1.
Rodriguez-Amaya DB: Natural Food Pigments and Colorants. Current Opinion in Food Science 2016, 7:20-26.
2.
Riaz M, Zia-Ul-Haq M, Saad B: Anthocyanins as Natural Colors. In: Anthocyanins and Human Health: Biomolecular and therapeutic aspects. Cham: Springer International Publishing; 2016: 47-55.
3.
Smeriglio A, Barreca D, Bellocco E, Trombetta D: Chemistry, Pharmacology and Health Benefits of Anthocyanins. Phytotherapy Research Ptr 2016, 30(8):1265-1286.
4.
Riaz M, Zia UHM, Saad B: Anthocyanins and Human Health: Biomolecular and therapeutic aspects; 2016.
5.
Krga I, Milenkovic D: Anthocyanins: From Sources and Bioavailability to Cardiovascular-Health Benefits and
Molecular Mechanisms of Action. Journal of Agricultural and Food Chemistry 2019, 67(7):1771-1783.
6.
Xu M, Bower KA, Wang S, Frank JA, Chen G, Ding M, Wang S, Shi X, Ke Z, Luo J: Cyanidin-3-Glucoside inhibits ethanol-induced invasion of breast cancer cells overexpressing
ErbB2. Molecular Cancer 2010, 9(1):285.
7.
Xie L, Su H, Sun C, Zheng X, Wei C: Recent advances in understanding the anti-obesity activity of anthocyanins and their
biosynthesis in microorganisms. Trends in Food Science & Technology 2017, 72:13-24.
8.
Holton TA, Cornish EC: Genetics and Biochemistry of Anthocyanin Biosynthesis. Plant Cell 1995, 7(7):1071-1083.
9.
Zhu L, Huang Y, Zhang Y, Xu C, Lu J, Wang Y: The growing season impacts the accumulation and composition of flavonoids in grape
skins in two-crop-a-year viticulture. Journal of food science and technology 2017, 54(9):2861-2870.
10.
Tirumale S, Wani NA: Biopigments: Fungal Pigments. In: Fungi and their Role in Sustainable Development: Current Perspectives. Springer; 2018: 413-426.
11.
Pandey RP, Parajuli P, Koffas MA, Sohng JK: Microbial production of natural and non-natural flavonoids: pathway engineering, directed
evolution and systems/synthetic biology. Biotechnology advances 2016, 34(5):634-662.
12.
Wang H, Li Y, Zhang K, Ma Y, Li P: Feasibility and transcriptomic analysis of betalain production by biomembrane surface
fermentation of Penicillium novae-zelandiae. AMB Express 2018, 8(1):4.
13.
Sarang H, Rajani P, Vasanthakumari MM, Kumara PM, Siva R, Ravikanth G, Uma Shaanker
R: An endophytic fungus, Gibberella moniliformis from Lawsonia inermis L. produces lawsone,
an orange-red pigment. Antonie van Leeuwenhoek 2017, 110(7):853-862.
14.
Li D, Fu D, Zhang Y, Ma X, Gao L, Wang X, Zhou D, Zhao K: Isolation, Purification, and Identification of Taxol and Related Taxanes from Taxol-Producing
Fungus Aspergillus niger subsp. taxi. J Microbiol Biotechnol 2017, 27(8):1379-1385.
15.
Mei YZ, Liu RX, Wang DP, Wang X, Dai CC: Biocatalysis and biotransformation of resveratrol in microorganisms. Biotechnology letters 2015, 37(1):9-18.
16.
Ein-Gil N, Ilan M, Carmeli S, Smith GW, Pawlik JR, Yarden O: Presence of Aspergillus sydowii, a pathogen of gorgonian sea fans in the marine sponge
Spongia obscura. The Isme Journal 2009, 3:752.
17.
Hallegraeff G, Coman F, Davies C, Hayashi A, McLeod D, Slotwinski A, Whittock L, Richardson
AJ: Australian Dust Storm Associated with Extensive <span class="named-content
genus-species" id="named-content-1">Aspergillus sydowii</span>
Fungal “Bloom” in Coastal Waters. Applied and Environmental Microbiology 2014, 80(11):3315.
18.
Klich MA: Identification of common Aspergillus species. Centraalbureau voor Schimmelcultures 2002.
19.
Geiser DM, Taylor JW, Ritchie KB, Smith GW: Cause of sea fan death in the West Indies. Nature 1998, 394(6689):137-138.
20.
González-Abradelo D, Pérez-Llano Y, Peidro-Guzmán H, Sánchez-Carbente MdR, Folch-Mallol
JL, Aranda E, Vaidyanathan VK, Cabana H, Gunde-Cimerman N, Batista-García RA: First demonstration that ascomycetous halophilic fungi (Aspergillus sydowii and Aspergillus
destruens) are useful in xenobiotic mycoremediation under high salinity conditions. Bioresource Technology 2019, 279:287-296.
21.
Tian J, Dong Q, Yu C, Zhao R, Wang J, Chen L: Biodegradation of the Organophosphate Trichlorfon and Its Major Degradation Products
by a Novel Aspergillus sydowii PA F-2. Journal of Agricultural and Food Chemistry 2016, 64(21):4280-4287.
22.
Alvarenga N, Birolli WG, Seleghim MHR, Porto ALM: Biodegradation of methyl parathion by whole cells of marine-derived fungi Aspergillus
sydowii and Penicillium decaturense. Chemosphere 2014, 117:47-52.
23.
Chung Y-M, Wei C-K, Chuang D-W, El-Shazly M, Hsieh C-T, Asai T, Oshima Y, Hsieh T-J,
Hwang T-L, Wu Y-C et al: An epigenetic modifier enhances the production of anti-diabetic and anti-inflammatory
sesquiterpenoids from Aspergillus sydowii. Bioorganic & Medicinal Chemistry 2013, 21(13):3866-3872.
24.
Zhou B, Ma C, Wang H, Xia T: Biodegradation of caffeine by whole cells of tea-derived fungi Aspergillus sydowii,
Aspergillus niger and optimization for caffeine degradation. BMC Microbiology 2018, 18(1):53.
25.
Trisuwan K, Rukachaisirikul V, Kaewpet M, Phongpaichit S, Hutadilok-Towatana N, Preedanon
S, Sakayaroj J: Sesquiterpene and xanthone derivatives from the sea fan-derived fungus Aspergillus
sydowii PSU-F154. J Nat Prod 2011, 74(7):1663-1667.
26.
He F, Han Z, Peng J, Qian PY, Qi SH: Antifouling indole alkaloids from two marine derived fungi. Nat Prod Commun 2013, 8(3):329-332.
27.
Matkar K, Chapla D, Divecha J, Nighojkar A, Madamwar D: Production of cellulase by a newly isolated strain of Aspergillus sydowii and its
optimization under submerged fermentation. International Biodeterioration & Biodegradation 2013, 78:24-33.
28.
Nanda G, Ghosh M: Physiological studies on xylose induction and glucose repression of xylanolytic enzymes
in Aspergillus sydowii MG49. FEMS Microbiology Letters 1994, 117(2):151-156.
29.
Mercer TR, Dinger ME, Mattick JS: Long non-coding RNAs: insights into functions. Nature Reviews Genetics 2009, 10:155.
30.
Liu J, Wang H, Chua N-H: Long noncoding RNA transcriptome of plants. Plant Biotechnology Journal 2015, 13(3):319-328.
31.
Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A,
Weigel D, García JA, Paz-Ares J: Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics 2007, 39:1033.
32.
Di C, Yuan J, Wu Y, Li J, Lin H, Hu L, Zhang T, Qi Y, Gerstein MB, Guo Y et al: Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating
expression, epigenetic and structural features. The Plant Journal 2014, 80(5):848-861.
33.
Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua N-H: Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in <em>Arabidopsis</em>. The Plant Cell 2012, 24(11):4333.
34.
Montoro P, Tuberoso CI, Perrone A, Piacente S, Cabras P, Pizza C: Characterisation by liquid chromatography-electrospray tandem mass spectrometry of
anthocyanins in extracts of Myrtus communis L. berries used for the preparation of
myrtle liqueur. J Chromatogr A 2006, 1112(1-2):232-240.
35.
Goudarzi M, Mir N, Mousavi-Kamazani M, Bagheri S, Salavati-Niasari M: Biosynthesis and characterization of silver nanoparticles prepared from two novel
natural precursors by facile thermal decomposition methods. Sci Rep 2016, 6:32539.
36.
Tan C, Selig MJ, Abbaspourrad A: Anthocyanin stabilization by chitosan-chondroitin sulfate polyelectrolyte complexation
integrating catechin co-pigmentation. Carbohydrate polymers 2018, 181:124-131.
37.
Fragoso S, Guasch J, Aceña L, Mestres M, Busto O: Prediction of red wine colour and phenolic parameters from the analysis of its grape
extract. International Journal of Food Science & Technology 2011, 46(12):2569-2575.
38.
Tsutsumi A, Horikoshi Y, Fushimi T, Saito A, Koizumi R, Fujii Y, Hu QQ, Hirota Y,
Aizawa K, Osakabe N: Acylated anthocyanins derived from purple carrot (Daucus carota L.) induce elevation
of blood flow in rat cremaster arteriole. Food & function 2019, 10(3):1726-1735.
39.
Yang L, Rong-Rong C, Ji-Li F, Ke Y: Total anthocyanins and cyanidin-3-O-glucoside contents and antioxidant activities
of purified extracts from eight different pigmented plants. Pharmacognosy Magazine 2019, 15(60):124.
40.
Dong T, Han R, Yu J, Zhu M, Zhang Y, Gong Y, Li Z: Anthocyanins accumulation and molecular analysis of correlated genes by metabolome
and transcriptome in green and purple asparaguses (Asparagus officinalis, L.). Food Chemistry 2019, 271:18-28.
41.
de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh
G, Asadollahi M, Askin M, Barry K et al: Comparative genomics reveals high biological diversity and specific adaptations in
the industrially and medically important fungal genus Aspergillus. Genome Biol 2017, 18(1):28.
42.
Kim D, Langmead B, Salzberg SL: HISAT: a fast spliced aligner with low memory requirements. Nat Methods 2015, 12(4):357-360.
43.
Li B, Dewey CN: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference
genome. BMC Bioinformatics 2011, 12:323.
44.
Pelletier MK, Murrell JR, Shirley BW: Characterization of flavonol synthase and leucoanthocyanidin dioxygenase genes in
Arabidopsis. Further evidence for differential regulation of "early" and "late" genes. Plant Physiol 1997, 113(4):1437-1445.
45.
Ferrer JL, Austin MB, Stewart C, Jr., Noel JP: Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiol Biochem 2008, 46(3):356-370.
46.
Ma L, Bajic VB, Zhang Z: On the classification of long non-coding RNAs. RNA Biol 2013, 10(6):925-933.
47.
Heo YM, Kim K, Kwon SL, Na J, Lee H, Jang S, Kim CH, Jung J, Kim JJ: Investigation of Filamentous Fungi Producing Safe, Functional Water-Soluble Pigments. Mycobiology 2018, 46(3):269-277.
48.
Delmulle T, De Maeseneire SL, De Mey M: Challenges in the microbial production of flavonoids. Phytochemistry Reviews 2018, 17(2):229-247.
49.
Goodrich JA, Kugel JF: Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 2006, 7(8):612-616.
50.
Lin Y, Jiang L, Chen Q, Li Y, Zhang Y, Luo Y, Zhang Y, Sun B, Wang X, Tang H: Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry
(Fragaria x ananassa) Provides New Insight into the Regulation of Anthocyanins Pathway. Plant Cell Physiol 2018.
51.
Chen Q, Liu X, Hu Y, Sun B, Hu Y, Wang X, Tang H, Wang Y: Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus. Int J Genomics 2018, 2018:8084032.
52.
Deng S, Cheng C, Liu Z, Chen Y, Zhang Z, Huang Y, Lin Y, Wang T, Lai Z: Comparative transcriptome analysis reveals a role for anthocyanin biosynthesis genes
in the formation of purple peel in Minhou wild banana (Musa itinerans Cheesman). The Journal of Horticultural Science and Biotechnology 2019, 94(2):184-200.
53.
Tang W, Zheng Y, Dong J, Yu J, Yue J, Liu F, Guo X, Huang S, Wisniewski M, Sun J et al: Comprehensive Transcriptome Profiling Reveals Long Noncoding RNA Expression and Alternative
Splicing Regulation during Fruit Development and Ripening in Kiwifruit (Actinidia
chinensis). Front Plant Sci 2016, 7:335.
54.
Bolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30(15):2114-2120.
55.
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359.
56.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 2015, 33(3):290-295.
57.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L,
Raychowdhury R, Zeng Q et al: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652.
58.
Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L: KOBAS 2.0: a web server for annotation and identification of enriched pathways and
diseases. Nucleic Acids Res 2011, 39(Web Server issue):W316-322.
59.
Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X et al: NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res 2018, 46(D1):D308-D314.
60.
Kang YJ, Yang DC, Kong L, Hou M, Meng YQ, Wei L, Gao G: CPC2: a fast and accurate coding potential calculator based on sequence intrinsic
features. Nucleic Acids Res 2017, 45(W1):W12-W16.
61.
Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y: Utilizing sequence intrinsic composition to classify protein-coding and long non-coding
transcripts. Nucleic Acids Res 2013, 41(17):e166.
62.
Li A, Zhang J, Zhou Z: PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved
k-mer scheme. BMC Bioinformatics 2014, 15:311.
63.
Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA et al: Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics 2019.
64.
Tafer H, Hofacker IL: RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 2008, 24(22):2657-2663.
65.
Li J, Ma W, Zeng P, Wang J, Geng B, Yang J, Cui Q: LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Brief Bioinform 2015, 16(5):806-812.
66.
Love MI, Huber W, Anders S: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014, 15(12):550.
67.
Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN,
Potter SC, Finn RD et al: The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 2019.
68.
Talavera G, Castresana J: Improvement of phylogenies after removing divergent and ambiguously aligned blocks
from protein sequence alignments. Syst Biol 2007, 56(4):564-577.
69.
Stamatakis A: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30(9):1312-1313.