1
|
Martins C, Jehangir M. A genomic glimpse of B chromosomes in cichlids. Genes Genomics 2021; 43:199-208. [PMID: 33547625 DOI: 10.1007/s13258-021-01049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND B chromosomes (Bs) are extra karyotype elements in addition to A chromosomes and are found in all major eukaryotic taxa. Among hundreds of investigated species, cichlid fishes have emerged as an interesting group of model and have contributed to unravel the complex biology of B chromosome. OBJECTIVE We review the current state of knowledge on B chromosome investigation in cichlid fish and discuss the recent genomic advances over gene and sequences hunting on Bs and their impact on the current concept of B chromosomes. RESULTS The Bs of cichlids have been under the subject of classical cytogenetics and high scale DNA, RNA and epigenetics analysis and a list of B chromosome genes and functional sequences has been generated. B chromosomes of cichlids are restricted to females in some species and are enriched with genes, relics of genes, transposable elements and sequences transcribing for many significant biological functions. Diverse potentially functional sequences have been described in the B chromosome of cichlids and could influence important biological characteristics as well seems to affect transcription and epigenetic modifications of the whole genome. CONCLUSION One of the most enigmatic characteristics of Bs in cichlids is their genic content related to cell cycle and chromosome structure, and their influence over sex rates. The relationship of Bs with cell cycle and sex determination looks like to be connected with the drive of the Bs during cell divisions.
Collapse
Affiliation(s)
- Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| |
Collapse
|
2
|
Clark FE, Kocher TD. Changing sex for selfish gain: B chromosomes of Lake Malawi cichlid fish. Sci Rep 2019; 9:20213. [PMID: 31882583 PMCID: PMC6934658 DOI: 10.1038/s41598-019-55774-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/02/2019] [Indexed: 01/16/2023] Open
Abstract
B chromosomes are extra, non-essential chromosomes present in addition to the normal complement of A chromosomes. Many species of cichlid fish in Lake Malawi carry a haploid, female-restricted B chromosome. Here we show that this B chromosome exhibits drive, with an average transmission rate of 70%. The offspring of B-transmitting females exhibit a strongly female-biased sex ratio. Genotyping of these offspring reveals the B chromosome carries a female sex determiner that is epistatically dominant to an XY system on linkage group 7. We suggest that this sex determiner evolved to enhance the meiotic drive of the B chromosome. This is some of the first evidence that female meiotic drive can lead to the invasion of new sex chromosomes solely to benefit the driver, and not to compensate for skewed sex ratios.
Collapse
Affiliation(s)
- Frances E Clark
- Department of Biology, University of Maryland College Park, College Park, MD, 20742, USA.
| | - Thomas D Kocher
- Department of Biology, University of Maryland College Park, College Park, MD, 20742, USA
| |
Collapse
|
3
|
Coan RLB, Martins C. Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata. Genes (Basel) 2018; 9:genes9060269. [PMID: 29882892 PMCID: PMC6027319 DOI: 10.3390/genes9060269] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/26/2022] Open
Abstract
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome.
Collapse
Affiliation(s)
- Rafael L B Coan
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
| |
Collapse
|
4
|
Perazzo GX, Noleto RB, Vicari MR, Gava A, Cestari MM. B chromosome polymorphism in South American cichlid. NEOTROPICAL BIODIVERSITY 2018. [DOI: 10.1080/23766808.2018.1429164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
| | - Rafael Bueno Noleto
- Department of Biology, State University of Paraná, União da Vitória, Paraná, Brazil
| | - Marcelo Ricardo Vicari
- Department of Structural, Molecular and Genetical Biology, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Adriana Gava
- Biological Sciences Institute, Federal University of Rio Grande, Rio Grande, Brazil
| | | |
Collapse
|
5
|
Carmello BO, Coan RLB, Cardoso AL, Ramos E, Fantinatti BEA, Marques DF, Oliveira RA, Valente GT, Martins C. The hnRNP Q-like gene is retroinserted into the B chromosomes of the cichlid fish Astatotilapia latifasciata. Chromosome Res 2017; 25:277-290. [PMID: 28776210 DOI: 10.1007/s10577-017-9561-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 11/27/2022]
Abstract
B chromosomes are dispensable elements observed in many eukaryotic species, including the African cichlid Astatotilapia latifasciata, which might have one or two B chromosomes. Although there have been many studies focused on the biology of these chromosomes, questions about the evolution, maintenance, and potential effects of these chromosomes remain. Here, we identified a variant form of the hnRNP Q-like gene inserted into the B chromosome of A. latifasciata that is characterized by a high copy number and intron-less structure. The absence of introns and presence of transposable elements with a reverse transcriptase domain flanking hnRNP Q-like sequences suggest that this gene was retroinserted into the B chromosome. RNA-Seq analysis did not show that the B variant retroinserted copies are transcriptionally active. However, RT-qPCR results showed variations in the canonical hnRNP Q-like copy expression levels among exons, tissues, sex, and B presence/absence. Although the patterns of transcription are not well understood, the exons of the B retrocopies were overexpressed, and a bias for female B+ expression was also observed. These results suggest that retroinsertion is an additional and important mechanism contributing to B chromosome formation. Furthermore, these findings indicate a bias towards female differential expression of B chromosome sequences, suggesting that B chromosomes and sex determination are somehow associated in cichlids.
Collapse
Affiliation(s)
- Bianca O Carmello
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Rafael L B Coan
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Bruno E A Fantinatti
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Diego F Marques
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Rogério A Oliveira
- Institute of Biosciences, Department of Biostatistics, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Guilherme T Valente
- Institute of Biosciences, Agronomic Science School, Department of Bioprocess and Biotechnology, Sao Paulo State University (UNESP), Botucatu, SP, 18610-307, Brazil
| | - Cesar Martins
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| |
Collapse
|
6
|
Clark FE, Conte MA, Ferreira-Bravo IA, Poletto AB, Martins C, Kocher TD. Dynamic Sequence Evolution of a Sex-Associated B Chromosome in Lake Malawi Cichlid Fish. J Hered 2016; 108:53-62. [PMID: 27630131 DOI: 10.1093/jhered/esw059] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/26/2016] [Indexed: 12/16/2022] Open
Abstract
B chromosomes are extra chromosomes found in many species of plants, animals, and fungi. B chromosomes often manipulate common cellular processes to increase their frequency, sometimes to the detriment of organismal fitness. Here, we characterize B chromosomes in several species of Lake Malawi cichlid fish. Whole genome sequencing of Metriaclima zebra "Boadzulu" individuals revealed blocks of sequence with unusually high sequence coverage, indicative of increased copy number of those sequences. These regions of high sequence coverage were found only in females. SNPs unique to the high copy number sequences permitted the design of specific amplification primers. These primers amplified fragments only in Metriaclima lombardoi individuals that carried a cytologically identified B chromosome (B-carriers), indicating these extra copies are located on the B chromosome. These same primers were used to identify B-carrying individuals in additional species from Lake Malawi. Across 7 species, a total of 43 B-carriers were identified among 323 females. B-carriers were exclusively female; no B chromosomes were observed in the 317 males surveyed from these species. Quantitative analysis of the copy number variation of B-specific sequence blocks suggests that B-carriers possess a single B chromosome, consistent with previous karyotyping of M. lombardoi A single B chromosome in B-carriers is consistent with 2 potential drive mechanisms: one involving nondisjunction and preferential segregation in a mitotic division prior to the germ-line, and the other involving preferential segregation during meiosis I.
Collapse
Affiliation(s)
- Frances E Clark
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Matthew A Conte
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Irani A Ferreira-Bravo
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Andreia B Poletto
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Cesar Martins
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Thomas D Kocher
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins).
| |
Collapse
|
7
|
Ramos É, Cardoso AL, Brown J, Marques DF, Fantinatti BEA, Cabral-de-Mello DC, Oliveira RA, O'Neill RJ, Martins C. The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. Chromosoma 2016; 126:313-323. [PMID: 27169573 DOI: 10.1007/s00412-016-0601-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/03/2016] [Accepted: 05/03/2016] [Indexed: 12/27/2022]
Abstract
Supernumerary chromosomes have been studied in many species of eukaryotes, including the cichlid fish, Astatotilapia latifasciata. However, there are many unanswered questions about the maintenance, inheritance, and functional aspects of supernumerary chromosomes. The cichlid family has been highlighted as a model for evolutionary studies, including those that focus on mechanisms of chromosome evolution. Individuals of A. latifasciata are known to carry up to two B heterochromatic isochromosomes that are enriched in repetitive DNA and contain few intact gene sequences. We isolated and characterized a transcriptionally active repeated DNA, called B chromosome noncoding DNA (BncDNA), highly represented across all B chromosomes of A. latifasciata. BncDNA transcripts are differentially processed among six different tissues, including the production of smaller transcripts, indicating transcriptional variation may be linked to B chromosome presence and sexual phenotype. The transcript lengths and lack of similarity with known protein/gene sequences indicate BncRNA might represent a novel long noncoding RNA family (lncRNA). The potential for interaction between BncRNA and known miRNAs were computationally predicted, resulting in the identification of possible binding of this sequence in upregulated miRNAs related to the presence of B chromosomes. In conclusion, Bnc is a transcriptionally active repetitive DNA enriched in B chromosomes with potential action over B chromosome maintenance in somatic cells and meiotic drive in gametic cells.
Collapse
Affiliation(s)
- Érica Ramos
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Adauto L Cardoso
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Judith Brown
- Allied Health Sciences Department and Institute for Systems Genomics, University of Connecticut, 06269, Storrs, CT, USA
| | - Diego F Marques
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Bruno E A Fantinatti
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Diogo C Cabral-de-Mello
- Department of Biology, Institute of Biosciences, Sao Paulo State University, 13506-900, Rio Claro, SP, Brazil
| | - Rogério A Oliveira
- Department of Biostatistics, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, 06269, Storrs, CT, USA
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil.
| |
Collapse
|
8
|
Pires LB, Sampaio TR, Dias AL. Mitotic and Meiotic Behavior of B Chromosomes in Crenicichla lepidota: New Report in the Family Cichlidae. J Hered 2015; 106:289-95. [PMID: 25790829 DOI: 10.1093/jhered/esv007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 01/30/2015] [Indexed: 11/14/2022] Open
Abstract
B chromosomes are additional genetic elements to the standard complement. They display distinctive features and have been found in 15% of eukaryote species. In this study, we analyzed 4 populations of Crenicichla lepidota from hydrographic system of Laguna dos Patos/RS (Brazil). All specimens showed 2n = 48 with 6m + 42st - a, FN = 54, with a secondary constriction on the first pair of the complement. Among the 18 samples analyzed, 6 individuals belonging to the Gasômetro and Saco da Alemoa populations presented 1-3 small-sized heterochromatic B chromosomes, with intra- and interindividual variation. Simple AgNORs coincident with 18S rDNA and CMA3 positive/DAPI negative sites were present in all populations. The extra chromosomes did not exhibit any 18S rDNA sites. The meiotic analyses showed heteropycnotic regions in leptotene and zygotene stages, which may be related to the presence of B chromosomes. During pachytene were found 24 bivalents and 1 spatially separated, as well as during metaphases I and diplotene, indicating that there is no association between B chromosomes and those of the A complement. During diakinesis, an unusual meiotic configuration was observed, revealing a proximity between the bivalent and chromosome B (univalent), that might be the result of a heterochromatin affinity between these chromosomes. In anaphase I, late migration of B chromosomes was detected. The low frequency of B chromosomes in the Cichlidae family and in Crenicichla suggests its recent origin in this group and may be ascribable to animal exposure to deleterious effects under certain environmental conditions. Moreover, this is the first report in C. lepidota.
Collapse
Affiliation(s)
- Larissa B Pires
- From the Depto de Biologia Geral, Universidade Estadual de Londrina, CCB, CEP 86051-970, Caixa Postal 6001, Londrina, Paraná, Brazil (Pires, Sampaio, and Dias)
| | - Tatiane R Sampaio
- From the Depto de Biologia Geral, Universidade Estadual de Londrina, CCB, CEP 86051-970, Caixa Postal 6001, Londrina, Paraná, Brazil (Pires, Sampaio, and Dias)
| | - Ana Lucia Dias
- From the Depto de Biologia Geral, Universidade Estadual de Londrina, CCB, CEP 86051-970, Caixa Postal 6001, Londrina, Paraná, Brazil (Pires, Sampaio, and Dias).
| |
Collapse
|
9
|
A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids. Gene 2015; 560:156-64. [PMID: 25639358 DOI: 10.1016/j.gene.2015.01.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 01/06/2023]
Abstract
Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity.
Collapse
|
10
|
Makunin AI, Dementyeva PV, Graphodatsky AS, Volobouev VT, Kukekova AV, Trifonov VA. Genes on B chromosomes of vertebrates. Mol Cytogenet 2014; 7:99. [PMID: 25538793 PMCID: PMC4274688 DOI: 10.1186/s13039-014-0099-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/05/2014] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND There is a growing body of evidence that B chromosomes, once regarded as totally heterochromatic and genetically inert, harbor multiple segmental duplications containing clusters of ribosomal RNA genes, processed pseudogenes and protein-coding genes. Application of novel molecular approaches further supports complex composition and possible phenotypic effects of B chromosomes. RESULTS Here we review recent findings of gene-carrying genomic segments on B chromosomes from different vertebrate groups. We demonstrate that the genetic content of B chromosomes is highly heterogeneous and some B chromosomes contain multiple large duplications derived from various chromosomes of the standard karyotype. Although B chromosomes seem to be mostly homologous to each other within a species, their genetic content differs between species. There are indications that some genomic regions are more likely to be located on B chromosomes. CONCLUSIONS The discovery of multiple autosomal genes on B chromosomes opens a new discussion about their possible effects ranging from sex determination to fitness and adaptation, their complex interactions with host genome and role in evolution.
Collapse
Affiliation(s)
- Alexey I Makunin
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Polina V Dementyeva
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
| | - Alexander S Graphodatsky
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Novosibirsk State University, Novosibirsk, Russia
| | - Vitaly T Volobouev
- />Museum National d’Histoire Naturelle, Origine, Structure et Evolution de la Biodiversite, Paris, France
| | - Anna V Kukekova
- />Department of Animal Sciences, The University of Illinois at Urbana-Champaign, Champaign, USA
| | - Vladimir A Trifonov
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
11
|
Henning F, Meyer A. The evolutionary genomics of cichlid fishes: explosive speciation and adaptation in the postgenomic era. Annu Rev Genomics Hum Genet 2014; 15:417-41. [PMID: 24898042 DOI: 10.1146/annurev-genom-090413-025412] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With more than 1,500 species, cichlid fishes provide textbook examples of recent and diverse adaptive radiations, rapid rates of speciation, and the parallel evolution of adaptive phenotypes among both recently and distantly related lineages. This extraordinary diversity has attracted considerable interest from researchers across several biological disciplines. Their broad phenotypic variation coupled with recent divergence makes cichlids an ideal model system for understanding speciation, adaptation, and phenotypic diversification. Genetic mapping, genome-wide analyses, and genome projects have flourished in the past decade and have added new insights on the question of why there are so many cichlids. These recent findings also show that the sharing of older DNA polymorphisms is extensive and suggest that linage sorting is incomplete and that adaptive introgression played a role in the African radiation. Here, we review the results of genetic and genomic research on cichlids in the past decade and suggest some potential avenues to further exploit the potential of the cichlid model system to provide a better understanding of the genomics of adaptation and speciation.
Collapse
Affiliation(s)
- Frederico Henning
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany;
| | | |
Collapse
|
12
|
Valente GT, Conte MA, Fantinatti BE, Cabral-de-Mello DC, Carvalho RF, Vicari MR, Kocher TD, Martins C. Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses. Mol Biol Evol 2014; 31:2061-72. [DOI: 10.1093/molbev/msu148] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|