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Cichlids

Cichlids are a diverse family of freshwater fish found predominantly in tropical regions of Africa and the Americas.
These vibrant, highly adaptable fish are renowned for their complex social behaviors, intricate parental care, and striking coloration.
The Cichlidae family includes over 1,700 species, ranging from the diminutive dwarf cichlids to the impressive Malawi cichlids.
Cichlids are popular in the aquarium hobby and play a signifcant role in many regional ecosystems.
Their remarkable evolutionary adaptations and unique phenotypes have made them a focal point for research in fields such as behavioral ecology, evolutionary biology, and conservation biology.

Most cited protocols related to «Cichlids»

1
Comparative Analysis of M. zebra Transcriptome Assemblies
GMAP [23 (link)] version 2014-12-06 was used to align existing RNA-seq transcriptome assemblies of eleven M. zebra tissues. The transcriptome assemblies were created using Trinity [24 (link)] as part of the cichlid genome project [13 (link)] and made available as supplementary information [25 ].
Three BAC clones that were previously sequenced and assembled using Sanger sequencing technology were aligned to the existing and newly produced assemblies for validation. These published BACs correspond to several opsin gene loci: SWS2A/SWS2B/LWS (GenBank accession JF262084.1, 107.6kbp), SWS1 (GenBank accession JF262085.1, 77.6kbp), and RH2B/RH2A (GenBank accession JF262089.1, 83.5kbp) [26 (link)]. The BAC sequences were aligned to the corresponding M_zebra_v0 and M_zebra_UMD1 assembly sequences using Gepard [27 (link)] version 1.30 to create dotplots for comparison.
Completeness of the intermediate and final M_zebra_UMD1 assemblies was assessed using CEGMA [28 (link)] version 2.5 optimized for vertebrate genomes (−−vrt). CEGMA relied on GeneWise version 2.4.1, HMMER version 3.1b1, and NCBI BLAST+ version 2.2.29+. The 248 mostly highly conserved core eukaryotic gene set provided by CEGMA was used.
The likelihoods of the intermediate and final M_zebra_UMD1 assemblies were evaluated using ALE [29 (link)]. Each of the Illumina libraries were aligned to the assemblies using Bowtie2 [30 (link)] version 2.0.2 with the ‘--very-sensitive’ preset parameter. The uncorrected PacBio reads were aligned to assemblies with BLASR version 1.3.1.127046 using the same parameters used above for PBJelly and the ‘-sam’ option to produce a SAM file for input to ALE. ALE was then run on each of the respective alignment files to produce likelihood and mapping statistics for each library.
Summary statistics of the assemblies were compiled using the assemblathon_stats.pl script [31 ].
Conte M.A, & Kocher T.D. (2015). An improved genome reference for the African cichlid, Metriaclima zebra. BMC Genomics, 16(1), 724.
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Publication 2015
Cichlids Clone Cells DNA Library Eukaryota FCER2 protein, human Genes Genetic Loci Genome RNA-Seq Rod Opsins Tissues Transcriptome Vertebrates Zebras
2
Nile Tilapia Genetic Map Construction
Offspring (n = 689) and parents from 41 full-sibling families belonging to the 20th, 24th, and 25th generations of the GST® strain were analyzed using a custom 57K SNP Axiom Nile Tilapia Genotyping Array (Affymetrix, Santa Clara, CA, USA) [23 (link)]. SNPs classified as “PolyHighRes” or “No-MinorHom” by Axiom Analysis Suite (Affymetrix, Santa Clara, CA, USA), and having a minor-allele frequency ≥0.05 and call rate ≥0.85 were used in genetic map construction (n = 40,548). Lep-MAP2 [97 (link)] was used to order these SNPs into LGs in a stepwise process beginning with SNPs being assigned to LGs using the “SeparateChromosomes” command. Logarithm of the odds (LOD) thresholds were adjusted until 22 LGs were generated, which correspond with the O. niloticus karyotype. Unassigned SNPs were subsequently added to LGs using the “JoinSingles” command and a more relaxed LOD threshold, and ordered within each LG using the “OrderMarkers” command.
Sequence flanking each SNP (2 × 35 nucleotides) was used to precisely position 40,190 SNPs to the O_niloticus_UMD1 assembly (NCBI accession MKQE00000000) and thereby integrate the linkage and physical maps. This revealed 22 additional contig misassemblies (i.e., contigs containing SNPs from different LGs) that were not detected in the original anchoring for O_niloticus_UMD1. These contigs were subsequently broken. Linkage information was subsequently used to order and orient contigs and build sequences for 22 Nile tilapia LGs in the new O_niloticus_UMD_NMBU assembly following the previous cichlid nomenclature [5 (link), 14 (link), 54 (link), 98 (link)].
LD results (r2 > 0.97) presented in Figs 4 and 5 and Additional file F were produced in PLINK2 version 1.90b3w [99 (link)] using the pedigree described above and SNP positions given in [23 (link)].
Conte M.A., Joshi R., Moore E.C., Nandamuri S.P., Gammerdinger W.J., Roberts R.B., Carleton K.L., Lien S, & Kocher T.D. (2019). Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. GigaScience, 8(4), giz030.
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Publication 2019
Asian Persons Chromosome Mapping Cichlids Figs Karyotype MAP2 protein, human Microtubule-Associated Proteins Nucleotides Oreochromis niloticus Parent Physical Examination Strains
3
Isolation of Pyrethroid-Resistant Aedes aegypti Strain
In order to study the effects of Vssc mutations S989P + V1016G (kdr) without the influence of other resistance mechanisms or strain variations, we needed a strain of A. aegypti that was closely related to a susceptible strain but containing kdr. To accomplish this, we used the following parental strains: Rockefeller (ROCK), an insecticide‐susceptible strain that has been reared in laboratories without exposure to insecticides for decades, which originated from the Caribbean,17 and Singapore (SP), a pyrethroid‐resistant strain in which the mechanisms of resistance have been well studied.14 Adult SP are 579‐fold resistant to permethrin (relative to ROCK) due to kdr and CYP‐mediated detoxification, whereas hydrolases and decreased penetration are not involved.14Mosquitoes were reared at 27 ± 1 °C and 70–80% relative humidity (RH). Females were blood‐fed using membrane‐covered water‐jacketed glass feeders with cow blood obtained locally. Adults were maintained on 10% sugar water in cages ∼ 35 × 25 × 25 cm holding ≤1000 mosquitoes. Larvae were reared in 27.5 × 21.5 × 7.5 cm containers with ∼ 2 L deionized water and fed Cichlid Gold fish food pellets (Hikari, Hayward, CA, USA) (ground pellets for first instar and medium size pellets for second to fourth instars). Food pellets were given daily, as needed depending on larval density (∼ 400–600) and instar.
The strain KDR:ROCK was isolated from crossing ROCK with SP followed by four backcrosses and genotype selections (see Section 2.2). KDR:ROCK is congenic to ROCK, but resistant to pyrethroids due to the Vssc mutations S989P + V1016G while containing no CYP‐mediated resistance. The procedure for isolating KDR:ROCK is illustrated in Fig. 1. In short, unmated SP females were crossed en masse with ROCK males. Unmated F1 females were backcrossed with ROCK and unmated BC1 females were genotyped for the presence of Vssc mutations S989P + V1016G (see Section 2.2). BC1 females that were heterozygous for P989 + G1016 (kdr) were backcrossed to ROCK males. This process was repeated for the BC2 and BC3 generations. At BC4, both males and unmated females were genotyped and individuals that were heterozygous for P989 + G1016 were reared en masse. Males and unmated females from the next generation were genotyped and individuals that were homozygous for P989 + G1016 were reared en masse. The resultant strain was named KDR:ROCK (Fig. 1).
Smith L.B., Kasai S, & Scott J.G. (2017). Voltage‐sensitive sodium channel mutations S989P + V1016G in Aedes aegypti confer variable resistance to pyrethroids, DDT and oxadiazines. Pest Management Science, 74(3), 737-745.
Publication 2017
Adult Blood Carbohydrates Caribbean People Cichlids Culicidae Females Food Gold Heterozygote Homozygote Humidity Hydrolase Insecticides Larva Males Metabolic Detoxication, Drug Mutation Parent Pellets, Drug Permethrin Pyrethroids Strains Tissue, Membrane
4
Vertebrate Genome Project assembly protocols
All 17 genomes were assembled with the VGP pipeline (Extended Data Fig. 2a) for benchmark purposes, with some uncurated. The pale spear-nosed bat, greater horseshoe bat, Canada lynx, platypus, male and female zebra finch, kākāpō, Anna’s hummingbird, Goode’s thornscrub tortoise, flier cichlid, and blunt-snouted clingfish assemblies were generated using the VGP pipeline 1.0 to 1.6 and curated for submission to NCBI and EBI public archives. The curated and submitted two-lined caecilian, zig-zag eel, climbing perch, channel bull blenny, eastern happy, and thorny skate assemblies were generated using a similar process developed in parallel (Supplementary Note 2). Two submitted curated versions of the female zebra finch were made, one using the standard VGP pipeline and the other using the VGP trio pipeline, so that comparative analyses could be performed by others.
Rhie A., McCarthy S.A., Fedrigo O., Damas J., Formenti G., Koren S., Uliano-Silva M., Chow W., Fungtammasan A., Kim J., Lee C., Ko B.J., Chaisson M., Gedman G.L., Cantin L.J., Thibaud-Nissen F., Haggerty L., Bista I., Smith M., Haase B., Mountcastle J., Winkler S., Paez S., Howard J., Vernes S.C., Lama T.M., Grutzner F., Warren W.C., Balakrishnan C.N., Burt D., George J.M., Biegler M.T., Iorns D., Digby A., Eason D., Robertson B., Edwards T., Wilkinson M., Turner G., Meyer A., Kautt A.F., Franchini P., Detrich HW I.I.I., Svardal H., Wagner M., Naylor G.J., Pippel M., Malinsky M., Mooney M., Simbirsky M., Hannigan B.T., Pesout T., Houck M., Misuraca A., Kingan S.B., Hall R., Kronenberg Z., Sović I., Dunn C., Ning Z., Hastie A., Lee J., Selvaraj S., Green R.E., Putnam N.H., Gut I., Ghurye J., Garrison E., Sims Y., Collins J., Pelan S., Torrance J., Tracey A., Wood J., Dagnew R.E., Guan D., London S.E., Clayton D.F., Mello C.V., Friedrich S.R., Lovell P.V., Osipova E., Al-Ajli F.O., Secomandi S., Kim H., Theofanopoulou C., Hiller M., Zhou Y., Harris R.S., Makova K.D., Medvedev P., Hoffman J., Masterson P., Clark K., Martin F., Howe K., Flicek P., Walenz B.P., Kwak W., Clawson H., Diekhans M., Nassar L., Paten B., Kraus R.H., Crawford A.J., Gilbert M.T., Zhang G., Venkatesh B., Murphy R.W., Koepfli K.P., Shapiro B., Johnson W.E., Di Palma F., Marques-Bonet T., Teeling E.C., Warnow T., Graves J.M., Ryder O.A., Haussler D., O’Brien S.J., Korlach J., Lewin H.A., Howe K., Myers E.W., Durbin R., Phillippy A.M, & Jarvis E.D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737-746.
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Publication 2021
Cattle Cichlids Females Finches Genome Lynx Males Perch Platypus, Duckbilled Rhinolophus Skates (Fish) Tortoises TRIO protein, human Zebras
5
Comprehensive Cichlid Isoform Annotation
Gene isoforms in the six species of cichlids were extracted from the assembled transcriptomes using ANGSD (Korneliussen etal. 2014 (link)) and BEDTools (Quinlan and Hall 2010 (link)). TransDecoder (http://transdecoder.github.io) was used to de novo annotate open reading frames ORFs in the expressed transcripts to ensure that they contained viable coding sequences (CDS). NCBI BLAST (Altschul etal. 1990 (link)) was used to align these CDS sequences to two related species of fish, Danio rerio and Gasterosteus aculeatus.
Singh P., Börger C., More H, & Sturmbauer C. (2017). The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation. Genome Biology and Evolution, 9(10), 2764-2781.
Publication 2017
Cichlids Exons Fishes Genes Open Reading Frames Protein Isoforms Transcriptome Zebrafish

Most recents protocols related to «Cichlids»

1
Nile Tilapia Genome Variant Calling
DNA-sequencing data per individual were quality filtered and adapters removed with Trimmomatic V0.36 (Bolger et al. 2014 (link)) in PE mode with the settings adapterfile:2:30:12:8:true MINLEN:30. Reads were mapped against the Nile tilapia (Oreochromis niloticus) genome assembly version 2 (RefSeq accession number GCF_001858045.1_ASM185804v2), which was the only cichlid genome assembly on chromosomal level available to us at the time. Prior to mapping, unplaced scaffolds of this genome assembly were concatenated lexicographically into an “UNPLACED” super chromosome. This customized reference was indexed with BWA V0.7.13 and individual DNA reads were aligned against it with bwa-mem under default parameters (Li and Durbin 2009 (link)). Alignments were coordinate-sorted and indexed with SAMtools 1.3.1 (Li et al. 2009 (link)). Variants were called with GATK’s V3.7 (McKenna et al. 2010 (link)) HaplotypeCaller (per individual and per chromosome), GenotypeGVCFs (per chromosome) and CatVariants (to merge all obtained VCF files). The final variants were filtered with GATK's VariantFiltration with settings “QD < 2.0”, “FS > 200.0”, “ReadPosRankSum < −20.0”, “SOR > 10.0”, “DP < 200” and “DP > 4,000” for indels and “MQ < 40.0”, “FS > 60.0”, “QD < 2.0”, “DP < 200”, “DP > 4,000”, ‘SOR > 7.5”, “MQRankSum < −12.5”, and “ReadPosRankSum < −10.0” for SNPs.
Lichilín N., Salzburger W, & Böhne A. (2023). No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni. G3: Genes|Genomes|Genetics, 13(3), jkad011.
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Publication 2023
Chromosomes Cichlids Genome INDEL Mutation Oreochromis niloticus Single Nucleotide Polymorphism
2
Nested 12S Metabarcoding for Environmental DNA
Library preparation was carried out following an established 12 S metabarcoding workflow previously developed at the University of Hull, the full protocol applied in this study can be viewed in Appendix S1, however, is summarized below:
Nested metabarcoding of DNA samples using a two‐step PCR protocol was performed at CUT, using multiplex identification (MID) tags in the first and second PCR steps as described in Kitson et al. (2019 (link)). PCR1 was performed in triplicate (3x PCR replicates per sample), amplifying a 106 bp fragment using published 12 S ribosomal RNA (rRNA) primers 12 S‐V5‐F (5′‐ACTGGGATTAGATACCCC‐3′) and 12 S‐V5‐R (5′‐TAGAACAGGCTCCTCTAG‐3′) (Kelly et al., 2014 (link); Riaz et al., 2011 (link)). Alongside DNA extracts PCR‐negative controls (Molecular Grade Water) were used throughout, and positive controls (DNA (0.05 ng μL−1) from the non‐native cichlid Maylandia zebra) were added to each plate outside of the eDNA prep area. All PCR replicates from each plate were pooled together to create sub‐libraries and purified with MagBIND RxnPure Plus magnetic beads (Omega Bio‐tek Inc.), following a double size selection protocol (Quail et al., 2009 (link)). Following this, a second shuttle PCR (PCR2) was performed on the PCR1 cleaned products to bind uniquely indexed Illumina adapters to each sub‐library. A second purification was then carried out on the PCR2 products with the Mag‐BIND RxnPure Plus magnetic beads (Omega Bio‐tek Inc.). Eluted DNA was then stored at 4°C until quantification and normalization. After normalization and pooling, the final library was then purified again (following the same protocol as the second clean‐up), quantified by qPCR using the NEBNext Library Quant Kit for Illumina (New England Biolabs Inc., Ipswich, MA, USA) and diluted to 4 nM. The final library was then loaded (with 10% PhiX) and sequenced on an Illumina MiSeq using a MiSeq Reagent Kit v3 (600 cycle) (Illumina Inc.) at CUT.
Sub‐library sequence reads were demultiplexed to sample level using a custom Python script. Tapirs, a reproducible workflow for the analysis of DNA metabarcoding data (https://github.com/EvoHull/Tapirs), was then used for taxonomic assignment of demultiplexed sequence reads. Reads were quality trimmed, merged, and clustered before taxonomic assignment against a curated national fish reference database. Taxonomic assignment used a lowest common ancestor approach based on basic local alignment search tool (BLAST) matches with minimum identity set at 98%. The full bioinformatics workflow is detailed in Appendix S1.
Griffiths N.P., Wright R.M., Hänfling B., Bolland J.D., Drakou K., Sellers G.S., Zogaris S., Tziortzis I., Dörflinger G, & Vasquez M.I. (2023). Integrating environmental DNA monitoring to inform eel (Anguilla anguilla) status in freshwaters at their easternmost range—A case study in Cyprus. Ecology and Evolution, 13(2), e9800.
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Publication 2023
Cichlids DNA, A-Form DNA, Environmental DNA Library Fishes Python Quail Ribosomes RNA primers Zebras
3
Fish Diversity and Fishing in the Upper Lufira River Basin
This study was conducted in the Upper Lufira River Basin (altitude: 1114–1160 m a.s.l.) (Fig. 1), which is localized across the mining hinterland area in the west of Haut-Katanga Province (in the south of the former Katanga Province). The climate type is equatorial savanna with a dry winter (type AW6: A, equatorial climate region; W, desert) following the classification of Köppen [43 ] and a rainy tropical climate with a rainy season extending from November to April [44 ]. Most precipitation falls from December to March [45 ]. The Upper Lufira River Basin is characterized by a great diversity of fish species, including members of the families Alestidae, Anabantidae, Amphilidae, Auchenoglanididae, Characidae, Clariidae, Cichlidae, Cyprinidae, Cyprinodontidae, Distichodontidae, Mochokidae, Mormyridae and Schilbeidae [46 , 47 ]. There is organized small-scale fishing for Coptodon rendalli (Boulenger, 1896), Oreochromis mweruensis Trewavas, 1983, Serranochromis macrocephalus Boulenger, 1899, Clarias gariepinus (Burchell, 1822) and Clarias ngamensis (Castelnau, 1861) [48 ]. Caught fishes are intended for human consumption, for a small part by the local population around the Upper Lufira River Basin and for most part by residents of bigger towns, such as Likasi and Lubumbashi.

Map of sampling sites in the Upper Lufira River Basin: along the Lufira River (Kaboko: 11°4′31.60″ S, 26°55′2.40″ E; Buta: 11°2′21.60″ S, 26°57′23.10″ E) and bordering two stretches of the Lufira River that have been dammed: Lake Tshangalele (Kisunka: 10°50′52.10″ S, 26°57′50.60″ E; Kapolowe Mission: 10°54′59.50″ S, 26°58′17.70″ E; Yuka: 10°56′25.30″ S, 26°58′53.40″ E; Mulandi: 10°57′36.64″ S, 27°6′44.88″ E) and Lake Koni (Koni: 10°43′3.65″ S, 27°17′3.24″ E)

Kasembele G.K., Manda A.C., Abwe E., Pariselle A., Bukinga F.M., Huyse T., Jorissen M.W., Vreven E.J., Luus-Powell W.J., Smit W.J., Sara J.R., Snoeks J, & Vanhove M.P. (2023). First record of monogenean fish parasites in the Upper Lufira River Basin (Democratic Republic of Congo): dactylogyrids and gyrodactylids infesting Oreochromis mweruensis, Coptodon rendalli and Serranochromis macrocephalus (Teleostei: Cichlidae). Parasites & Vectors, 16, 48.
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Publication 2023
Characidae Cichlids Climate Cyprinidae Cyprinodontidae Family Member Fishes Homo sapiens Macrocephaly Mormyridae Rain Rivers Tropical Climate
4
Ae. aegypti Rearing and Synchronization
The Ae. aegypti CR and ROCK strains were maintained with a 12 h light:dark photoperiod at 27°C and 80% relative humidity. Larvae were fed 1 pellet of Cichlid Gold® Fish Food (Hikari , Himeji, Japan) per 50 larvae [69 (link)]. Eggs were vacuum hatched in a 1L flask in diH2O for 30 minutes to maximize synchronized development. After 24 h, larvae were sorted to a density of 200 larvae/1L of diH2O. After eclosion, mosquitoes were maintained on 10% sucrose using cotton wicks.
Jacobs E., Chrissian C., Rankin-Turner S., Wear M., Camacho E., Scott J.G., Broderick N.A., McMeniman C.J., Stark R.E, & Casadevall A. (2023). Cuticular profiling of insecticide resistant Aedes aegypti. bioRxiv.
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Publication Preprint 2023
Cichlids Culicidae Eggs Food Gold Gossypium Humidity Larva Light Strains Sucrose Vacuum
5
Optimizing Aedes aegypti Larval Rearing
Ae. aegypti (Florida strain, F15-19 originating from Fort Myers, Florida) eggs were hatched under a vacuum for 1500 s, provided with a pinch of ground fish diet (Cichlid gold, Hikari, Kasai, Japan). At 20 hours post-hatch, 1st instar larvae were pooled and counted into small, medium, and large containers (Table 1).
First, we counted larvae into containers to maintain a constant density of 0.20 larva/ml. We manipulated diet amount available in these containers by providing larvae with 0.10, 0.30, 0.50 mg diet/larva daily (hereafter referred to as low, medium, and high) each day until the last larvae pupated. Diet was powdered finely to avoid particles settling on the floor of the container and was distributed evenly across the container. There were five replicate containers per food amount (Table 1).
Secondly, larvae were reared using these same container sizes at either low (0.20 larvae/ml) or high (1.40 larvae/ml) density. These densities are in line with previous studies capturing density dependent effects in Ae. aegypti (S1 Table). In pilot experiments, there was no increase in winglength when larvae were provided more than 0.70 mg/larva/day (S1 Fig). Trays were provided with a surplus of diet (>3.5 mg/larva/day). This is seven times the amount of diet/ml presented in the ‘high’ diet treatment from the first experiment. After 7 days, water from containers was replaced each day prior to feeding to prevent fouling [21 ]. There were four to five replicates per density/container size treatment (Table 2). In all experiments, the diet in each tub was spread evenly across the surface of the water.
Qureshi A., Keen E., Brown G, & Cator L. (2023). The size of larval rearing container modulates the effects of diet amount and larval density on larval development in Aedes aegypti. PLOS ONE, 18(1), e0280736.
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Publication 2023
Cichlids Diet DNA Replication Eggs Fishes Gold Larva Strains Vacuum

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More about "Cichlids"

Cichlids are a diverse family of freshwater fish, known for their vibrant colors, complex social behaviors, and remarkable evolutionary adaptations.
These tropical fish are predominantly found in Africa and the Americas, with over 1,700 species ranging from the diminutive dwarf cichlids to the impressive Malawi cichlids.
Cichlids are a popular choice in the aquarium hobby, captivating hobbyists with their stunning appearances and intricate parental care.
These fish play a significant role in many regional ecosystems, making them a focal point for research in fields such as behavioral ecology, evolutionary biology, and conservation biology.
When studying cichlids, researchers may utilize various tools and techniques, including Antibiotic–antimycotic solution, MS-222 (a fish anesthetic), DAPI (a fluorescent stain for nucleic acids), X-Tek HMXST 225 (a micro-CT scanning system), Alexa Fluor 488 conjugated Donkey anti-mouse secondary antibody (for immunofluorescence), FBS (Fetal Bovine Serum), Fetal calf serum, and CSM1816 cryostat (for tissue sectioning).
The use of RNAlater, a RNA stabilization reagent, can also be beneficial for preserving genetic samples.
PubCompare.ai's AI-driven platform can assist researchers in optimizing their cichlid studies by providing access to a wide range of protocols from literature, pre-prints, and patents.
The platform's intelligent comparisons can help identify the best protocols and products for specific research needs, enhancing reproducibility and accuracy.