1
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Blackmon H, Jonika MM, Alfieri JM, Fardoun L, Demuth JP. Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera. J Hered 2024; 115:173-182. [PMID: 38181226 PMCID: PMC10936555 DOI: 10.1093/jhered/esae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/04/2024] [Indexed: 01/07/2024] Open
Abstract
Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an important role to chromosomal mutations. When the effective population size (Ne) is small, the efficacy of selection is weakened, and the likelihood of fixing underdominant mutations by genetic drift is greater. Thus, it is possible that ecological and phenotypic transitions that modulate Ne facilitate the fixation of chromosome changes, increasing the rate of karyotype evolution. We synthesize all available chromosome number data in Coleoptera and estimate the impact of traits expected to change Ne on the rate of karyotype evolution in the family Carabidae and 12 disparate clades from across Coleoptera. Our analysis indicates that in Carabidae, wingless clades have faster rates of chromosome number increase. Additionally, our analysis indicates clades exhibiting multiple traits expected to reduce Ne, including strict inbreeding, oligophagy, winglessness, and island endemism, have high rates of karyotype evolution. Our results suggest that chromosome number changes are likely fixed by genetic drift despite an initial fitness cost and that chromosomal speciation models may be important to consider in clades with very small Ne.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, United States
| | - Michelle M Jonika
- Department of Biology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
| | - James M Alfieri
- Department of Biology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, United States
| | - Leen Fardoun
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Jeffery P Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
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2
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Xu X, Wang C, Xu C, Yuan J, Wang G, Wu Y, Huang C, Jing H, Yang P, Xu L, Peng S, Shan F, Xia X, Jin F, Hou F, Wang J, Mi D, Ren Y, Liu Y, Irwin DM, Li X, Chen W, Li G. Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii). Mol Ecol Resour 2024; 24:e13896. [PMID: 37955396 DOI: 10.1111/1755-0998.13896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome-wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.
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Affiliation(s)
- Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yajiang Wu
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Shiming Peng
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Fen Shan
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Xiaochao Xia
- Guangdong Wildlife Monitoring, Rescue and Conservation Center, Guangzhou, China
| | - Fuyuan Jin
- Guangdong Maoming Forest Park Administrative Office, Maoming, China
| | - Fanghui Hou
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an, China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- Guangzhou Zoo, Guangzhou, China
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3
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dos Santos AG, Souza JFDSE, Soares SC, Nakayama CM, Feldberg E. Chromosomal characterization of three species of Serrasalmini (Serrasalmidae: Characiformes). Genet Mol Biol 2023; 46:e20230088. [PMID: 37992304 PMCID: PMC10664975 DOI: 10.1590/1678-4685-gmb-2023-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
The tribe Serrasalmini is a diverse group with paraphyletic genera and taxonomic uncertainties. Several studies have been carried out in this group of fish in order to understand this problem, including the cytogenetic approach. In this study, three species of a clade of Serrasalmini were characterized cytogenetically - Pristobrycon striolatus, Catoprion absconditus and Pygopristis denticulatus. The three species presented diploid number (2n) equal to 62 chromosomes, of one and two arms, with karyotypic formulas and species-specific fundamental numbers. Heterochromatin is centromeric and terminal (bi-telomeric) in most chromosomes, with a conspicuous interstitial block at pair 1 (m) in all three species. The nucleolar organizer regions were multiple and C-band positive, and their location was confirmed via 18S ribosomal DNA mapping; however, with additional sites. The 5S rDNA was located in interstitial region of long arm of pair 1 (m), in the three species (homeologous). Moreover, we observed synteny between 18S and 5S in the species C. absconditus and P. denticulatus, which, according to fiber-FISH, are interspersed. Thus, the maintenance of 2n (62) evidences the diversification of chromosomal formulas within the clade by non-Robertsonian rearrangements and reflects the paraphyly of the related species.
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Affiliation(s)
- Alan Gomes dos Santos
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
| | - José Francisco de Sousa e Souza
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
| | - Simone Cardoso Soares
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
| | - Celeste Mutuko Nakayama
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de
Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de
Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
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4
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Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. Evolution 2023; 77:2504-2511. [PMID: 37738212 DOI: 10.1093/evolut/qpad169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/04/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years-the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.
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Affiliation(s)
- Melissa A Toups
- Department of Life and Environmental Sciences, Bournemouth University, Poole, United Kingdom
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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5
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Li A, Yang Q, Li R, Dai X, Cai K, Lei Y, Jia K, Jiang Y, Zan L. Chromosome-level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity. Mol Ecol 2023; 32:1323-1334. [PMID: 35467052 DOI: 10.1111/mec.16483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/29/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The takin (Budorcas taxicolor) is one of the largest bovid herbivores in the subfamily Caprinae. The takin is at high risk of extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed the first reference genome of Bu. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb, which were anchored onto 25+XY chromosomes. We found that the takin was more closely related to muskox than to other Caprinae species. Compared to the common ancestral karyotype of bovidae (2n = 60), we found the takin (2n = 52) experienced four chromosome fusions and one large translocation. Furthermore, we resequenced nine golden takins from the main distribution area, the Qinling Mountains, and identified 3.3 million single nucleotide polymorphisms. The genetic diversity of takin was very low (θπ = 0.00028 and heterozygosity =0.00038), among the lowest detected in domestic and wild mammals. Takin genomes showed a high inbreeding coefficient (FROH =0.217), suggesting severe inbreeding depression. The demographic history showed that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into their evolution.
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Affiliation(s)
- Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qimeng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuelei Dai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Keli Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinghu Lei
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Kangsheng Jia
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
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6
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Schott SCQ, Glugoski L, Azambuja M, Moreira-Filho O, Vicari MR, Nogaroto V. Comparative Cytogenetic and Sequence Analysis of U Small Nuclear RNA Genes in Three Ancistrus Species (Siluriformes: Loricariidae). Zebrafish 2022; 19:200-209. [PMID: 36099209 DOI: 10.1089/zeb.2022.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ancistrus presents a wide karyotypic diversity, resulting from numeric and structural chromosomal rearrangements. It has been proposed that some genome-specific regions containing repetitive units could organize prone-to-break DNA sites in Loricariidae, triggering chromosomal rearrangements such as Robertsonian fusions (Rb fusions), centric fissions, translocations, and inversions. The tandemly repeats of the small nuclear RNAs (snRNAs) gene families are considered good cytogenetic markers for understanding chromosomal remodeling events among closely related species, but these snRNAs have been scarcely analyzed in Ancistrus. This study presented the nucleotide sequencing and comparative in situ location of U snRNA sequences from Ancistrus aguaboensis, Ancistrus cf. multispinis, and Ancistrus sp. (2n = 50, 52, and 50, respectively), aiming to provide information about snRNA clusters in the genome and chromosome evolution in Ancistrus. U snRNA nucleotide sequences of Ancistrus presented identity to orthologous copies and folded their secondary structures correctly. In situ localization and karyotyping of the three Ancistrus species revealed clustered copies of U2 and U5 snRNA gene families to a single chromosome site, one chromosome pair bearing U1 snRNA sequence, and one main locus of U4 snRNA sequence, besides scattered signals along the chromosomes. Previous studies related the participation of the rRNA gene families in centric fusion events, contributing to chromosome rearrangements and karyotype plasticity present in Loricariidae. In this study, homeologies in U snRNA loci chromosomal locations were detected, indicating the occurrence of conserved sites of these gene families in these three Ancistrus species with 2n = 50 or 52 chromosomes.
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Affiliation(s)
| | - Larissa Glugoski
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Matheus Azambuja
- Departamento de Genética, Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
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7
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Steinberg ER, Bressa MJ, Mudry MD. Sex chromosome systems in Neotropical Primates: What have we learnt so far from cytogenetics and genomics? J Evol Biol 2022; 35:1589-1600. [PMID: 35731796 DOI: 10.1111/jeb.14039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/10/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022]
Abstract
Neotropical Primates (Platyrrhini) show great diversity in their life histories, ecology, behaviour and genetics. This diversity extends to their chromosome complements, both to autosomes and to sex chromosomes. In this contribution, we will review what is currently known about sex chromosomes in this group, both from cytogenetic and from genomic evidence. The X and Y chromosomes in Neotropical Primates, also known as New World Monkeys, have striking structural differences compared with Old World Monkeys when Catarrhini sex chromosomes are considered. The XY bivalent displays a different meiotic behaviour in prophase I, and their Y chromosome shows extensive genomic differences. Even though the most widespread sex chromosome system is the XX/XY and thus considered the ancestral one for Platyrrhini, modifications of this sexual system are observed within this group. Multiple sex chromosome systems originated from Y-autosome translocations were described in several genera (Aotus, Callimico and Alouatta). In the howler monkeys, genus Alouatta, an independent origin of the sexual systems in South American and Mesoamerican species was postulated. All the above-mentioned evidence suggests that the Y chromosome of Platyrrhini has a different evolutionary history compared with the Catarrhini Y. There is still much to understand regarding their sex chromosome systems.
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Affiliation(s)
- Eliana Ruth Steinberg
- Grupo de Investigación en Biología Evolutiva (GIBE). Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - María José Bressa
- Grupo de Citogenética de Insectos. Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Marta Dolores Mudry
- Grupo de Investigación en Biología Evolutiva (GIBE). Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología, Genética y Evolución (EGE), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
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8
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Lv M, Zhang Y, Liu K, Li C, Wang J, Fan G, Liu X, Yang H, Liu C, Mahboob S, Liu J, Shao C. A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon. Front Genet 2020; 11:581161. [PMID: 33329719 PMCID: PMC7729161 DOI: 10.3389/fgene.2020.581161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
Anglerfishes are a highly diverse group of species with unique characteristics. Here, we report the first chromosome-level genome of a species in the order Lophiiformes, the yellow goosefish (Lophius litulon), obtained by whole genome shotgun sequencing and high-throughput chromatin conformation capture. Approximately 97.20% of the assembly spanning 709.23 Mb could be anchored to 23 chromosomes with a contig N50 of 164.91 kb. The BUSCO value was 95.4%, suggesting that the quality of the assembly was high. A comparative gene family analysis identified expanded and contracted gene families, and these may be associated with adaptation to the benthic environment and the lack of scales in the species. A majority of positively selected genes were related to metabolic processes, suggesting that digestive and metabolic system evolution expanded the diversity of yellow goosefish prey. Our study provides a valuable genetic resource for understanding the mechanisms underlying the unique features of the yellow goosefish and for investigating anglerfish evolution.
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Affiliation(s)
- Meiqi Lv
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Changlin Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shahid Mahboob
- Department of Zoology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Junnian Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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9
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Zattera ML, Gazolla CB, Soares ADA, Gazoni T, Pollet N, Recco-Pimentel SM, Bruschi DP. Evolutionary Dynamics of the Repetitive DNA in the Karyotypes of Pipa carvalhoi and Xenopus tropicalis (Anura, Pipidae). Front Genet 2020; 11:637. [PMID: 32793276 PMCID: PMC7385237 DOI: 10.3389/fgene.2020.00637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023] Open
Abstract
The large amphibian genomes contain numerous repetitive DNA components that have played an important role in the karyotypic diversification of this vertebrate group. Hypotheses based on the presumable primitive karyotype (2n = 20) of the anurans of the family Pipidae suggest that they have evolved principally through intrachromosomal rearrangements. Pipa is the only South American pipid, while all the other genera are found in Africa. The divergence of the South American lineages from the African ones occurred at least 136 million years ago and is thought to have had a strong biogeographic component. Here, we tested the potential of the repetitive DNA to enable a better understanding of the differentiation of the karyotype among the family Pipidae and to expand our capacity to interpret the chromosomal evolution in this frog family. Our results indicate a long history of conservation in the chromosome bearing the H3 histone locus, corroborating inferences on the chromosomal homologies between the species in pairs 6, 8, and 9. The chromosomal distribution of the microsatellite motifs also provides useful markers for comparative genomics at the chromosome level between Pipa carvalhoi and Xenopus tropicalis, contributing new insights into the evolution of the karyotypes of these species. We detected similar patterns in the distribution and abundance of the microsatellite arrangements, which reflect the shared organization in the terminal/subterminal region of the chromosomes between these two species. By contrast, the microsatellite probes detected a differential arrangement of the repetitive DNA among the chromosomes of the two species, allowing longitudinal differentiation of pairs that are identical in size and morphology, such as pairs 1, 2, 4, and 5. We also found evidence of the distinctive composition of the repetitive motifs of the centromeric region between the species analyzed in the present study, with a clear enrichment of the (CA) and (GA) microsatellite motifs in P. carvalhoi. Finally, microsatellite enrichment in the pericentromeric region of chromosome pairs 6, 8, and 9 in the P. carvalhoi karyotype, together with interstitial telomeric sequences (ITS), validate the hypothesis that pericentromeric inversions occurred during the chromosomal evolution of P. carvalhoi and reinforce the role of the repetitive DNA in the remodeling of the karyotype architecture of the Pipidae.
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Affiliation(s)
- Michelle Louise Zattera
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Camilla Borges Gazolla
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Amanda de Araújo Soares
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Thiago Gazoni
- Universidade Estadual Paulista (Unesp), Campus Rio Claro, Rio Claro, Brazil
| | - Nicolas Pollet
- Laboratoire Evolution Genomes Comportement Ecologie, CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Daniel Pacheco Bruschi
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
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10
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Tapisso JT, Gabriel SI, Cerveira AM, Britton-Davidian J, Ganem G, Searle JB, Ramalhinho MDG, Mathias MDL. Spatial and Temporal Dynamics of Contact Zones Between Chromosomal Races of House Mice, Mus musculus domesticus, on Madeira Island. Genes (Basel) 2020; 11:E748. [PMID: 32640559 DOI: 10.3390/genes11070748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 01/29/2023] Open
Abstract
Analysis of contact zones between parapatric chromosomal races can help our understanding of chromosomal divergence and its influence on the speciation process. Monitoring the position and any movement of contact zones can allow particular insights. This study investigates the present (2012-2014) and past (1998-2002) distribution of two parapatric house mouse chromosomal races-PEDC (Estreito da Calheta) and PADC (Achadas da Cruz)-on Madeira Island, aiming to identify changes in the location and width of their contact. We also extended the 1998-2002 sampling area into the range of another chromosomal race-PLDB (Lugar de Baixo). Clinal analysis indicates no major geographic alterations in the distribution and chromosomal characteristics of the PEDC and PADC races but exhibited a significant shift in position of the Rb (7.15) fusion, resulting in the narrowing of the contact zone over a 10+ year period. We discuss how this long-lasting contact zone highlights the role of landscape on mouse movements, in turn influencing the chromosomal characteristics of populations. The expansion of the sampling area revealed new chromosomal features in the north and a new contact zone in the southern range involving the PEDC and PLDB races. We discuss how different interacting mechanisms (landscape resistance, behaviour, chromosomal incompatibilities, meiotic drive) may help to explain the pattern of chromosomal variation at these contacts between chromosomal races.
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11
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Garcia F, Biedma L, Calzada J, Román J, Lozano A, Cortés F, Godoy JA, Ruiz-Herrera A. Chromosomal Differentiation in Genetically Isolated Populations of the Marsh-Specialist Crocidura suaveolens (Mammalia: Soricidae). Genes (Basel) 2020; 11:E270. [PMID: 32131436 DOI: 10.3390/genes11030270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost limit of its distributional range, in the Gulf of Cádiz (Iberian Peninsula). In this area, C. suaveolens is restricted to genetically isolated populations associated to the tidal marches of five rivers (Guadiana, Piedras, Odiel, Tinto and Guadalquivir). This particular distributional range provides a unique opportunity to investigate whether genetic differentiation and habitat specialization was accompanied by chromosomal variation. In this context, the main objective of this study was to determinate the chromosomal characteristics of the habitat-specialist C. suaveolens in Southwestern Iberia, as a way to understand the evolutionary history of this species in the Iberian Peninsula. A total of 41 individuals from six different populations across the Gulf of Cádiz were collected and cytogenetically characterized. We detected four different karyotypes, with diploid numbers (2n) ranging from 2n = 40 to 2n = 43. Two of them (2n = 41 and 2n = 43) were characterized by the presence of B-chromosomes. The analysis of karyotype distribution across lineages and populations revealed an association between mtDNA population divergence and chromosomal differentiation. C. suaveolens populations in the Gulf of Cádiz provide a rare example of true karyotypic polymorphism potentially associated to genetic isolation and habitat specialization in which to investigate the evolutionary significance of chromosomal variation in mammals and their contribution to phenotypic and ecological divergence.
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Palacios-Gimenez OM, Milani D, Song H, Marti DA, López-León MD, Ruiz-Ruano FJ, Camacho JPM, Cabral-de-Mello DC. Eight Million Years of Satellite DNA Evolution in Grasshoppers of the Genus Schistocerca Illuminate the Ins and Outs of the Library Hypothesis. Genome Biol Evol 2020; 12:88-102. [PMID: 32211863 PMCID: PMC7093836 DOI: 10.1093/gbe/evaa018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2020] [Indexed: 12/21/2022] Open
Abstract
Satellite DNA (satDNA) is an abundant class of tandemly repeated noncoding sequences, showing high rate of change in sequence, abundance, and physical location. However, the mechanisms promoting these changes are still controversial. The library model was put forward to explain the conservation of some satDNAs for long periods, predicting that related species share a common collection of satDNAs, which mostly experience quantitative changes. Here, we tested the library model by analyzing three satDNAs in ten species of Schistocerca grasshoppers. This group represents a valuable material because it diversified during the last 7.9 Myr across the American continent from the African desert locust (Schistocerca gregaria), and this thus illuminates the direction of evolutionary changes. By combining bioinformatic and cytogenetic, we tested whether these three satDNA families found in S. gregaria are also present in nine American species, and whether differential gains and/or losses have occurred in the lineages. We found that the three satDNAs are present in all species but display remarkable interspecies differences in their abundance and sequences while being highly consistent with genus phylogeny. The number of chromosomal loci where satDNA is present was also consistent with phylogeny for two satDNA families but not for the other. Our results suggest eminently chance events for satDNA evolution. Several evolutionary trends clearly imply either massive amplifications or contractions, thus closely fitting the library model prediction that changes are mostly quantitative. Finally, we found that satDNA amplifications or contractions may influence the evolution of monomer consensus sequences and by chance playing a major role in driftlike dynamics.
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Affiliation(s)
- Octavio M Palacios-Gimenez
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Hojun Song
- Department of Entomology, Texas A&M University
| | - Dardo A Marti
- Laboratorio de Genética Evolutiva, IBS, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, CONICET, Posadas, Argentina
| | - Maria D López-León
- Departamento de Genética, Facultad de Ciencias, UGR - Univ de Granada, Spain
| | - Francisco J Ruiz-Ruano
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
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13
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Micolino R, Cristiano MP, Cardoso DC. Karyotype and putative chromosomal inversion suggested by integration of cytogenetic and molecular data of the fungus-farming ant Mycetomoellerius iheringi Emery, 1888. Comp Cytogenet 2020; 14:197-210. [PMID: 32431788 PMCID: PMC7225177 DOI: 10.3897/compcytogen.v14i2.49846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/28/2020] [Indexed: 05/11/2023]
Abstract
Comparative cytogenetic analyses are being increasingly used to collect information on species evolution, for example, diversification of closely related lineages and identification of morphologically indistinguishable species or lineages. Here, we have described the karyotype of the fungus-farming ant Mycetomoellerius iheringi Emery, 1888 and investigated its evolutionary relationships on the basis of molecular and cytogenetic data. The M. iheringi karyotype consists of 2n = 20 chromosomes (2K = 18M + 2SM). We also demonstrated that this species has the classical insect TTAGG telomere organization. Phylogenetic reconstruction showed that M. iheringi is phylogenetically closer to M. cirratus Mayhé-Nunes & Brandão, 2005 and M. kempfi Fowler, 1982. We compared M. iheringi with other congeneric species such as M. holmgreni Wheeler, 1925 and inferred that M. iheringi probably underwent a major pericentric inversion in one of its largest chromosomes, making it submetacentric. We discussed our results in the light of the phylogenetic relationships and chromosomal evolution.
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Affiliation(s)
- Ricardo Micolino
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990,Curitiba, PR, BrazilUniversidade Federal do ParanáCuritibaBrazil
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, BrazilUniversidade Federal de Ouro PretoOuro PretoBrazil
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, BrazilUniversidade Federal de Ouro PretoOuro PretoBrazil
| | - Danon Clemes Cardoso
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990,Curitiba, PR, BrazilUniversidade Federal do ParanáCuritibaBrazil
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, BrazilUniversidade Federal de Ouro PretoOuro PretoBrazil
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14
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Gama JM, Gazolla CB, de Souza DY, Recco-Pimentel SM, Bruschi DP. Recurrent variation in the active NOR sites in the monkey frogs of the genus Pithecopus Cope, 1866 (Phyllomedusidae, Anura). Comp Cytogenet 2019; 13:325-338. [PMID: 31681462 PMCID: PMC6817578 DOI: 10.3897/compcytogen.v13i4.37687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Treefrogs of the genus Pithecopus Cope, 1866 exhibit expressive chromosomal homogeneity which contrasts with a high variation frequency of the nucleolus organizer region (NOR) related to the group. Currently, the genus contains eleven species and no chromosomal data are available on P. palliatus Peters, 1873, P. ayeaye Lutz, 1966 and P. megacephalus Miranda-Ribeiro, 1926. Here, we describe the karyotypes of these three species based on Giemsa staining, C-banding, silver impregnation and in situ hybridization (FISH). We were also analyze the evolutionary dynamic of the NOR-bearing chromosome in species of genus under a phylogenetic view. The results indicate that P. palliatus, P. ayeaye, and P. megacephalus have similar karyotypes, which are typical of the genus Pithecopus. In P. palliatus the NOR was detected in the pericentromeric region of pair 9p whereas in P. ayeaye and P. megacephalus we report cases of the multiple NOR sites in karyotypes. In P. ayeaye the NOR was detected in the pericentromeric region of pair 9p in both homologues and additional sites was detected in pairs 3q, 4p, and 8q, all confirmed by FISH experiments. Already in P. megacephalus the NOR sites were detected in pericentromeric region homologues of pair 8q and additionally in one chromosome of pair 13q. A comparative overview of all the Pithecopus karyotypes analyzed up to now indicates the recurrence of the NOR-bearing chromosome pairs and the position of the NORs sites on these chromosomes. We hypothesized that this feature is a result of a polymorphic condition present in the common ancestor of Pithecopus. In such case, the lineages derived from polymorphic ancestor have reached fixation independently after divergence of lineages, resulting in a high level of homoplasy observed in this marker. Our findings help to fill the gaps in the understanding of the karyotype of the genus Pithecopus and reinforce the role of the evolutionary dynamics of the rDNA genes in karyotype diversification in this group.
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Affiliation(s)
- Joana Moura Gama
- Programa de Pós-Graduação em Genética (PPG-GEN). Departamento de Genética, Universidade Federal do Paraná (UFPR), Setor de Biológicas, Av. Coronel Francisco H. Dos Santos, 100, 81531-980, Curitiba, PR, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Camilla Borges Gazolla
- Programa de Pós-Graduação em Genética (PPG-GEN). Departamento de Genética, Universidade Federal do Paraná (UFPR), Setor de Biológicas, Av. Coronel Francisco H. Dos Santos, 100, 81531-980, Curitiba, PR, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Deborah Yasmin de Souza
- Programa de Pós-Graduação em Genética (PPG-GEN). Departamento de Genética, Universidade Federal do Paraná (UFPR), Setor de Biológicas, Av. Coronel Francisco H. Dos Santos, 100, 81531-980, Curitiba, PR, BrazilUniversidade Federal do ParanáCuritibaBrazil
| | - Shirlei Maria Recco-Pimentel
- Departamento de Biologia Estrutural and Funcional, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária, 13083-863, Campinas, SP, BrazilUniversidade Estadual de CampinasCampinasBrazil
| | - Daniel Pacheco Bruschi
- Programa de Pós-Graduação em Genética (PPG-GEN). Departamento de Genética, Universidade Federal do Paraná (UFPR), Setor de Biológicas, Av. Coronel Francisco H. Dos Santos, 100, 81531-980, Curitiba, PR, BrazilUniversidade Federal do ParanáCuritibaBrazil
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Pizzaia D, Oliveira-Maekawa VM, Martins AR, Mondin M, Aguiar-Perecin MLR. Karyotype structure and NOR activity in Brazilian Smilax Linnaeus, 1753 species (Smilacaceae). Comp Cytogenet 2019; 13:245-263. [PMID: 31528267 PMCID: PMC6715645 DOI: 10.3897/compcytogen.v13i3.35775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
The genus Smilax Linnaeus, 1753 (Smilacaceae) is a large genus of dioecious plants distributed in tropical, subtropical and temperate regions. Some Smilax species have medicinal importance and their identification is important for the control of raw material used in the manufacture of phytotherapeutical products. The karyotypes of seven Brazilian Smilax species were investigated. Mitotic metaphases of roots from young plants were analysed in Feulgen-stained preparations. The karyotypes were asymmetric and modal with 2n = 2x = 32 chromosomes gradually decreasing in size. In S. goyazana A De Candolle & C De Candolle, 1878, a polyploid species, 2n = 4x = 64. In all the species, the large and medium-sized chromosomes were subtelocentric and submetacentric and the small chromosomes were submetacentric or metacentric. Their karyotypes were quite similar, with differences in the arm ratio of some chromosomes. S. fluminensis Steudel, 1841 differed from the other species by having a large metacentric chromosome 1. These findings suggest that evolution occurred without drastic changes in the chromosomal structure in the species analyzed. Terminal secondary constrictions were visualized on the short arm of some chromosomes, but they were detected only in one homologue of each pair. Due to the terminal location and the degree of chromosome condensation, secondary constrictions were not visualized in some species. The nucleolus organizer regions (NORs) were mapped by silver-staining and fluorescent in situ hybridization (FISH) in S. rufescens Grisebach, 1842 and S. fluminensis. Silver-staining and FISH signals were colocalized on the short arms of six chromosomes in S. rufescens and four chromosomes in S. fluminensis. In FISH preparations, one of the largest chromosomes had the secondary constrictions highly decondensed in some cells. This finding and the heteromorphism observed in Feulgen-stained chromosomes suggest that differential rRNA gene expression between homologous rDNA loci can occur in some cells, resulting in different degrees of ribosomal chromatin decondensation. The presence of a heteromorphic chromosome pair in S. rufescens, S. polyantha Grisebach, 1842 and S. goyazana suggests a chromosomal sex determination in these dioecious species.
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Affiliation(s)
- Daniel Pizzaia
- Department of Genetics, Luiz de Queiroz College of Agriculture, ESALQ, University of São Paulo, Avenida Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil
| | - Vanessa M Oliveira-Maekawa
- Department of Plant Biology, The University of Campinas, UNICAMP, Barão Geraldo, 13083-970, Campinas, SP, Brazil
| | - Aline R Martins
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture, ESALQ, University of São Paulo, Avenida Pádua Dias,11 13418-900, Piracicaba, SP, Brazil
| | - Mateus Mondin
- Department of Genetics, Luiz de Queiroz College of Agriculture, ESALQ, University of São Paulo, Avenida Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil
| | - Margarida L R Aguiar-Perecin
- Department of Genetics, Luiz de Queiroz College of Agriculture, ESALQ, University of São Paulo, Avenida Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil
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16
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Bruschi DP, Sousa DY, Soares A, de Carvalho KA, Busin CS, Ficanha NC, Lima AP, Andrade GV, Recco-Pimentel SM. Comparative cytogenetics of nine populations of the Rhinella genus (Anura, Bufonidae) with a highlight on their conservative karyotype. Genet Mol Biol 2019; 42:445-451. [PMID: 31259364 PMCID: PMC6726150 DOI: 10.1590/1678-4685-gmb-2018-0139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/17/2018] [Indexed: 11/21/2022] Open
Abstract
The genus Rhinella is one of the most diverse groups of bufonid toads, currently composed by 93 valid species and naturally distributed throughout different Neotropical ecoregions. Here, we analyze nine Brazilian populations of toads representing species of the Rhinella margaritifera and Rhinella marina groups. These new data include the first description of the R. hoogmoedi and R. proboscidae karyotypes, as well as other taxonomically unresolved forms. Chromosomal analysis of the populations revealed pronounced chromosomal uniformity (2n=22), including the diploid number and chromosomal morphology. Three different NOR-bearing chromosomes were identified: in the subterminal region of pair 10q in R. hoogmoedi, Rhinella sp. 1 and Rhinella sp. 2, in subterminal region of 7p in R. proboscidae and Rhinella cf. margaritifera while in R. henseli and R. icterica was detected in interstitial region of 7p. Karyotypic uniformity of the genus permits the inference of interspecific chromosome homologies and evolutionary changes in the NOR-bearing chromosome may represent an informative character in species group level. The review of the cytogenetic data of the Rhinella species together with the new karyotypes reported here contributes to the understanding of the chromosomal evolution of these toads, which karyotypes are highly conserved despite the ample distribution of many forms.
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Affiliation(s)
- Daniel Pacheco Bruschi
- Departamento de Genética, Setor de Ciências Biológicas,
Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
- Departamento de Biologia Estrutural e Funcional, Instituto de
Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP,
Brazil
| | - Deborah Yasmim Sousa
- Departamento de Genética, Setor de Ciências Biológicas,
Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
| | - Amanda Soares
- Departamento de Genética, Setor de Ciências Biológicas,
Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
| | - Klélia Aparecida de Carvalho
- Departamento de Genética e Evolução, Microbiologia e
Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP),
Campinas, SP, Brazil
| | - Carmen Sílvia Busin
- Instituto de Ciências Biológicas, Programa de Pós-Graduação em
Ciências Ambientais (PPGCiAmb), Universidade de Passo Fundo (UPF), Passo Fundo,
RS, Brazil
| | - Natália Cristine Ficanha
- Instituto de Ciências Biológicas, Programa de Pós-Graduação em
Ciências Ambientais (PPGCiAmb), Universidade de Passo Fundo (UPF), Passo Fundo,
RS, Brazil
| | | | - Gilda Vasconcellos Andrade
- Departamento de Biologia, Centro de Ciências Biológicas e da
Saúde, Universidade Federal do Maranhão (UFMA), São Luís, MA, Brazil
| | - Shirlei Maria Recco-Pimentel
- Departamento de Biologia Estrutural e Funcional, Instituto de
Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP,
Brazil
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17
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Piscor D, Pozzobon APB, Fernandes CA, Centofante L, Parise-Maltempi PP. Molecular Clock as Insight to Estimate the Evolutionary History and Times of Divergence for 10 Nominal Astyanax Species (Characiformes, Characidae): An Evolutionary Approach in Species with 2n = 36, 46, 48, and 50 Chromosomes. Zebrafish 2018; 16:98-105. [PMID: 30358520 DOI: 10.1089/zeb.2018.1647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Astyanax is a genus with a wide distribution ranging from the south United States to north of Patagonia (Argentina). The available cytogenetic data on Astyanax indicate a high karyotypic diversity, with diploid number of 36-52 chromosomes, presence of B chromosomes, heterochromatin polymorphism, and variations with respect to the number and localization of nucleolar organizer regions (NORs) and 18S and 5S ribosomal DNA sites. In the present study, we estimated the evolutionary history and times of divergence for 10 nominal Astyanax species from the South and Central/North American (Cna) continents, which present distinct chromosomal characteristics, based on molecular clocks inferred from mitochondrial DNA sequence. The molecular clock results indicate the origin of three distinct clades (Humeral dark spot [Hds]; Diffuse humeral spot [Dhs]; Cna group) during the late Miocene about 11.2 million years ago (Mya). Thus, Astyanax mexicanus (Cna) represent a species that diverged a long time ago (∼8.6 Mya) from the Hds group, and Astyanax schubarti is the oldest species (∼6.5 Mya) among the Dhs species.
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Affiliation(s)
- Diovani Piscor
- 1 Laboratório de Citogenética, Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Rio Claro, Brazil.,2 Universidade Estadual de Mato Grosso do Sul (UEMS), Unidade de Mundo Novo, Mundo Novo, Brazil
| | - Allan Pierre Bonetti Pozzobon
- 3 Universidade Federal do Rio de Janeiro (UFRJ), Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé (NUPEM/UFRJ), Macaé, Brazil
| | | | - Liano Centofante
- 4 Laboratório de Genética Animal, Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Patricia Pasquali Parise-Maltempi
- 1 Laboratório de Citogenética, Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Rio Claro, Brazil
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Lukhtanov VA, Dincă V, Friberg M, Šíchová J, Olofsson M, Vila R, Marec F, Wiklund C. Versatility of multivalent orientation, inverted meiosis, and rescued fitness in holocentric chromosomal hybrids. Proc Natl Acad Sci U S A 2018; 115:E9610-9. [PMID: 30266792 DOI: 10.1073/pnas.1802610115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chromosomal rearrangements (e.g., fusions/fissions) have the potential to drive speciation. However, their accumulation in a population is generally viewed as unlikely, because chromosomal heterozygosity should lead to meiotic problems and aneuploid gametes. Canonical meiosis involves segregation of homologous chromosomes in meiosis I and sister chromatid segregation during meiosis II. In organisms with holocentric chromosomes, which are characterized by kinetic activity distributed along almost the entire chromosome length, this order may be inverted depending on their metaphase I orientation. Here we analyzed the evolutionary role of this intrinsic versatility of holocentric chromosomes, which is not available to monocentric ones, by studying F1 to F4 hybrids between two chromosomal races of the Wood White butterfly (Leptidea sinapis), separated by at least 24 chromosomal fusions/fissions. We found that these chromosomal rearrangements resulted in multiple meiotic multivalents, and, contrary to the theoretical prediction, the hybrids displayed relatively high reproductive fitness (42% of that of the control lines) and regular behavior of meiotic chromosomes. In the hybrids, we also discovered inverted meiosis, in which the first and critical stage of chromosome number reduction was replaced by the less risky stage of sister chromatid separation. We hypothesize that the ability to invert the order of the main meiotic events facilitates proper chromosome segregation and hence rescues fertility and viability in chromosomal hybrids, potentially promoting dynamic karyotype evolution and chromosomal speciation.
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Cacheux L, Ponger L, Gerbault-Seureau M, Loll F, Gey D, Richard FA, Escudé C. The Targeted Sequencing of Alpha Satellite DNA in Cercopithecus pogonias Provides New Insight Into the Diversity and Dynamics of Centromeric Repeats in Old World Monkeys. Genome Biol Evol 2018; 10:1837-1851. [PMID: 29860303 PMCID: PMC6061836 DOI: 10.1093/gbe/evy109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alpha satellite is the major repeated DNA element of primate centromeres. Specific evolutionary mechanisms have led to a great diversity of sequence families with peculiar genomic organization and distribution, which have till now been studied mostly in great apes. Using high throughput sequencing of alpha satellite monomers obtained by enzymatic digestion followed by computational and cytogenetic analysis, we compare here the diversity and genomic distribution of alpha satellite DNA in two related Old World monkey species, Cercopithecus pogonias and Cercopithecus solatus, which are known to have diverged about 7 Ma. Two main families of monomers, called C1 and C2, are found in both species. A detailed analysis of our data sets revealed the existence of numerous subfamilies within the centromeric C1 family. Although the most abundant subfamily is conserved between both species, our fluorescence in situ hybridization (FISH) experiments clearly show that some subfamilies are specific for each species and that their distribution is restricted to a subset of chromosomes, thereby pointing to the existence of recurrent amplification/homogenization events. The pericentromeric C2 family is very abundant on the short arm of all acrocentric chromosomes in both species, pointing to specific mechanisms that lead to this distribution. Results obtained using two different restriction enzymes are fully consistent with a predominant monomeric organization of alpha satellite DNA that coexists with higher order organization patterns in the C. pogonias genome. Our study suggests a high dynamics of alpha satellite DNA in Cercopithecini, with recurrent apparition of new sequence variants and interchromosomal sequence transfer.
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Affiliation(s)
- Lauriane Cacheux
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Loïc Ponger
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Michèle Gerbault-Seureau
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - François Loll
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Delphine Gey
- Service de Systématique Moléculaire, UMS 2700 CNRS, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Florence Anne Richard
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Université Versailles St-Quentin, Montigny-le-Bretonneux, France
| | - Christophe Escudé
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
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20
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Barby FF, Ráb P, Lavoué S, Ezaz T, Bertollo LAC, Kilian A, Maruyama SR, Aguiar de Oliveira E, Artoni RF, Santos MH, Ilesanmi Jegede O, Hatanaka T, Tanomtong A, Liehr T, Cioffi MDB. From Chromosomes to Genome: Insights into the Evolutionary Relationships and Biogeography of Old World Knifefishes (Notopteridae; Osteoglossiformes). Genes (Basel) 2018; 9:E306. [PMID: 29921830 PMCID: PMC6027293 DOI: 10.3390/genes9060306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 01/13/2023] Open
Abstract
In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family.
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Affiliation(s)
- Felipe Faix Barby
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic.
| | - Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan.
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Canberra, ACT 2617, Australia.
| | - Sandra Regina Maruyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Mateus Henrique Santos
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil.
| | - Oladele Ilesanmi Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25 Mubi. Adamawa State, Nigeria.
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen 40002, Thailand.
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany.
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
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21
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Nirchio M, Paim FG, Milana V, Rossi AR, Oliveira C. Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes). Front Genet 2018; 9:17. [PMID: 29459882 PMCID: PMC5807406 DOI: 10.3389/fgene.2018.00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 01/15/2018] [Indexed: 11/13/2022] Open
Abstract
Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.
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Affiliation(s)
- Mauro Nirchio
- Facultad de Ciencias Agropecuarias, Universidad Técnica de Machala, Machala, Ecuador
| | - Fabilene G. Paim
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São Paulo, Brazil
| | - Valentina Milana
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Anna R. Rossi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”, São Paulo, Brazil
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22
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Prizon AC, Bruschi DP, Borin-Carvalho LA, Cius A, Barbosa LM, Ruiz HB, Zawadzki CH, Fenocchio AS, Portela-Castro ALDB. Hidden Diversity in the Populations of the Armored Catfish Ancistrus Kner, 1854 (Loricariidae, Hypostominae) from the Paraná River Basin Revealed by Molecular and Cytogenetic Data. Front Genet 2017; 8:185. [PMID: 29225612 PMCID: PMC5705632 DOI: 10.3389/fgene.2017.00185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/07/2017] [Indexed: 12/01/2022] Open
Abstract
Only one species of armored catfish, Ancistrus cirrhosus Valenciennes 1836, has been historically described in the basin of the Paraná River, from Misiones (Argentina). However, the ample variation found in the morphology and coloration of the populations sampled in the tributaries of the Brazilian state of Paraná makes it difficult to establish the real taxonomic status and evolutionary history of the Ancistrus specimens, suggesting that A. cirrhosus is not the only species found in this basin. By combining data on mitochondrial DNA (COI gene) and chromosomal markers from different Ancistrus populations, totaling 144 specimens, in the tributaries of the Paraná, and specimens from Misiones (type-locality of A. cirrhosus), we detected five distinct evolutionary lineages. All the specimens were 2n = 50, but had four distinct karyotype formulae. The results of the Generalized Mixed Yule Coalescent (GYMC) and the genetic distances (uncorrected P-values) between lineages ranged from 3 to 5%. Clusters of 18S rDNA were observed in a single chromosome pair in seven populations of Ancistrus, but at different positions, in some cases, in synteny with the 5S rDNA sites. Multiple 5S sites were observed in all populations. Overall, the cytogenetic data reinforce the genetic evidence of the diversification of lineages, and indicate the existence of candidate species in the study region. The evidence indicates that at least four candidate species of the Ancistrus may coexist in the Paraná basin besides A. cirrhosus. Overall, our results provide a comprehensive scenario for the genetic variation among Ancistrus populations and reinforce the conclusion that the true diversity of the freshwater fish of the Neotropical regions has been underestimated.
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Affiliation(s)
- Ana C Prizon
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Daniel P Bruschi
- Laboratório de Citogenética Animal e Mutagênese Ambioental, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luciana A Borin-Carvalho
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Andréa Cius
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Ligia M Barbosa
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | - Henrique B Ruiz
- Departamento de Biologia/Nupélia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Claudio H Zawadzki
- Departamento de Biologia/Nupélia, Universidade Estadual de Maringá, Maringá, Brazil
| | - Alberto S Fenocchio
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Ana L de Brito Portela-Castro
- Laboratório de Citogenética de Vertebrados, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
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Zlotina A, Dedukh D, Krasikova A. Amphibian and Avian Karyotype Evolution: Insights from Lampbrush Chromosome Studies. Genes (Basel) 2017; 8:genes8110311. [PMID: 29117127 PMCID: PMC5704224 DOI: 10.3390/genes8110311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 01/04/2023] Open
Abstract
Amphibian and bird karyotypes typically have a complex organization, which makes them difficult for standard cytogenetic analysis. That is, amphibian chromosomes are generally large, enriched with repetitive elements, and characterized by the absence of informative banding patterns. The majority of avian karyotypes comprise a small number of relatively large macrochromosomes and numerous tiny morphologically undistinguishable microchromosomes. A good progress in investigation of amphibian and avian chromosome evolution became possible with the usage of giant lampbrush chromosomes typical for growing oocytes. Due to the giant size, peculiarities of organization and enrichment with cytological markers, lampbrush chromosomes can serve as an opportune model for comprehensive high-resolution cytogenetic and cytological investigations. Here, we review the main findings on chromosome evolution in amphibians and birds that were obtained using lampbrush chromosomes. In particular, we discuss the data on evolutionary chromosomal rearrangements, accumulation of polymorphisms, evolution of sex chromosomes as well as chromosomal changes during clonal reproduction of interspecies hybrids.
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Affiliation(s)
- Anna Zlotina
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Dmitry Dedukh
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg 199034, Russia.
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24
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Favarato RM, Ribeiro LB, Feldberg E, Matoso DA. Chromosomal Mapping of Transposable Elements of the Rex Family in the Bristlenose Catfish, Ancistrus (Siluriformes, Loricariidae), from the Amazonian Region. J Hered 2017; 108:254-261. [PMID: 27940473 DOI: 10.1093/jhered/esw084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/02/2016] [Indexed: 11/13/2022] Open
Abstract
Repetitive DNA sequences are present in the genome of basically every known organism, and transposable elements (TE) are one of the most representative sequences involved in chromosomal rearrangements and the genomic evolution of eukaryotes. In fish, the non-LTR retrotransposon TEs, Rex1, Rex3, and Rex6, are widely distributed in fish genomes and are the best-characterized TEs in several species. In the current study, three of these retroelements were physically mapped, through fluorescent in situ hybridization (FISH), in 7 species (71 specimens) of the genus Ancistrus, known as bristlenose catfish: Ancistrus ranunculus, Ancistrus sp. 1 "Purus," Ancistrus sp. 2 "Catalão," Ancistrus dolichopterus, Ancistrus maximus, Ancistrus aff. dolichopterus, and Ancistrus dubius. Rex1, Rex3, and Rex6 showed a cluster distribution, mainly in the terminal and pericentromeric portions, in heterochromatic and euchromatic regions, and did not occur in sexual chromosomes; however, the number and position of the clusters varied between species. This TE distribution suggests its implication in the karyotypic evolution of these species, without affecting the rise of sexual chromosome systems in Ancistrus, in view of their chromosomal variation.
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Affiliation(s)
- Ramon Marin Favarato
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
| | - Leila Braga Ribeiro
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil.,Centro de Ciências da Saúde, Universidade Federal de Roraima, Boa Vista, Brazil
| | - Eliana Feldberg
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
| | - Daniele Aparecida Matoso
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
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25
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Lara Kamei MCDS, Baumgärtner L, Paiva S, Zawadzki CH, Martins-Santos IC, Portela-Castro ALDB. Chromosomal Diversity of Three Species of Hypostomus Lacépède, 1803 (Siluriformes, Loricariidae), from the Paraná River Basin, Brazil: A Species Complex in Hypostomus ancistroides Reinforced by a ZZ/ZW Sex Chromosome System. Zebrafish 2017; 14:357-363. [PMID: 28609254 DOI: 10.1089/zeb.2017.1429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hypostomus shows wide morphological patterns, corroborated by great chromosomal diversity that has suggested the existence of new species, especially from small tributaries. Cytogenetic analysis has contributed to estimate a cryptic diversity providing important data for taxonomic and evolutionary studies. Cytogenetic techniques were carried out on species from a small tributary of Ivaí River, Keller River (upper Paraná River basin): Hypostomus aff. ancistroides, Hypostomus topavae, and Hypostomus aff. hermanni that presented 2n = 68, 80, and 72 chromosomes, respectively. Each species showed the same diploid number from previous descriptions for other populations but different karyotype formulas, and Hypostomus aff. ancistroides had a ZZ/ZW sex chromosome system. Multiple NORs (nucleolar organizer regions) and pericentromeric heterochromatin blocks were found in the three species. Moreover, each of them showed species-specific heterochromatins. Multiple 5S rDNA sites were detected in Hypostomus aff. ancistroides and H. topavae, whereas Hypostomus aff. hermanni had only one pair bearing these sites. In addition to the divergence in the karyotype formulas, chromosomal markers used showed karyotype differences in the three species related to other respective populations studied. Furthermore, the first description of a ZZ/ZW system for Hypostomus aff. ancistroides reinforces the hypothesis that it may correspond to a species complex and yet, confirming an unknown cryptic diversity existent in small rivers.
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Affiliation(s)
| | - Lucas Baumgärtner
- 2 Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Cascavel, Brazil
| | - Suzana Paiva
- 3 Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá , Maringá, Brazil
| | - Cláudio Henrique Zawadzki
- 4 Departamento de Biologia/Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupélia), Universidade Estadual de Maringá , Maringá, Brazil
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Blanco DR, Vicari MR, Lui RL, Traldi JB, Bueno V, Martinez JDF, Brandão H, Oyakawa OT, Moreira Filho O. Karyotype Diversity and Evolutionary Trends in Armored Catfish Species of the Genus Harttia (Siluriformes: Loricariidae). Zebrafish 2017; 14:169-176. [PMID: 28060676 DOI: 10.1089/zeb.2016.1377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most species of the genus Harttia inhabits the headwaters of small tributaries, but some species are restricted to the main channel of some rivers. This feature, combined with limited dispersal ability, leads to the formation of small isolated populations with reduced gene flow. Currently, there are 23 taxonomically defined and recognized species, and 17 of these are found in Brazil, distributed in several hydrographic basins. Despite this diversity, few chromosomal data for the species belonging to this genus are found in the literature. Thus, this study analyzed, by classical and molecular cytogenetics methodologies, the chromosomal diversity of this genus, to discuss the processes that are involved in the evolution and karyotype differentiation of the species of the group. Seven species of Harttia were analyzed: H. kronei, H. longipinna, H. gracilis, H. punctata, H. loricariformis, H. torrenticola, and H. carvalhoi. The chromosomal diversity found in these species includes different diploid and fundamental numbers, distinct distribution of several repetitive sequences, the presence of supernumerary chromosomes in H. longipinna and multiple sex chromosome systems of the type XX/XY1Y2 in H. carvalhoi and X1X1X2X2/X1X2Y in H. punctata. Lastly, our data highlight the genus Harttia as an excellent model for evolutionary studies.
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Affiliation(s)
- Daniel Rodrigues Blanco
- 1 Coordenação do Curso de Ciências Biológicas, Universidade Tecnológica Federal do Paraná , Santa Helena (PR), Brazil
| | - Marcelo Ricardo Vicari
- 2 Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa , Ponta Grossa (PR), Brazil
| | - Roberto Laridondo Lui
- 3 Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Cascavel (PR), Brazil
| | - Josiane Baccarin Traldi
- 1 Coordenação do Curso de Ciências Biológicas, Universidade Tecnológica Federal do Paraná , Santa Helena (PR), Brazil
| | - Vanessa Bueno
- 1 Coordenação do Curso de Ciências Biológicas, Universidade Tecnológica Federal do Paraná , Santa Helena (PR), Brazil
| | | | - Heleno Brandão
- 1 Coordenação do Curso de Ciências Biológicas, Universidade Tecnológica Federal do Paraná , Santa Helena (PR), Brazil
| | - Osvaldo Takeshi Oyakawa
- 5 Museu de Zoologia da Universidade de São Paulo, Universidade de São Paulo , São Paulo (SP), Brazil
| | - Orlando Moreira Filho
- 6 Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Carlos (SP), Brazil
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27
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Gerstein AC, Lim H, Berman J, Hickman MA. Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen. Evolution 2017; 71:1025-1038. [PMID: 28195309 DOI: 10.1111/evo.13205] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/27/2017] [Indexed: 12/18/2022]
Abstract
Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is maintained over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term "ploidy drive." We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes (measured as total nuclear DNA through flow cytometry) in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Improvements in fitness often ran counter to changes in genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged toward diploidy (the baseline ploidy of C. albicans). Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.
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Affiliation(s)
- Aleeza C Gerstein
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Microbiology & Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota
| | - Heekyung Lim
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Judith Berman
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Microbiology & Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota.,Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Meleah A Hickman
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia
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28
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Takagui FH, Moura LFD, Ferreira DC, Centofante L, Vitorino CDA, Bueno V, Margarido VP, Venere PC. Karyotype Diversity in Doradidae (Siluriformes, Doradoidea) and Presence of the Heteromorphic ZZ/ZW Sex Chromosome System in the Family. Zebrafish 2017; 14:236-243. [PMID: 28192063 DOI: 10.1089/zeb.2016.1368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Karyotypes and other chromosomal markers as revealed by conventional and molecular cytogenetic protocols in four species of the catfish family Doradidae from the Araguaia-Tocantins river basin, namely Hassar wilderi, Leptodoras cataniae, Tenellus leporhinus and Tenellus trimaculatus were examined. All species had diploid chromosome number 2n = 58 and karyotypes dominated by biarmed chromosomes, simple NOR phenotype, that is, one chromosome pair bearing this site in terminal position, but some differences in karyotypes and distribution of constitutive heterochromatin, position of rDNA sites. Such characteristics appeared species-specific. A ZZ/ZW sex chromosome system was found in Tenellus trimaculatus, resulting likely from the amplification of the heterochromatin, followed by a paracentric inversion. Our results confirmed low karyotype differentiation observed until now among representatives of this endemic catfish family.
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Affiliation(s)
- Fábio Hiroshi Takagui
- 1 Laboratório de Citogenética Animal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina , Londrina, Brazil
| | - Lucas Ferreira de Moura
- 2 Laboratório de Ictiologia, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso , Pontal do Araguaia, Brazil
| | - Daniela Cristina Ferreira
- 3 Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
| | - Liano Centofante
- 3 Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
| | - Carla de Andrade Vitorino
- 4 Programa de Pós Graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
| | - Vanessa Bueno
- 5 Universidade Tecnológica Federal do Paraná , Prolongamento da Rua Cerejeira s/n, Paraná, Brazil
| | - Vladimir Pavan Margarido
- 6 Laboratório de Citogenética de peixes, Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná , Paraná, Brazil
| | - Paulo Cesar Venere
- 3 Laboratório de Citogenética e Genética Animal, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil .,4 Programa de Pós Graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso , Cuiabá, Brazil
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Orengo DJ, Puerma E, Papaceit M, Segarra C, Aguadé M. Dense gene physical maps of the non-model species Drosophila subobscura. Chromosome Res 2017; 25:145-154. [PMID: 28078516 DOI: 10.1007/s10577-016-9549-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 11/29/2022]
Abstract
The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism. These maps are based on 462 markers: 115, 236, and 111 markers for elements A, C, and E, respectively. The availability of these dense maps will facilitate genome assembly and will thus greatly contribute to obtaining a good reference genome, which is a required step for D. subobscura to attain the model species status. The comparative analysis of these physical maps and those obtained from the D. pseudoobscura and D. melanogaster genomes allowed us to infer the number of fixed inversions and chromosomal evolutionary rates for each pairwise comparison. For all three elements, rates inferred from the more closely related species were higher than those inferred from the more distantly related species, which together with results of relative-rate tests point to an acceleration in the D. subobscura lineage at least for elements A and E.
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Affiliation(s)
- Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Papaceit
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Carmen Segarra
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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Giménez MD, Förster DW, Jones EP, Jóhannesdóttir F, Gabriel SI, Panithanarak T, Scascitelli M, Merico V, Garagna S, Searle JB, Hauffe HC. A Half-Century of Studies on a Chromosomal Hybrid Zone of the House Mouse. J Hered 2016; 108:25-35. [PMID: 27729448 DOI: 10.1093/jhered/esw061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
The first natural chromosomal variation in the house mouse was described nearly 50 years ago in Val Poschiavo on the Swiss side of the Swiss-Italian border in the Central Eastern Alps. Studies have extended into neighboring Valtellina, and the house mice of the Poschiavo-Valtellina area have been subject to detailed analysis, reviewed here. The maximum extent of this area is 70 km, yet it has 4 metacentric races and the standard 40-chromosome telocentric race distributed in a patchwork fashion. The metacentric races are characterized by highly reduced diploid numbers (2n = 22-26) resulting from Robertsonian fusions, perhaps modified by whole-arm reciprocal translocations. The races hybridize and the whole Poschiavo-Valtellina area can be considered a "hybrid zone." The studies of this area have provided insights into origin of races within hybrid zones, gene flow within hybrid zones and the possibility of speciation in hybrid zones. This provides a case study of how chromosomal rearrangements may impact the genetic structure of populations and their diversification.
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Affiliation(s)
- Mabel D Giménez
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Daniel W Förster
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Eleanor P Jones
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Fríða Jóhannesdóttir
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Sofia I Gabriel
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Thadsin Panithanarak
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Moira Scascitelli
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Valeria Merico
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Silvia Garagna
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Jeremy B Searle
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Heidi C Hauffe
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
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Oliveira LC, de Oliveira MDSP, Davide LC, Torres GA. Karyotype and genome size in Euterpe Mart. (Arecaceae) species. Comp Cytogenet 2016; 10:17-25. [PMID: 27186334 PMCID: PMC4856922 DOI: 10.3897/compcytogen.v10i1.5522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
Euterpe (Martius, 1823), a genus from Central and South America, has species with high economic importance in Brazil, because of their palm heart and fruits, known as açaí berries. Breeding programs have been conducted to increase yield and establish cultivation systems to replace the extraction of wild material. These programs need basic information about the genome of these species to better explore the available genetic variability. The aim of this study was to compare Euterpe edulis (Martius, 1824), Euterpe oleracea (Martius, 1824) and Euterpe precatoria (Martius, 1842), with regard to karyotype, type of interphase nucleus and nuclear DNA amount. Metaphase chromosomes and interphase nuclei from root tip meristematic cells were obtained by the squashing technique and solid stained for microscope analysis. The DNA amount was estimated by flow cytometry. There were previous reports on the chromosome number of Euterpe edulis and Euterpe oleracea, but chromosome morphology of these two species and the whole karyotype of Euterpe precatoria are reported for the first time. The species have 2n=36, a number considered as a pleisomorphic feature in Arecoideae since the modern species, according to floral morphology, have the lowest chromosome number (2n=28 and 2n=30). The three Euterpe species also have the same type of interphase nuclei, classified as semi-reticulate. The species differed on karyotypic formulas, on localization of secondary constriction and genome size. The data suggest that the main forces driving Euterpe karyotype evolution were structural rearrangements, such as inversions and translocations that alter chromosome morphology, and either deletion or amplification that led to changes in chromosome size.
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Affiliation(s)
- Ludmila Cristina Oliveira
- Universidade Federal de Lavras, Campus Universitário, Caixa Postal 3037, CEP 37200-000, Lavras-MG, Brasil
| | | | - Lisete Chamma Davide
- Embrapa Amazônia Oriental, Trav. Dr. Enéas Pinheiro, s/n°, Bairro Marco, CEP 66095-100, Caixa Postal 48, Belém-PA, Brasil
| | - Giovana Augusta Torres
- Universidade Federal de Lavras, Campus Universitário, Caixa Postal 3037, CEP 37200-000, Lavras-MG, Brasil
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Blackmon H, Hardy NB, Ross L. The evolutionary dynamics of haplodiploidy: Genome architecture and haploid viability. Evolution 2015; 69:2971-8. [PMID: 26462452 PMCID: PMC4989469 DOI: 10.1111/evo.12792] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 02/07/2023]
Abstract
Haplodiploid reproduction, in which males are haploid and females are diploid, is widespread among animals, yet we understand little about the forces responsible for its evolution. The current theory is that haplodiploidy has evolved through genetic conflicts, as it provides a transmission advantage to mothers. Male viability is thought to be a major limiting factor; diploid individuals tend to harbor many recessive lethal mutations. This theory predicts that the evolution of haplodiploidy is more likely in male heterogametic lineages with few chromosomes, as genes on the X chromosome are often expressed in a haploid environment, and the fewer the chromosome number, the greater the proportion of the total genome that is X-linked. We test this prediction with comparative phylogenetic analyses of mites, among which haplodiploidy has evolved repeatedly. We recover a negative correlation between chromosome number and haplodiploidy, find evidence that low chromosome number evolved prior to haplodiploidy, and that it is unlikely that diplodiploidy has reevolved from haplodiploid lineages of mites. These results are consistent with the predicted importance of haploid male viability.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, University of Texas, Arlington, Box 19498, Arlington, Texas, 76019
| | - Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, 36849
| | - Laura Ross
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.
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Neiman M, Beaton MJ, Hessen DO, Jeyasingh PD, Weider LJ. Endopolyploidy as a potential driver of animal ecology and evolution. Biol Rev Camb Philos Soc 2015; 92:234-247. [PMID: 26467853 DOI: 10.1111/brv.12226] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 01/20/2023]
Abstract
Endopolyploidy - the existence of higher-ploidy cells within organisms that are otherwise of a lower ploidy level (generally diploid) - was discovered decades ago, but remains poorly studied relative to other genomic phenomena, especially in animals. Our synthetic review suggests that endopolyploidy is more common in animals than often recognized and probably influences a number of fitness-related and ecologically important traits. In particular, we argue that endopolyploidy is likely to play a central role in key traits such as gene expression, body and cell size, and growth rate, and in a variety of cell types, including those responsible for tissue regeneration, nutrient storage, and inducible anti-predator defences. We also summarize evidence for intraspecific genetic variation in endopolyploid levels and make the case that the existence of this variation suggests that endopolyploid levels are likely to be heritable and thus a potential target for natural selection. We then discuss why, in light of evident benefits of endopolyploidy, animals remain primarily diploid. We conclude by highlighting key areas for future research such as comprehensive evaluation of the heritability of endopolyploidy and the adaptive scope of endopolyploid-related traits, the extent to which endopolyploid induction incurs costs, and characterization of the relationships between environmental variability and endopolyploid levels.
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Affiliation(s)
- Maurine Neiman
- Department of Biology, University of Iowa, 143 Biology Building, Iowa City, IA 52242, U.S.A
| | - Margaret J Beaton
- Biology Department, Mount Allison University, Sackville, NB E4L 1G7, Canada
| | - Dag O Hessen
- Department of Biosciences, University of Oslo, Box 1066, Blindern, 0316 Oslo, Norway
| | - Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, U.S.A
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, 730 Van Vleet Oval, Room 304, Norman, OK 73019, U.S.A
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Sánchez-Guillén RA, Capilla L, Reig-Viader R, Martínez-Plana M, Pardo-Camacho C, Andrés-Nieto M, Ventura J, Ruiz-Herrera A. On the origin of Robertsonian fusions in nature: evidence of telomere shortening in wild house mice. J Evol Biol 2015; 28:241-9. [PMID: 25491286 DOI: 10.1111/jeb.12568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 01/31/2023]
Abstract
The role of telomere shortening to explain the occurrence of Robertsonian (Rb) fusions, as well as the importance of the average telomere length vs. the proportion of short telomeres, especially in nature populations, is largely unexplored. In this study, we have analysed telomere shortening in nine wild house mice from the Barcelona Rb system with diploid numbers ranging from 29 to 40 chromosomes. We also included two standard (2n=40) laboratory mice for comparison. Our data showed that the average telomere length (considering all chromosomal arms) is influenced by both the diploid number and the origin of the mice (wild vs. laboratory). In detail, we detected that wild mice from the Rb Barcelona system (fused and standard) present shorter telomeres than standard laboratory mice. However, only wild mice with Rb fusions showed a high proportion of short telomeres (only in p-arms), thus revealing the importance of telomere shortening in the origin of the Rb fusions in the Barcelona system. Overall, our study confirms that the number of critically short telomeres, and not a simple reduction in the average telomere length, is more likely to lead to the origin of Rb fusions in the Barcelona system and ultimately in nature.
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Affiliation(s)
- R A Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
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Emadzade K, Jang TS, Macas J, Kovařík A, Novák P, Parker J, Weiss-Schneeweiss H. Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae). Ann Bot 2014; 114:1597-608. [PMID: 25169019 PMCID: PMC4273535 DOI: 10.1093/aob/mcu178] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Chromosomal evolution, including numerical and structural changes, is a major force in plant diversification and speciation. This study addresses genomic changes associated with the extensive chromosomal variation of the Mediterranean Prospero autumnale complex (Hyacinthaceae), which includes four diploid cytotypes each with a unique combination of chromosome number (x = 5, 6, 7), rDNA loci and genome size. METHODS A new satellite repeat PaB6 has previously been identified, and monomers were reconstructed from next-generation sequencing (NGS) data of P. autumnale cytotype B(6)B(6) (2n = 12). Monomers of all other Prospero cytotypes and species were sequenced to check for lineage-specific mutations. Copy number, restriction patterns and methylation levels of PaB6 were analysed using Southern blotting. PaB6 was localized on chromosomes using fluorescence in situ hybridization (FISH). KEY RESULTS The monomer of PaB6 is 249 bp long, contains several intact and truncated vertebrate-type telomeric repeats and is highly methylated. PaB6 is exceptional because of its high copy number and unprecedented variation among diploid cytotypes, ranging from 10(4) to 10(6) copies per 1C. PaB6 is always located in pericentromeric regions of several to all chromosomes. Additionally, two lineages of cytotype B(7)B(7) (x = 7), possessing either a single or duplicated 5S rDNA locus, differ in PaB6 copy number; the ancestral condition of a single locus is associated with higher PaB6 copy numbers. CONCLUSIONS Although present in all Prospero species, PaB6 has undergone differential amplification only in chromosomally variable P. autumnale, particularly in cytotypes B(6)B(6) and B(5)B(5). These arose via independent chromosomal fusions from x = 7 to x = 6 and 5, respectively, accompanied by genome size increases. The copy numbers of satellite DNA PaB6 are among the highest in angiosperms, and changes of PaB6 are exceptionally dynamic in this group of closely related cytotypes of a single species. The evolution of the PaB6 copy numbers is discussed, and it is suggested that PaB6 represents a recent and highly dynamic system originating from a small pool of ancestral repeats.
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Affiliation(s)
- Khatere Emadzade
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Jiří Macas
- Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
| | - Ales Kovařík
- Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Petr Novák
- Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic
| | - John Parker
- Cambridge University Botanic Garden, Cambridge CB2 1JF, UK
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Marques A, Banaei-Moghaddam AM, Klemme S, Blattner FR, Niwa K, Guerra M, Houben A. B chromosomes of rye are highly conserved and accompanied the development of early agriculture. Ann Bot 2013; 112:527-34. [PMID: 23739836 PMCID: PMC3718213 DOI: 10.1093/aob/mct121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/16/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Supernumerary B chromosomes (Bs) represent a specific type of selfish genetic element. As Bs are dispensable for normal growth, it is expected to observe B polymorphisms among populations. To address whether Bs maintained in geographically distinct populations of cultivated and weedy rye are polymorphic, the distribution patterns and the transcriptional activity of different B-located repeats were analysed. METHODS Bs of cultivated and weedy rye from seven origins were analysed by fluorescence in situ hybridization (FISH) with probes specific for the pericentromeric and interstitial regions as well as the B-specific non-disjunction control region. The DNA replication, chromatin composition and transcription behaviour of the non-disjunction regions were determined. To address whether the B-marker repeats E3900 and D1100 have diverged genotypes of different origin at the sequence level, the genomic sequences of both repeats were compared between cultivated rye and weedy rye from five different origins. KEY RESULTS B chromosomes in cultivated and weedy rye have maintained a similar molecular structure at the level of subspecies. The high degree of conservation of the non-disjunction control region regarding its transcription activity, histone composition and replication underlines the functional importance of this chromosome region for the maintenance of Bs. The conserved chromosome structure suggests a monophyletic origin of the rye B. As Bs were found in different countries, it is likely that Bs were frequently present in the seed material used in early agriculture. CONCLUSIONS The surprisingly conserved chromosome structure suggests that although the rye Bs experienced rapid evolution including multiple rearrangements at the early evolutionary stages, this process has slowed significantly and may have even ceased during its recent evolution.
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Affiliation(s)
- André Marques
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, UFPE, Brazil
| | - Ali M. Banaei-Moghaddam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Sonja Klemme
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Frank R. Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Katsumasa Niwa
- Laboratory of Plant Breeding, Faculty of Agriculture, Tokyo University of Agriculture, Japan
| | - Marcelo Guerra
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, UFPE, Brazil
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
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Prakhongcheep O, Chaiprasertsri N, Terada S, Hirai Y, Srikulnath K, Hirai H, Koga A. Heterochromatin blocks constituting the entire short arms of acrocentric chromosomes of Azara's owl monkey: formation processes inferred from chromosomal locations. DNA Res 2013; 20:461-70. [PMID: 23761219 PMCID: PMC3789557 DOI: 10.1093/dnares/dst023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Centromeres and telomeres of higher eukaryotes generally contain repetitive sequences, which often form pericentric or subtelomeric heterochromatin blocks. C-banding analysis of chromosomes of Azara's owl monkey, a primate species, showed that the short arms of acrocentric chromosomes consist mostly or solely of constitutive heterochromatin. The purpose of the present study was to determine which category, pericentric, or subtelomeric is most appropriate for this heterochromatin, and to infer its formation processes. We cloned and sequenced its DNA component, finding it to be a tandem repeat sequence comprising 187-bp repeat units, which we named OwlRep. Subsequent hybridization analyses revealed that OwlRep resides in the pericentric regions of a small number of metacentric chromosomes, in addition to the short arms of acrocentric chromosomes. Further, in the pericentric regions of the acrocentric chromosomes, OwlRep was observed on the short-arm side only. This distribution pattern of OwlRep among chromosomes can be simply and sufficiently explained by assuming (i) OwlRep was transferred from chromosome to chromosome by the interaction of pericentric heterochromatin, and (ii) it was amplified there as subtelomeric heterochromatin. OwlRep carries several direct and inverted repeats within its repeat units. This complex structure may lead to a higher frequency of chromosome scission and may thus be a factor in the unique distribution pattern among chromosomes. Neither OwlRep nor similar sequences were found in the genomes of the other New World monkey species we examined, suggesting that OwlRep underwent rapid amplification after the divergence of the owl monkey lineage from lineages of the other species.
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Gornung E, Mosconi F, Annesi F, Castiglia R. The first cytogenetic description of Euleptes europaea (Gené, 1839) from Northern Sardinia reveals the highest diploid chromosome number among sphaerodactylid geckos (Sphaerodactylidae, Squamata). Comp Cytogenet 2013; 7:153-161. [PMID: 24260697 PMCID: PMC3833756 DOI: 10.3897/compcytogen.v7i2.4881] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/27/2013] [Indexed: 06/02/2023]
Abstract
The karyotype of a sphaerodactylid gecko Euleptes europaea (Gené, 1839) was assembled for the first time in this species. It is made of 2n = 42 gradually decreasing in size chromosomes, the highest chromosome number so far acknowledged in the family Sphaerodactylidae. The second chromosome pair of the karyotype appears slightly heteromorphic in the male individual. Accordingly, FISH with a telomeric probe revealed an uneven distribution of telomeric repeats on the two homologues of this pair, which may be indicative of an XY sex-determination system in the species, to be further investigated.
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Affiliation(s)
- Ekaterina Gornung
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Università di Roma “La Sapienza”, Via Alfonso Borelli 50 – 00161 – Roma – Italia
| | - Fabio Mosconi
- Cooperativa Myosotis c/o Museo Civico di Zoologia di Roma, Via Aldrovandi 18 – 00197 – Roma – Italia
| | - Flavia Annesi
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Università di Roma “La Sapienza”, Via Alfonso Borelli 50 – 00161 – Roma – Italia
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Università di Roma “La Sapienza”, Via Alfonso Borelli 50 – 00161 – Roma – Italia
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Romanenko SA, Perelman PL, Trifonov VA, Graphodatsky AS. Chromosomal evolution in Rodentia. Heredity (Edinb) 2012; 108:4-16. [PMID: 22086076 PMCID: PMC3238120 DOI: 10.1038/hdy.2011.110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 11/08/2022] Open
Abstract
Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution.
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Affiliation(s)
- S A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.
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Gornung E, Bezerra AMR, Castiglia R. Comparative chromosome mapping of the rRNA genes and telomeric repeats in three Italian pine voles of the Microtus savii s.l. complex (Rodentia, Cricetidae). Comp Cytogenet 2011; 5:247-257. [PMID: 24260633 PMCID: PMC3833774 DOI: 10.3897/compcytogen.v5i3.1429] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 06/23/2011] [Indexed: 06/02/2023]
Abstract
The Microtus (Terricola) savii s. l. complex is a group of five species/subspecies of the Italian pine voles, which diverged at different times either with or without chromosomal differentiation. The evidence of chromosomal diversification has so far concerned the shape of the sex chromosomes, especially the X chromosome. Three taxa of the group, Microtus savii savii, Microtus savii nebrodensis, and Microtus savii tolfetanus have identical karyotypes with metacentric X chromosomes. The X chromosomes of Microtus brachycercus and Microtus brachycercus niethammericus are, respectively, subtelocentric and acrocentric in shape. The Microtus savii complex has been long an object of conventional karyological studies, but comparative molecular cytogenetic data were completely missing. Therefore, we conducted a comparative chromosomal mapping of rRNA genes (rDNA) and telomeric repeats in three of the five taxa of the group: Microtus savii savii, Microtus savii nebrodensis, and Microtus brachycercus niethammericus, each of which belongs to a distinct mitochondrial clade.The survey revealed that differentiation of the clades was accompanied by remarkable changes with regard to the number and locations of the rDNA sites. Thus, Microtus savii savii and Microtus savii nebrodensis have especially high numbers of rDNA sites, which are located in the centromeric regions of, correspondingly, 18 and 13 chromosome pairs, whereas Microtus brachycercus niethammericus shows variable (8-10) and heteromorphic rDNA sites on both centromeric and telomeric regions. Interstitial telomeric sites (ITS), which are believed to indicate possible breakpoints of recurring chromosomal rearrangements, are present on the largest biarmed chromosomes and on the metacentric X chromosomes in Microtus savii savii and Microtus savii nebrodensis. These preliminary results are discussed in the context of recent advances in phylogeny of the group, as well as the rDNA genomic organization and X chromosome rearrangements in the genus Microtus.
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Affiliation(s)
- Ekaterina Gornung
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, University of Rome “Sapienza”, via Alfonso Borelli 50, 00161, Rome, Italy
| | | | - Riccardo Castiglia
- Departamento de Zoologia, Universidade de Brasília, 70910–900, Brasília, DF, Brazil
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Wülker WF, Kiknadze I, Istomina A. Karyotypes of Chironomus Meigen (Diptera: Chironomidae) species from Africa. Comp Cytogenet 2011; 5:23-46. [PMID: 24260617 PMCID: PMC3833731 DOI: 10.3897/compcytogen.v5i1.975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 03/15/2011] [Indexed: 06/02/2023]
Abstract
The karyotypes of six African Chironomus species (Chironomus alluaudi Kieffer, 1913, Chironomus transvaalensis Kieffer, 1923, Chironomus sp. Nakuru, Chironomus formosipennis Kieffer, 1908, Chironomus prope pulcher Wiedemann, 1830, Chironomus sp. Kisumu) were investigated; four of these karyotypes were described for the first time (Chironomus sp. Nakuru, Chironomus formosipennis, Chironomus prope pulcher, Chironomus sp. Kisumu). Of the six Chironomus karyotypes, three had "pseudothummi" cytocomplex chromosome arms combinations AE CD BF G (Chironomus alluaudi, Chironomus transvaalensis, Chironomus sp. Nakuru), two had "thummi"cytocomplex arms combinations AB CD EF G (Chironomus formosipennis, Chironomus prope pulcher), and one had "parathummi"armcombinations AC BF DE G (Chironomus sp. Kisumu). Thus, three of the ten main cytocomplexes known were detected in Africa. Detailed photomaps of all chromosome arms, with the exception of arms B and G, were prepared for the karyotypes of Chironomus alluaudi, Chironomus transvaalensis, Chironomus sp. Nakuru, Chironomus prope pulcher; the karyotypes of Chironomus formosipennis, Chironomus sp. Kisumucould only be fragmentarily mapped. Endemic African banding sequences were characteristic for most of the chromosomal arms in all species studied. However, basic sequences, which can be present in different Chironomus species on different continents (Wülker, 1980; Kiknadze et al. 2008), were also detected also in several African species (Chironomus alluaudi, Chironomus sp. Nakuru, and Chironomus formosipennis). The banding sequences of African species studied allow discussion of the derivation of modern banding patterns from hypothetical species, living before separation of cytocomplexes and continents.
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Affiliation(s)
| | - I.I. Kiknadze
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Lavrentiev pr. 10, Russia
| | - A.G. Istomina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Lavrentiev pr. 10, Russia
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Gifalli-Iughetti C, Koiffmann CP. Synteny of human chromosomes 14 and 15 in the platyrrhines (Primates, Platyrrhini). Genet Mol Biol 2009; 32:786-91. [PMID: 21637455 PMCID: PMC3036896 DOI: 10.1590/s1415-47572009005000069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 03/11/2009] [Indexed: 11/22/2022] Open
Abstract
In order to study the intra- and interspecific variability of the 14/15 association in Platyrrhini, we analyzed 15 species from 13 genera, including species that had not been described yet. The DNA libraries of human chromosomes 14 and 15 were hybridized to metaphases of Alouatta guariba clamitans, A. caraya, A. sara, Ateles paniscus chamek, Lagothrix lagothricha, Brachyteles arachnoides, Saguinus midas midas, Leontopithecus chrysomelas, Callimico goeldii, Callithrix sp., Cebus apella, Aotus nigriceps, Cacajao melanocephalus,Chiropotes satanas and Callicebus caligatus. The 14/15 hybridization pattern was present in 13 species, but not in Alouatta sara that showed a 14/15/14 pattern and Aotus nigriceps that showed a 15/14/15/14 pattern. In the majority of the species, the HSA 14 homologue retained synteny for the entire chromosome, whereas the HSA 15 homologue displayed fragmented segments. Within primates, the New World monkeys represent the taxon with the highest variability in chromosome number (2n = 16 to 62). The presence of the HSA 14/15 association in all species and subspecies studied herein confirms that this association is the ancestral condition for platyrrhines and that this association has been retained in most platyrrhines, despite the occurrence of extensive inter- and intrachromosomal rearrangements in this infraorder of Primates.
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Affiliation(s)
- Cristiani Gifalli-Iughetti
- Centro de Estudos do Genoma Humano, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP Brazil
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Abstract
For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.
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Affiliation(s)
- J L Bennetzen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA
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Abstract
It has long been suspected that maize is the product of an historical tetraploid event. Several observations support this possibility, including the fact that the maize genome contains duplicated chromosomal segments with colinear gene arrangements. Some of the genes from these duplicated segments have been sequenced. In this study, we examine the pattern of sequence divergence among 14 pairs of duplicated genes. We compare the pattern of divergence to patterns predicted by four models of the evolution of the maize genome-autotetraploidy, genomic allotetraploidy, segmental allotetraploidy, and multiple segmental duplications. Our analyses indicate that coalescent times for duplicated sequences fall into two distinct groups, corresponding to roughly 20.5 and 11.4 million years. This observation strongly discounts the possibility that the maize genome is the product of a genomic allotetraploid event, and it is also difficult to reconcile with either autotetraploidy or multiple independent segmental duplications. However, the presence of two (and only two) coalescent times is predicted by the segmental allotetraploid model. If the maize genome is the product of a segmental allotetraploid event, as these data suggest, then its two diploid progenitors diverged roughly 20.5 million years ago (Mya), and the allotetraploid event probably occurred approximately 11.4 Mya. Comparison of maize and sorghum sequences suggests that one of the two ancestral diploids shares a more recent common ancestor with sorghum than it does with the other ancestral diploid.
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Affiliation(s)
- B S Gaut
- Department of Plant Sciences and Center for Theoretical and Applied Genetics, Rutgers University, New Brunswick, NJ 08903, USA
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