective pressure dominates the synonymous codon usage in parvoviridae. Virus Genes, 46:10-19.
Shpaer EG (1986) Constraints on codon context in Escherichia coli genes. Their possible role in modulating the effieincy of translation. Journal of Molecular Biology, 188: 555-564.
Sookruksawong S, Sun F, Liu Z, Tassanakajon A (2013) RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei. Developmental and Comparative Immunology, 41: 523–533.
Spinelli J, Mahnken C, Steinberg M (1979) Alternate sources of proteins for fish meal in salmonid diets. In: Halver JE, Tiews K (Editors), Finfish nutrition and fishfeed technology, Vol 2. Heenemann, Berlin, pp. 131-147.
Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U et al. (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature, 466: 720-726.
Stottrup JG, Norsker NH (1997) Production and use of copepods in marine fish larviculture. Aquaculture, 155: 231-247.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M and Kumar S (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28: 2731-2739.
Tan Q, Brusgaard K, Kruse TA, Oakeley E, Hemmings B, Beck-Nielsen H, Hansen L, Gaster M (2004) Correspondence analysis of microarray time-course data in case-control design. Journal of Biology Informatics, 37: 358-365.
Tarrant AM, Baumgartner MF, Verslycke T, Johnson CL (2008) Differential gene expression in diapausing and active Calanus finmarchicus (Copepoda). Marine Ecology Progress Series, 355: 193-207.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics, 4: 41.
Tekaia F, Yeramoan E, Dujon B (2002) Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: A global picture with correspondence analysis. Gene, 297:51-60.
Tew KS, Chang WB, Lin CH, Liu JK, Wong TY,Yeh CH Kuo J (2008) Synonymous codon usage in marine pico-cyanobacterium Synechococcus sp. WH8102. Platax, 5: 1-13.
Tillman JA, Seybold SJ, Jurenka RA, Blomquist GJ (1999) Insect pheromones–an overview of biosynthesis and endocrine regulation. Insect Biochemistry and Molecular biology, 29: 481-514.
Tjensvoll K (2006) Studies on the mitochondrial genome and rDNA genes from the salmon louse, Lepeophtheirus salmonis. PhD Thesis, University of Bergen, Norway.
Tjensvoll K, Hodneland K, Nilsen F, Nylund A (2005) Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed. Gene, 353: 218-230.
Towle DW, Henry RP, Terwilliger NB (2011) Microarray-detected changes in gene expression in gills of green crabs (Carcinus maenas) upon dilution of environmental salinity. Comparative Biochemistry and Physiology, Part D 6: 115-125.
Vargas-Albores F, Martinez-Martinez A, Aguilar-Campos J, Jimenez-Vega F (2009) The expression of protein disulfide isomerase from Litopenaeus vannamei hemocytes is regulated by bacterial inoculation. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 4: 141-146.
Vijay N, Poelstra JW, Künstner A, Wolf JBW (2013) Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology, 22: 620-634.
Wald N, Alroy M, Botzman M, Margalit H (2012) Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the ENCoded amino acids. Nucleic Acids Research, 40: 7074-7083.
Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS (2010) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics, 11: 400.
Watanabe T, Arakawa T, Kitajima C, Fukusho K, Fujita S (1978) Nutritional quality of living feed from the viewpoint of essential fatty acids for fish. Bulletin of the Japanese Society of Scientific Fisheries, 44: 1223-1227.
Wei WL, Qi XQ, Wang LH, Zhang YX, Hua W, Li DH, Lü HX, Zhang XR (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics, 12: 451.
Weihrauch D, Ziegler A, Siebers D, Towle DW (2001) Molecular characterization of V-type H+-ATPase (B-subunit) in gills of euryhaline crabs and its physiological role in osmoregulatory ion uptake. The Journal of Experimental Biology, 204: 25-37.
Wong GK, Wang J, Tao L, Tan J, Zhang J, Passey DA, Yu J (2002) Compositional gradients in gramineae genes. Genome Research, 12: 851-856.
Wright F (1990) The effective number of codons used in a gene. Gene, 87: 23-29.
Xia ZH, Xu HM, Zhai JL, Li DJ, He CZ, Huang X (2011) RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Molecular Biology, 77: 299-308.
Xue S, Liu Y, Zhang Y, Sun Y, Geng X, Sun J (2013) Sequencing and de novo analysis of the hemocytes transcriptome in Litopenaeus vannamei pesponse to White Spot Syndrome Virus infection. PLoS One, 8: e76718.
Yang Q, Sun F, Yang Z, Li H (2014) Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications. BioMed Research International, 2014: 1-12.
Yasuike M, Leong J, Jantzen SG, von Schalburg KR, Nilsen F, Jones SR, Koop BF (2012) Genomic resources for sea lice: Analysis of ESTs and mitochondrial genomes. Marine Biotechnology, 14: 155-166.
Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: A web tool for plotting GO annotations. Nucleic Acids Research, 34: W293-2937.
Yotoko KSC, Bonatoo SL (2007) A phylogenomic appraisal of the evolutionary relationship of mycoplasmas. Genetics and Molecular Biology, 30: 270-276.
Zeng D, Chen X, Xie D, ZhaoY, Yang C, Li Y , Ma N, Peng M, Yang Q, Liao Z et al. (2013) Transcriptome analysis of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Taura syndrome Virus (TSV) experimental infection. PLoS ONE, 28: e57515.
Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829.
Zhang Y, Chen J, Tang X, Wang F, Jiang L, Xiong X, Wang M, Rong M, Liu Z, Liang S (2010) Transcriptome analysis of the venom glands of the Chinese wolf spider Lycosa singoriensis. Zoology, 113: 10-18.
Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: A comparative study. BMC Bioinformatics, 12 Suppl 14: S2.
林慧君 (2000) 模糊許水蚤(Pseudodiaptomus annandalei)形態發育及溫度、鹽度、藻類對其生長之影響。國立東華大學生物多樣性及演化研究所。碩士論文。
洪健文 (2012) 矽藻二次代謝物poly unsaturated aldehyde 對橈足類Acartia bilobata 游泳行為之影響。碩士論文。國立台灣海洋大學海洋生物研究所。1-35。
張文炳 (1992) 橈腳類短角異劍水蚤之生理生態學研究。國立台灣大學海洋研究所。博士論文。
許登瑋 (2008) 不同食物對橈足類短角異劍水蚤族群成長及脂肪酸組成之影響。國立臺灣大學漁業科學研究所。碩士論文。
潘國文 (2009) 日本虎斑猛水蚤之基因表現與功能性基因庫篩選。國立臺灣大學漁業科學研究所。碩士論文。