1
|
Guimarães EMC, Viana PF, Pinheiro-Figliuolo VS, Marajó L, de Sousa E Souza JF, Feldberg E. Repetitive DNA Mapping Reveals Multiple Sex Chromosomes X1X1X2X2/X1X2Y in Pseudotylosurus microps (Günther 1866) (Beloniformes, Teleostei) from the Amazon. Sex Dev 2025; 18:70-80. [PMID: 39993387 DOI: 10.1159/000544037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 02/05/2025] [Indexed: 02/26/2025] Open
Abstract
INTRODUCTION Needlefish (Belonidae family) comprises 44 known species distributed worldwide. These species are predominantly marine but include estuarine representatives and 12 freshwater species. Among the recognized species, 8 are endemic to South American rivers. Cytogenetic studies of Belonidae are scarce and mostly limited to describing the diploid chromosome number (2n) and karyotypic structure. METHODS We used classical and molecular cytogenetic markers to karyotypically characterize Pseudotylosurus microps to understand the evolutionary processes of Belonidae species in the Amazon basin. RESULTS P. microps exhibited different diploid numbers between males (2n = 47, 3m + 3sm + 41st/a FN = 53) and females (2n = 48, 4m + 4sm + 40st/a FN = 56). Our study revealed the first case of multiple sex chromosomes in the Belonidae family. CONCLUSION These findings describe a multiple sex chromosome system of the type X1X1X2X2/X1X2Y. The C-banding pattern and 5S rDNA mapping suggest that this system likely resulted from a tandem fusion between a homolog of pair 1 and a homolog of pair 3, producing a large acrocentric Y chromosome. We propose that karyotypic changes due to internal chromosomal rearrangements, as observed in P. microps, can lead to species diversification and, in some cases, the emergence of a heteromorphic and multiple sex chromosome system.
Collapse
Affiliation(s)
- Erika Milena Corrêa Guimarães
- Postgraduate Program in Genetics, Conservation and Evolutionary Biology - PPG-GCBEv, Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Patrik Ferreira Viana
- Postgraduate Program in Genetics, Conservation and Evolutionary Biology - PPG-GCBEv, Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Vanessa Susan Pinheiro-Figliuolo
- Postgraduate Program in Genetics, Conservation and Evolutionary Biology - PPG-GCBEv, Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Leandro Marajó
- Postgraduate Program in Genetics, Conservation and Evolutionary Biology - PPG-GCBEv, Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - José Francisco de Sousa E Souza
- Postgraduate Program in Genetics, Conservation and Evolutionary Biology - PPG-GCBEv, Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Eliana Feldberg
- Postgraduate Program in Genetics, Conservation and Evolutionary Biology - PPG-GCBEv, Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
- Laboratory of Animal Genetics, Biodiversity Coordination, National Institute of Amazonian Research (INPA), Manaus, Brazil
| |
Collapse
|
2
|
Yang F, Cao LJ, Nguyen P, Ma ZZ, Chen JC, Song W, Wei SJ. Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths. Genome Res 2025; 35:66-77. [PMID: 39762048 PMCID: PMC11789632 DOI: 10.1101/gr.279569.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 11/26/2024] [Indexed: 01/24/2025]
Abstract
Sex chromosomes can expand through fusion with autosomes, thereby acquiring unique evolutionary patterns. In butterflies and moths (Lepidoptera), these sex chromosome-autosome (SA) fusions occur relatively frequently, suggesting possible evolutionary advantages. Here, we investigated how SA fusion affects chromosome features and molecular evolution in leafroller moths (Lepidoptera: Tortricidae). Phylogenomic analysis showed that Tortricidae diverged ∼124 million years ago, accompanied by an SA fusion between the Merian elements M(20 + 17) and MZ. In contrast to partial autosomal fusions, the fused neo-Z Chromosome developed a hierarchical architecture, in which the three elements exhibit heterogeneous sequence features and evolutionary patterns. Specifically, the M17 part had a distinct base composition and chromatin domains. Unlike M20 and MZ, M17 was expressed at the same levels as autosomes in both sexes, compensating for the lost gene dosage in females. Concurrently, the SA fusion drove M17 as an evolutionary hotspot, accelerating the evolution of several genes related to ecological adaptation (e.g., ABCCs) and facilitating the divergence of closely related species, whereas the undercompensated M20 did not show such an effect. Thus, accelerated evolution under a novel pattern of dosage compensation may have favored the adaptive radiation of this group. This study demonstrates the association between a karyotype variant and adaptive evolution and explains the recurrent SA fusion in the Lepidoptera.
Collapse
Affiliation(s)
- Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Institute of Zoology, Chinese Academy of Science, Beijing 100101, China
| | - Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 Ceske Budejovice, Czech Republic
| | - Zhong-Zheng Ma
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China;
| |
Collapse
|
3
|
Palmer Droguett DH, Fletcher M, Alston BT, Kocher S, Cabral-de-Mello DC, Wright AE. Neo-Sex Chromosome Evolution in Treehoppers Despite Long-Term X Chromosome Conservation. Genome Biol Evol 2024; 16:evae264. [PMID: 39657114 DOI: 10.1093/gbe/evae264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 11/20/2024] [Accepted: 12/04/2024] [Indexed: 12/17/2024] Open
Abstract
Sex chromosomes follow distinct evolutionary trajectories compared to the rest of the genome. In many cases, sex chromosomes (X and Y or Z and W) significantly differentiate from one another resulting in heteromorphic sex chromosome systems. Such heteromorphic systems are thought to act as an evolutionary trap that prevents subsequent turnover of the sex chromosome system. For old, degenerated sex chromosome systems, chromosomal fusion with an autosome may be one way that sex chromosomes can "refresh" their sequence content. We investigated these dynamics using treehoppers (hemipteran insects of the family Membracidae), which ancestrally have XX/X0 sex chromosomes. We assembled the most complete reference assembly for treehoppers to date for Umbonia crassicornis and employed comparative genomic analyses of 12 additional treehopper species to analyze X chromosome variation across different evolutionary timescales. We find that the X chromosome is largely conserved, with one exception being an X-autosome fusion in Calloconophora caliginosa. We also compare the ancestral treehopper X with other X chromosomes in Auchenorrhyncha (the clade containing treehoppers, leafhoppers, spittlebugs, cicadas, and planthoppers), revealing X conservation across more than 300 million years. These findings shed light on chromosomal evolution dynamics in treehoppers and the role of chromosomal rearrangements in sex chromosome evolution.
Collapse
Affiliation(s)
- Daniela H Palmer Droguett
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Micah Fletcher
- Department of Ecology and Evolutionary Biology, the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ben T Alston
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Sarah Kocher
- Department of Ecology and Evolutionary Biology, the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Diogo C Cabral-de-Mello
- Department of General and Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Alison E Wright
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| |
Collapse
|
4
|
Mora P, Hospodářská M, Voleníková AC, Koutecký P, Štundlová J, Dalíková M, Walters JR, Nguyen P. Sex-biased gene content is associated with sex chromosome turnover in Danaini butterflies. Mol Ecol 2024; 33:e17256. [PMID: 38180347 PMCID: PMC11628659 DOI: 10.1111/mec.17256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here, we investigate the evolutionary origin of the previously reported Danaus neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of Tirumala septentrionis (subtribe Danaina), Ideopsis similis (Amaurina), Idea leuconoe (Euploeina) and Lycorea halia (Itunina) and identified their Z-linked scaffolds. We found that the Danaus neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the Melitaea cinxia chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in I. similis and independent fusion occurred between ancestral Z chromosome and McChr12 in L. halia. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analysing the genomic distribution of sex-biased genes in I. leuconoe and L. halia. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both I. leuconoe and L. halia appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z varies across tissues and species.
Collapse
Affiliation(s)
- Pablo Mora
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Present address:
University of JaénJaénSpain
| | - Monika Hospodářská
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Institute of EntomologyBiology Centre of the Czech Academy of SciencesČeské BudějoviceCzech Republic
| | | | - Petr Koutecký
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Jana Štundlová
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Martina Dalíková
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKansasUSA
| | - James R. Walters
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKansasUSA
| | - Petr Nguyen
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Institute of EntomologyBiology Centre of the Czech Academy of SciencesČeské BudějoviceCzech Republic
| |
Collapse
|
5
|
Rueda-M N, Pardo-Diaz C, Montejo-Kovacevich G, McMillan WO, Kozak KM, Arias CF, Ready J, McCarthy S, Durbin R, Jiggins CD, Meier JI, Salazar C. Genomic evidence reveals three W-autosome fusions in Heliconius butterflies. PLoS Genet 2024; 20:e1011318. [PMID: 39024186 PMCID: PMC11257349 DOI: 10.1371/journal.pgen.1011318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
Collapse
Affiliation(s)
- Nicol Rueda-M
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Krzysztof M. Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
- Museum of Vertebrate Zoology, Berkeley, California, United States of America
| | - Carlos F. Arias
- Smithsonian Tropical Research Institute, Panama City, Panama
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, Washington DC, United States of America
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará - UFPA, Belém, Brazil
- Centre for Advanced Studies of Biodiversity - CEABIO, Belém, Brazil
| | - Shane McCarthy
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Richard Durbin
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Joana I. Meier
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| |
Collapse
|
6
|
Cao LJ, Yang F, Chen JC, Wei SJ. Nuclear and mitochondrial genomes of the plum fruit moth Grapholita funebrana. Sci Data 2024; 11:692. [PMID: 38926434 PMCID: PMC11208415 DOI: 10.1038/s41597-024-03522-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The plum fruit moth Grapholita funebrana (Tortricidae, Lepidoptera) is an important pest of many wild and cultivated stone fruits and other plants in the family Rosaceae. Here, we assembled its nuclear and mitochondrial genomes using Illumina, Nanopore, and Hi-C sequencing technologies. The nuclear genome size is 570.9 Mb, with a repeat rate of 51.28%, and a BUCSO completeness of 97.7%. The karyotype for males is 2n = 56. We identified 17,979 protein-coding genes, 5,643 tRNAs, and 94 rRNAs. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomes provide resources to understand the genetics, ecology, and genome evolution of the tortricid moths.
Collapse
Affiliation(s)
- Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| |
Collapse
|
7
|
Han MJ, Luo C, Hu H, Lin M, Lu K, Shen J, Ren J, Ye Y, Westhof E, Tong X, Dai F. Multiple independent origins of the female W chromosome in moths and butterflies. SCIENCE ADVANCES 2024; 10:eadm9851. [PMID: 38896616 PMCID: PMC11186504 DOI: 10.1126/sciadv.adm9851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of the lepidopteran W chromosome remains poorly understood. Here, we assemble the genome from females down to the chromosome level of a model insect (Bombyx mori) and identify a W chromosome of approximately 10.1 megabase using a newly developed tool. In addition, we identify 3593 genes that were not previously annotated in the genomes of B. mori. Comparisons of 21 lepidopteran species (including 17 ZW and four Z0 systems) and three trichopteran species (Z0 system) reveal that the formation of Ditrysia W involves multiple mechanisms, including previously proposed canonical and noncanonical models, as well as a newly proposed mechanism called single-Z turnover. We conclude that there are multiple independent origins of the W chromosome in the Ditrysia (most moths and all butterflies) of Lepidoptera.
Collapse
Affiliation(s)
- Min-Jin Han
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Chaorui Luo
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Hai Hu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Meixing Lin
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Kunpeng Lu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Jianghong Shen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Jianyu Ren
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Yanzhuo Ye
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Eric Westhof
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire, UPR9002 CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Xiaoling Tong
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
8
|
van’t Hof AE, Whiteford S, Yung CJ, Yoshido A, Zrzavá M, de Jong MA, Tan KL, Zhu D, Monteiro A, Brakefield PM, Marec F, Saccheri IJ. Zygosity-based sex determination in a butterfly drives hypervariability of Masculinizer. SCIENCE ADVANCES 2024; 10:eadj6979. [PMID: 38701204 PMCID: PMC11067997 DOI: 10.1126/sciadv.adj6979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Nature has devised many ways of producing males and females. Here, we report on a previously undescribed mechanism for Lepidoptera that functions without a female-specific gene. The number of alleles or allele heterozygosity in a single Z-linked gene (BaMasc) is the primary sex-determining switch in Bicyclus anynana butterflies. Embryos carrying a single BaMasc allele develop into WZ (or Z0) females, those carrying two distinct alleles develop into ZZ males, while (ZZ) homozygotes initiate female development, have mismatched dosage compensation, and die as embryos. Consequently, selection against homozygotes has favored the evolution of spectacular allelic diversity: 205 different coding sequences of BaMasc were detected in a sample of 246 females. The structural similarity of a hypervariable region (HVR) in BaMasc to the HVR in Apis mellifera csd suggests molecular convergence between deeply diverged insect lineages. Our discovery of this primary switch highlights the fascinating diversity of sex-determining mechanisms and underlying evolutionary drivers.
Collapse
Affiliation(s)
- Arjen E. van’t Hof
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Sam Whiteford
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Carl J. Yung
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Maaike A. de Jong
- Netherlands eScience Center, Science Park 402, 1098 XH Amsterdam, Netherlands
| | - Kian-Long Tan
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Dantong Zhu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | | | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Ilik J. Saccheri
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| |
Collapse
|
9
|
Wang Y, Yao Y, Zhang Y, Qian X, Guo D, Coates BS. A chromosome-level genome assembly of the soybean pod borer: insights into larval transcriptional response to transgenic soybean expressing the pesticidal Cry1Ac protein. BMC Genomics 2024; 25:355. [PMID: 38594617 PMCID: PMC11005160 DOI: 10.1186/s12864-024-10216-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Genetically modified (GM) crop plants with transgenic expression of Bacillus thuringiensis (Bt) pesticidal proteins are used to manage feeding damage by pest insects. The durability of this technology is threatened by the selection for resistance in pest populations. The molecular mechanism(s) involved in insect physiological response or evolution of resistance to Bt is not fully understood. RESULTS To investigate the response of a susceptible target insect to Bt, the soybean pod borer, Leguminivora glycinivorella (Lepidoptera: Tortricidae), was exposed to soybean, Glycine max, expressing Cry1Ac pesticidal protein or the non-transgenic parental cultivar. Assessment of larval changes in gene expression was facilitated by a third-generation sequenced and scaffolded chromosome-level assembly of the L. glycinivorella genome (657.4 Mb; 27 autosomes + Z chromosome), and subsequent structural annotation of 18,197 RefSeq gene models encoding 23,735 putative mRNA transcripts. Exposure of L. glycinivorella larvae to transgenic Cry1Ac G. max resulted in prediction of significant differential gene expression for 204 gene models (64 up- and 140 down-regulated) and differential splicing among isoforms for 10 genes compared to unexposed cohorts. Differentially expressed genes (DEGs) included putative peritrophic membrane constituents, orthologs of Bt receptor-encoding genes previously linked or associated with Bt resistance, and those involved in stress responses. Putative functional Gene Ontology (GO) annotations assigned to DEGs were significantly enriched for 36 categories at GO level 2, respectively. Most significantly enriched cellular component (CC), biological process (BP), and molecular function (MF) categories corresponded to vacuolar and microbody, transport and metabolic processes, and binding and reductase activities. The DEGs in enriched GO categories were biased for those that were down-regulated (≥ 0.783), with only MF categories GTPase and iron binding activities were bias for up-regulation genes. CONCLUSIONS This study provides insights into pathways and processes involved larval response to Bt intoxication, which may inform future unbiased investigations into mechanisms of resistance that show no evidence of alteration in midgut receptors.
Collapse
Affiliation(s)
- Yangzhou Wang
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yao Yao
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yunyue Zhang
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xueyan Qian
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Dongquan Guo
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Brad S Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, 532 Science II, 2310 Pammel Dr., Ames, IA, 50011, USA.
| |
Collapse
|
10
|
Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M. Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. Nat Ecol Evol 2024; 8:777-790. [PMID: 38383850 PMCID: PMC11009112 DOI: 10.1038/s41559-024-02329-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes and show that the chromosomes of extant lepidopterans are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact through 250 million years of evolution and diversification. Against this stable background, eight lineages have undergone extensive reorganization either through numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions often involve small, repeat-rich Merian elements and the sex-linked element. Our results reveal the constraints on genome architecture in Lepidoptera and provide a deeper understanding of chromosomal rearrangements in eukaryotic genome evolution.
Collapse
Affiliation(s)
| | - Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
| |
Collapse
|
11
|
Rovatsos M, Mazzoleni S, Augstenová B, Altmanová M, Velenský P, Glaw F, Sanchez A, Kratochvíl L. Heteromorphic ZZ/ZW sex chromosomes sharing gene content with mammalian XX/XY are conserved in Madagascan chameleons of the genus Furcifer. Sci Rep 2024; 14:4898. [PMID: 38418601 PMCID: PMC10901801 DOI: 10.1038/s41598-024-55431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
Chameleons are well-known lizards with unique morphology and physiology, but their sex determination has remained poorly studied. Madagascan chameleons of the genus Furcifer have cytogenetically distinct Z and W sex chromosomes and occasionally Z1Z1Z2Z2/Z1Z2W multiple neo-sex chromosomes. To identify the gene content of their sex chromosomes, we microdissected and sequenced the sex chromosomes of F. oustaleti (ZZ/ZW) and F. pardalis (Z1Z1Z2Z2/Z1Z2W). In addition, we sequenced the genomes of a male and a female of F. lateralis (ZZ/ZW) and F. pardalis and performed a comparative coverage analysis between the sexes. Despite the notable heteromorphy and distinctiveness in heterochromatin content, the Z and W sex chromosomes share approximately 90% of their gene content. This finding demonstrates poor correlation of the degree of differentiation of sex chromosomes at the cytogenetic and gene level. The test of homology based on the comparison of gene copy number variation revealed that female heterogamety with differentiated sex chromosomes remained stable in the genus Furcifer for at least 20 million years. These chameleons co-opted for the role of sex chromosomes the same genomic region as viviparous mammals, lacertids and geckos of the genus Paroedura, which makes these groups excellent model for studies of convergent and divergent evolution of sex chromosomes.
Collapse
Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | | | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Munich, Germany
| | - Antonio Sanchez
- Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
12
|
Scarparo G, Palanchon M, Brelsford A, Purcell J. Social antagonism facilitates supergene expansion in ants. Curr Biol 2023; 33:5085-5095.e4. [PMID: 37979579 PMCID: PMC10860589 DOI: 10.1016/j.cub.2023.10.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/07/2023] [Accepted: 10/25/2023] [Indexed: 11/20/2023]
Abstract
Antagonistic selection has long been considered a major driver of the formation and expansion of sex chromosomes. For example, sexually antagonistic variation on an autosome can select for suppressed recombination between that autosome and the sex chromosome, leading to a neo-sex chromosome. Autosomal supergenes, chromosomal regions containing tightly linked variants affecting the same complex trait, share similarities with sex chromosomes, raising the possibility that sex chromosome evolution models can explain the evolution of genome structure and recombination in other contexts. We tested this premise in a Formica ant species, wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. We discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is in strong linkage disequilibrium with one chromosome 3 haplotype (P2) found in multi-queen (polygyne) colonies. We suggest that queen miniaturization is strongly disfavored in the single-queen (monogyne) background and is thus socially antagonistic. As such, divergent selection experienced by ants living in alternative social "environments" (monogyne and polygyne) may have contributed to the emergence of a genetic polymorphism on chromosome 9 and associated queen-size dimorphism. Consequently, an ancestral polygyne-associated haplotype may have expanded to include the polymorphism on chromosome 9, resulting in a larger region of suppressed recombination spanning two chromosomes. This process is analogous to the formation of neo-sex chromosomes and consistent with models of expanding regions of suppressed recombination. We propose that miniaturized queens, 16%-20% smaller than queens without 9r, could be incipient intraspecific social parasites.
Collapse
Affiliation(s)
- Giulia Scarparo
- Department of Entomology, University of California, Riverside, 165 Entomology Bldg. Citrus Drive, Riverside, CA 92521, USA.
| | - Marie Palanchon
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, 2710 Life Science Bldg., Riverside, CA 92521, USA
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, 2710 Life Science Bldg., Riverside, CA 92521, USA
| | - Jessica Purcell
- Department of Entomology, University of California, Riverside, 165 Entomology Bldg. Citrus Drive, Riverside, CA 92521, USA.
| |
Collapse
|
13
|
Pospíšilová K, Van't Hof AE, Yoshido A, Kružíková R, Visser S, Zrzavá M, Bobryshava K, Dalíková M, Marec F. Masculinizer gene controls male sex determination in the codling moth, Cydia pomonella. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 160:103991. [PMID: 37536576 DOI: 10.1016/j.ibmb.2023.103991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
The molecular mechanisms of sex determination in moths and butterflies (Lepidoptera) with female heterogamety (WZ/ZZ) are poorly understood, except in the silkworm Bombyx mori. However, the Masculinizer (Masc) gene that controls male development and dosage compensation in B. mori, appears to be conserved in Lepidoptera, as its masculinizing function was recently confirmed in several moth species. In this work, we investigated the role of the Masc gene in sex determination of the codling moth Cydia pomonella (Tortricidae), a globally important pest of pome fruits and walnuts. The gene structure of the C. pomonella Masc ortholog, CpMasc, is similar to B. mori Masc. However, unlike B. mori, we identified 14 splice variants of CpMasc in the available transcriptomes. Subsequent screening for sex specificity and genetic variation using publicly available data and RT-PCR revealed three male-specific splice variants. Then qPCR analysis of these variants revealed sex-biased expression showing a peak only in early male embryos. Knockdown of CpMasc by RNAi during early embryogenesis resulted in a shift from male-to female-specific splicing of the C. pomonella doublesex (Cpdsx) gene, its downstream effector, in ZZ embryos, leading to a strongly female-biased sex ratio. These data clearly demonstrate that CpMasc functions as a masculinizing gene in the sex-determining cascade of C. pomonella. Our study also showed that CpMasc transcripts are provided maternally, as they were detected in unfertilized eggs after oviposition and in mature eggs dissected from virgin females. This finding is unique, as maternal provision of mRNA has rarely been studied in Lepidoptera.
Collapse
Affiliation(s)
- Kristýna Pospíšilová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Arjen E Van't Hof
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic.
| | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic.
| | - Renata Kružíková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Sander Visser
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; School of Science and Engineering, University of Groningen, 9700 CC, Groningen, the Netherlands.
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Kseniya Bobryshava
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic.
| |
Collapse
|
14
|
Kitano J, Ansai S, Fujimoto S, Kakioka R, Sato M, Mandagi IF, Sumarto BKA, Yamahira K. A Cryptic Sex-Linked Locus Revealed by the Elimination of a Master Sex-Determining Locus in Medaka Fish. Am Nat 2023; 202:231-240. [PMID: 37531272 DOI: 10.1086/724840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
AbstractSex chromosomes rapidly turn over in several taxonomic groups. Sex chromosome turnover is generally thought to start with the appearance of a new sex-determining gene on an autosome while an old sex-determining gene still exists, followed by the fixation of the new one. However, we do not know how prevalent the transient state is, where multiple sex-determining loci coexist within natural populations. Here, we removed a Y chromosome with a master male-determining gene DMY from medaka fish using high temperature-induced sex-reversed males. After four generations, the genomic characteristics of a sex chromosome were found on one chromosome, which was an autosome in the original population. Thus, the elimination of a master sex-determining locus can reveal a cryptic locus with a possible sex-determining effect, which can be the seed for sex chromosome turnover. Our results suggest that populations that seem to have a single-locus XY system may have other chromosomal regions with sex-determining effects. In conclusion, the coexistence of multiple sex-determining genes in a natural population may be more prevalent than previously thought. Experimental elimination of a master sex-determining locus may serve as a promising method for finding a locus that can be a protosex chromosome.
Collapse
|
15
|
Pazhenkova EA, Lukhtanov VA. Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera. Chromosome Res 2023; 31:16. [PMID: 37300756 DOI: 10.1007/s10577-023-09725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
In the evolution of many organisms, periods of slow genome reorganization (= chromosomal conservatism) are interrupted by bursts of numerous chromosomal changes (= chromosomal megaevolution). Using comparative analysis of chromosome-level genome assemblies, we investigated these processes in blue butterflies (Lycaenidae). We demonstrate that the phase of chromosome number conservatism is characterized by the stability of most autosomes and dynamic evolution of the sex chromosome Z, resulting in multiple variants of NeoZ chromosomes due to autosome-sex chromosome fusions. In contrast during the phase of rapid chromosomal evolution, the explosive increase in chromosome number occurs mainly through simple chromosomal fissions. We show that chromosomal megaevolution is a highly non-random canalized process, and in two phylogenetically independent Lysandra lineages, the drastic parallel increase in number of fragmented chromosomes was achieved, at least partially, through reuse of the same ancestral chromosomal breakpoints. In species showing chromosome number doubling, we found no blocks of duplicated sequences or duplicated chromosomes, thus refuting the hypothesis of polyploidy. In the studied taxa, long blocks of interstitial telomere sequences (ITSs) consist of (TTAGG)n arrays interspersed with telomere-specific retrotransposons. ITSs are sporadically present in rapidly evolving Lysandra karyotypes, but not in the species with ancestral chromosome number. Therefore, we hypothesize that the transposition of telomeric sequences may be triggers of the rapid chromosome number increase. Finally, we discuss the hypothetical genomic and population mechanisms of chromosomal megaevolution and argue that the disproportionally high evolutionary role of the Z sex chromosome can be additionally reinforced by sex chromosome-autosome fusions and Z-chromosome inversions.
Collapse
Affiliation(s)
- Elena A Pazhenkova
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya Nab. 1, 199034, St. Petersburg, Russia.
| |
Collapse
|
16
|
Pazhenkova EA, Lukhtanov VA. Whole-Genome Analysis Reveals the Dynamic Evolution of Holocentric Chromosomes in Satyrine Butterflies. Genes (Basel) 2023; 14:437. [PMID: 36833364 PMCID: PMC9956908 DOI: 10.3390/genes14020437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are poorly understood. Here, we analyzed chromosome-scale genome assemblies to identify structural rearrangements between karyotypes of satyrine butterfly species. For the species pair Erebia ligea-Maniola jurtina, sharing the ancestral diploid karyotype 2n = 56 + ZW, we demonstrate a high level of chromosomal macrosynteny and nine inversions separating these species. We show that the formation of a karyotype with a low number of chromosomes (2n = 36 + ZW) in Erebia aethiops was based on ten fusions, including one autosome-sex chromosome fusion, resulting in a neo-Z chromosome. We also detected inversions on the Z sex chromosome that were differentially fixed between the species. We conclude that chromosomal evolution is dynamic in the satyrines, even in the lineage that preserves the ancestral chromosome number. We hypothesize that the exceptional role of Z chromosomes in speciation may be further enhanced by inversions and sex chromosome-autosome fusions. We argue that not only fusions/fissions but also inversions are drivers of the holocentromere-mediated mode of chromosomal speciation.
Collapse
Affiliation(s)
- Elena A. Pazhenkova
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
| |
Collapse
|
17
|
Marajó L, Viana PF, Ferreira AMV, Py-Daniel LHR, Cioffi MDB, Sember A, Feldberg E. Chromosomal rearrangements and the first indication of an ♀X 1 X 1 X 2 X 2 /♂X 1 X 2 Y sex chromosome system in Rineloricaria fishes (Teleostei: Siluriformes). JOURNAL OF FISH BIOLOGY 2023; 102:443-454. [PMID: 36427042 DOI: 10.1111/jfb.15275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Rineloricaria is the most diverse genus within the freshwater fish subfamily Loricariinae, and it is widely distributed in the Neotropical region. Despite limited cytogenetic data, records from southern and south-eastern Brazil suggest a high rate of chromosomal rearrangements in this genus, mirrored in remarkable inter- and intraspecific karyotype variability. In the present work, we investigated the karyotype features of Rineloricaria teffeana, an endemic representative from northern Brazil, using both conventional and molecular cytogenetic techniques. We revealed different diploid chromosome numbers (2n) between sexes (33♂/34♀), which suggests the presence of an ♀X1 X1 X2 X2 /♂X1 X2 Y multiple sex chromosome system. The male-limited Y chromosome was the largest and the only biarmed element in the karyotype, implying Y-autosome fusion as the most probable mechanism behind its origination. C-banding revealed low amounts of constitutive heterochromatin, mostly confined to the (peri)centromeric regions of most chromosomes (including the X2 and the Y) but also occupying the distal regions of a few chromosomal pairs. The chromosomal localization of the 18S ribosomal DNA (rDNA) clusters revealed a single site on chromosome pair 4, which was adjacent to the 5S rDNA cluster. Additional 5S rDNA loci were present on the autosome pair 8, X1 chromosome, and in the presumed fusion point on the Y chromosome. The probe for telomeric repeat motif (TTAGGG)n revealed signals of variable intensities at the ends of all chromosomes except for the Y chromosome, where no detectable signals were evidenced. Male-to-female comparative genomic hybridization revealed no sex-specific or sex-biased repetitive DNA accumulations, suggesting a presumably low level of neo-Y chromosome differentiation. We provide evidence that rDNA sites might have played a role in the formation of this putative multiple sex chromosome system and that chromosome fusions originate through different mechanisms among different Rineloricaria species.
Collapse
Affiliation(s)
- Leandro Marajó
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Alex Matheus Viana Ferreira
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Lúcia Helena Rapp Py-Daniel
- Coleção de Peixes, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Libechov, Czech Republic
| | - Eliana Feldberg
- Laboratório de Genética Animal, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| |
Collapse
|
18
|
Höök L, Näsvall K, Vila R, Wiklund C, Backström N. High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.). Chromosome Res 2023; 31:2. [PMID: 36662301 PMCID: PMC9859909 DOI: 10.1007/s10577-023-09713-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023]
Abstract
Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling.
Collapse
Affiliation(s)
- L Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
| | - K Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
| | - R Vila
- Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - C Wiklund
- Department of Zoology, Division of Ecology, Stockholm University, Stockholm, Sweden
| | - N Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| |
Collapse
|
19
|
Gasparotto AE, Milani D, Martí E, Ferretti ABSM, Bardella VB, Hickmann F, Zrzavá M, Marec F, Cabral-de-Mello DC. A step forward in the genome characterization of the sugarcane borer, Diatraea saccharalis: karyotype analysis, sex chromosome system and repetitive DNAs through a cytogenomic approach. Chromosoma 2022; 131:253-267. [PMID: 36219241 DOI: 10.1007/s00412-022-00781-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022]
Abstract
Moths of the family Crambidae include a number of pests that cause economic losses to agricultural crops. Despite their economic importance, little is known about their genome architecture and chromosome evolution. Here, we characterized the chromosomes and repetitive DNA of the sugarcane borer Diatraea saccharalis using a combination of low-pass genome sequencing, bioinformatics, and cytogenetic methods, focusing on the sex chromosomes. Diploid chromosome numbers differed between the sexes, i.e., 2n = 33 in females and 2n = 34 in males. This difference was caused by the occurrence of a WZ1Z2 trivalent in female meiosis, indicating a multiple sex-chromosome system WZ1Z2/Z1Z1Z2Z2. A strong interstitial telomeric signal was observed on the W chromosome, indicating a fusion of the ancestral W chromosome with an autosome. Among repetitive DNAs, transposable elements (TEs) accounted for 39.18% (males) to 41.35% (females), while satDNAs accounted for only 0.214% (males) and 0.215% (females) of the genome. FISH mapping revealed different chromosomal organization of satDNAs, such as single localized clusters, spread repeats, and non-clustered repeats. Two TEs mapped by FISH were scattered. Although we found a slight enrichment of some satDNAs in the female genome, they were not differentially enriched on the W chromosome. However, we found enriched FISH signals for TEs on the W chromosome, suggesting their involvement in W chromosome degeneration and differentiation. These data shed light on karyotype and repetitive DNA dynamics due to multiple chromosome fusions in D. saccharalis, contribute to the understanding of genome structure in Lepidoptera and are important for future genomic studies.
Collapse
Affiliation(s)
- Ana E Gasparotto
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Ana Beatriz S M Ferretti
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Frederico Hickmann
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, (USP/ESALQ), University of São Paulo, Piracicaba, SP, Brazil
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil.
- Department of Experimental Biology, Genetics Area, University of Jaen, Paraje las Lagunillas s/n, 23071, Jaen, Spain.
| |
Collapse
|
20
|
Sigeman H, Zhang H, Ali Abed S, Hansson B. A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds. J Evol Biol 2022; 35:1797-1805. [PMID: 36156325 PMCID: PMC10087220 DOI: 10.1111/jeb.14096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/03/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Abstract
We report the discovery of a novel neo-sex chromosome in an African warbler, Sylvietta brachyura (northern crombec; Macrosphenidae). This species is part of the Sylvioidea superfamily, where four separate autosome-sex chromosome translocation events have previously been discovered via comparative genomics of 11 of the 22 families in this clade. Our discovery here resulted from analyses of genomic data of single species-representatives from three additional Sylvioidea families (Macrosphenidae, Pycnonotidae and Leiothrichidae). In all three species, we confirmed the translocation of a part of chromosome 4A to the sex chromosomes, which originated basally in Sylvioidea. In S. brachyura, we found that a part of chromosome 8 has been translocated to the sex chromosomes, forming a unique neo-sex chromosome in this lineage. Furthermore, the non-recombining part of 4A in S. brachyura is smaller than in other Sylvioidea species, which suggests that recombination continued along this region after the fusion event in the Sylvioidea ancestor. These findings reveal additional sex chromosome diversity among the Sylvioidea, where five separate translocation events are now confirmed.
Collapse
Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Lund, Sweden.,Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Hongkai Zhang
- Department of Biology, Lund University, Lund, Sweden
| | | | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
21
|
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: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
22
|
Abstract
Organisms mount the cellular stress response whenever environmental parameters exceed the range that is conducive to maintaining homeostasis. This response is critical for survival in emergency situations because it protects macromolecular integrity and, therefore, cell/organismal function. From an evolutionary perspective, the cellular stress response counteracts severe stress by accelerating adaptation via a process called stress-induced evolution. In this Review, we summarize five key physiological mechanisms of stress-induced evolution. Namely, these are stress-induced changes in: (1) mutation rates, (2) histone post-translational modifications, (3) DNA methylation, (4) chromoanagenesis and (5) transposable element activity. Through each of these mechanisms, organisms rapidly generate heritable phenotypes that may be adaptive, maladaptive or neutral in specific contexts. Regardless of their consequences to individual fitness, these mechanisms produce phenotypic variation at the population level. Because variation fuels natural selection, the physiological mechanisms of stress-induced evolution increase the likelihood that populations can avoid extirpation and instead adapt under the stress of new environmental conditions.
Collapse
Affiliation(s)
- Elizabeth A Mojica
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
| | - Dietmar Kültz
- Department of Animal Science, University of California, Davis, One Shields Avenue, Meyer Hall, Davis, CA 95616, USA
| |
Collapse
|
23
|
Cao LJ, Song W, Chen JC, Fan XL, Hoffmann AA, Wei SJ. Population genomic signatures of the oriental fruit moth related to the Pleistocene climates. Commun Biol 2022; 5:142. [PMID: 35177826 PMCID: PMC8854661 DOI: 10.1038/s42003-022-03097-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/31/2022] [Indexed: 12/31/2022] Open
Abstract
The Quaternary climatic oscillations are expected to have had strong impacts on the evolution of species. Although legacies of the Quaternary climates on population processes have been widely identified in diverse groups of species, adaptive genetic changes shaped during the Quaternary have been harder to decipher. Here, we assembled a chromosome-level genome of the oriental fruit moth and compared genomic variation among refugial and colonized populations of this species that diverged in the Pleistocene. High genomic diversity was maintained in refugial populations. Demographic analysis showed that the effective population size of refugial populations declined during the penultimate glacial maximum (PGM) but remained stable during the last glacial maximum (LGM), indicating a strong impact of the PGM rather than the LGM on this pest species. Genome scans identified one chromosomal inversion and a mutation of the circadian gene Clk on the neo-Z chromosome potentially related to the endemicity of a refugial population. In the colonized populations, genes in pathways of energy metabolism and wing development showed signatures of selection. These different genomic signatures of refugial and colonized populations point to multiple impacts of Quaternary climates on adaptation in an extant species.
Collapse
Affiliation(s)
- Li-Jun Cao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Wei Song
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
- Beijing Key Laboratory for Forest Pests Control, Beijing Forestry University, Beijing, 100083, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Xu-Lei Fan
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China.
| |
Collapse
|
24
|
Shakya SB, Wang-Claypool CY, Cicero C, Bowie RCK, Mason NA. Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila Alpestris). Mol Ecol 2022; 31:1783-1799. [PMID: 35048444 DOI: 10.1111/mec.16357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/16/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
Genetic structure and phenotypic variation among populations is affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD dataset of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment.
Collapse
Affiliation(s)
- Subir B Shakya
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nicholas A Mason
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| |
Collapse
|
25
|
Rovatsos M, Gamble T, Nielsen SV, Georges A, Ezaz T, Kratochvíl L. Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200102. [PMID: 34304587 PMCID: PMC8310713 DOI: 10.1098/rstb.2020.0102] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2020] [Indexed: 12/25/2022] Open
Abstract
Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here, we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32-72 Ma, one species in particular, Burton's legless lizard (Lialis burtonis), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
Collapse
Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Charles University, Prague, CZ 12844, Czech Republic
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
- Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI 53233, USA
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Stuart V. Nielsen
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Lukáš Kratochvíl
- Department of Ecology, Charles University, Prague, CZ 12844, Czech Republic
| |
Collapse
|
26
|
Sember A, Nguyen P, Perez MF, Altmanová M, Ráb P, Cioffi MDB. Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: state of the art and future challenges. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200098. [PMID: 34304595 PMCID: PMC8310710 DOI: 10.1098/rstb.2020.0098] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Despite decades of cytogenetic and genomic research of dynamic sex chromosome evolution in teleost fishes, multiple sex chromosomes have been largely neglected. In this review, we compiled available data on teleost multiple sex chromosomes, identified major trends in their evolution and suggest further trajectories in their investigation. In a compiled dataset of 440 verified records of fish sex chromosomes, we counted 75 multiple sex chromosome systems with 60 estimated independent origins. We showed that male-heterogametic systems created by Y-autosome fusion predominate and that multiple sex chromosomes are over-represented in the order Perciformes. We documented a striking difference in patterns of differentiation of sex chromosomes between male and female heterogamety and hypothesize that faster W sex chromosome differentiation may constrain sex chromosome turnover in female-heterogametic systems. We also found no significant association between the mechanism of multiple sex chromosome formation and percentage of uni-armed chromosomes in teleost karyotypes. Last but not least, we hypothesized that interaction between fish populations, which differ in their sex chromosomes, can drive the evolution of multiple sex chromosomes in fishes. This underlines the importance of broader inter-population sampling in studies of fish sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Petr Nguyen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Manolo F. Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
| |
Collapse
|
27
|
Mongue AJ, Hansen ME, Walters JR. Support for faster and more adaptive Z chromosome evolution in two divergent lepidopteran lineages. Evolution 2021; 76:332-345. [PMID: 34463346 PMCID: PMC9291949 DOI: 10.1111/evo.14341] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/21/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
The rateof divergence for Z or X chromosomes is usually observed to be greater than autosomes, but the proposed evolutionary causes for this pattern vary, as do empirical results from diverse taxa. Even among moths and butterflies (Lepidoptera), which generally share a single-origin Z chromosome, the handful of available studies give mixed support for faster or more adaptive evolution of the Z chromosome, depending on the species assayed. Here, we examine the molecular evolution of Z chromosomes in two additional lepidopteran species: the Carolina sphinx moth and the monarch butterfly, the latter of which possesses a recent chromosomal fusion yielding a segment of newly Z-linked DNA. We find evidence for both faster and more adaptive Z chromosome evolution in both species, although this effect is strongest in the neo-Z portion of the monarch sex chromosome. The neo-Z is less male-biased than expected of a Z chromosome, and unbiased and female-biased genes drive the signal for adaptive evolution here. Together these results suggest that male-biased gene accumulation and haploid selection have opposing effects on long-term rates of adaptation and may help explain the discrepancies in previous findings as well as the repeated evolution of neo-sex chromosomes in Lepidoptera.
Collapse
Affiliation(s)
- Andrew J Mongue
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH93FL, United Kingdom
| | - Megan E Hansen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
| | - James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
| |
Collapse
|
28
|
Visser S, Voleníková A, Nguyen P, Verhulst EC, Marec F. A conserved role of the duplicated Masculinizer gene in sex determination of the Mediterranean flour moth, Ephestia kuehniella. PLoS Genet 2021; 17:e1009420. [PMID: 34339412 PMCID: PMC8360546 DOI: 10.1371/journal.pgen.1009420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/12/2021] [Accepted: 06/22/2021] [Indexed: 12/28/2022] Open
Abstract
Sex determination in the silkworm, Bombyx mori, is based on Feminizer (Fem), a W-linked Fem piRNA that triggers female development in WZ individuals, and the Z-linked Masculinizer (Masc), which initiates male development and dosage compensation in ZZ individuals. While Fem piRNA is missing in a close relative of B. mori, Masc determines sex in several representatives of distant lepidopteran lineages. We studied the molecular mechanisms of sex determination in the Mediterranean flour moth, Ephestia kuehniella (Pyralidae). We identified an E. kuehniella Masc ortholog, EkMasc, and its paralog resulting from a recent duplication, EkMascB. Both genes are located on the Z chromosome and encode a similar Masc protein that contains two conserved domains but has lost the conserved double zinc finger domain. We developed PCR-based genetic sexing and demonstrated a peak in the expression of EkMasc and EkMascB genes only in early male embryos. Simultaneous knock-down experiments of both EkMasc and EkMascB using RNAi during early embryogenesis led to a shift from male- to female-specific splicing of the E. kuehniella doublesex gene (Ekdsx), their downstream effector, in ZZ embryos and resulted in a strong female-biased sex-ratio. Our results thus confirmed the conserved role of EkMasc and/or EkMascB in masculinization. We suggest that the C-terminal proline-rich domain, we have identified in all functionally confirmed Masc proteins, in conjunction with the masculinizing domain, is important for transcriptional regulation of sex determination in Lepidoptera. The function of the Masc double zinc finger domain is still unknown, but appears to have been lost in E. kuehniella. The sex-determining cascade in the silkworm, Bombyx mori, differs greatly from those of other insects. In B. mori, female development is initiated by Fem piRNA expressed from the W chromosome during early embryogenesis. Fem piRNA silences Masculinizer (Masc) thereby blocking the male pathway resulting in female development. It is currently unknown whether this cascade is conserved across Lepidoptera. In the Mediterranean flour moth, Ephestia kuehniella, we identified an ortholog of Masc and discovered its functional duplication on the Z chromosome, which has not yet been found in any other lepidopteran species. We provide two lines of evidence that the EkMasc and/or EkMascB genes play an essential role in masculinization: (i) they show a peak of expression during early embryogenesis in ZZ but not in WZ embryos and (ii) their simultaneous silencing by RNAi results in female-specific splicing of the E. kuehniella doublesex gene (Ekdsx) in ZZ embryos and in a female-biased sex ratio. Our results suggest a conserved role of the duplicated Masc gene in sex determination of E. kuehniella.
Collapse
Affiliation(s)
- Sander Visser
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Anna Voleníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Eveline C. Verhulst
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- * E-mail:
| |
Collapse
|
29
|
Provazníková I, Hejníčková M, Visser S, Dalíková M, Carabajal Paladino LZ, Zrzavá M, Voleníková A, Marec F, Nguyen P. Large-scale comparative analysis of cytogenetic markers across Lepidoptera. Sci Rep 2021; 11:12214. [PMID: 34108567 PMCID: PMC8190105 DOI: 10.1038/s41598-021-91665-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/24/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.
Collapse
Affiliation(s)
- Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Hejníčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Sander Visser
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | | | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - František Marec
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
| |
Collapse
|
30
|
Cabral-de-Mello DC, Zrzavá M, Kubíčková S, Rendón P, Marec F. The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths. Front Genet 2021; 12:661417. [PMID: 33859676 PMCID: PMC8042265 DOI: 10.3389/fgene.2021.661417] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.
Collapse
Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, Brazil.,Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Magda Zrzavá
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | | | - Pedro Rendón
- IAEA-TCLA-Consultant-USDA-APHIS-Moscamed Program Guatemala, Guatemala City, Guatemala
| | - František Marec
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| |
Collapse
|
31
|
Aguirre C, Olivares N, Hinrichsen P. An Efficient Duplex PCR Method for Sex Identification of the European Grapevine Moth Lobesia botrana (Lepidoptera: Tortricidae) at Any Developmental Stage. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:2505-2510. [PMID: 32676656 DOI: 10.1093/jee/toaa155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 06/11/2023]
Abstract
Many genetic studies in insects require sex identification of individuals in all developmental stages. The most common sex chromosome system in lepidopterans is WZ/ZZ; the W chromosome is present only in females. Based on two W chromosome-specific short sequences (CpW2 and CpW5) described in Cydia pomonella (L.) (Lepidoptera: Tortricidae), we identified homologous female-specific sequences in Lobesia botrana Den. & Schiff, a polyphagous and very harmful species present in Chile since 2008. From this starting point, we extended the sequence information using the inverse PCR method, identifying the first W-specific sequences described up to now for the moth. Finally, we developed a duplex PCR method for rapid and sensitive determination of sex in L. botrana from larva to adult. The method showed a detection limit of 1 pg of genomic DNA; a blind panel of samples exhibited exact correspondence with the morphological identification. These results will be very useful for studies requiring sex-specific analyses at any developmental stage, contributing also to the understanding of gene expression in the insect, as well as to the eventual development of control protocols against the moth, such as the development of genetic sexing strains for the implementation of the sterile insect technique.
Collapse
Affiliation(s)
- Carlos Aguirre
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| | - Natalia Olivares
- Instituto de Investigaciones Agropecuarias, INIA-La Cruz, La Cruz, Quillota, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| |
Collapse
|
32
|
Ahmad SF, Jehangir M, Cardoso AL, Wolf IR, Margarido VP, Cabral-de-Mello DC, O'Neill R, Valente GT, Martins C. B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes. BMC Genomics 2020; 21:656. [PMID: 32967626 PMCID: PMC7509943 DOI: 10.1186/s12864-020-07072-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of the extra, non-essential karyotype elements, commonly known as supernumerary or B chromosomes (Bs). The non-Mendelian inheritance and non-pairing abilities of B chromosomes make them an interesting model for genomics studies, thus bringing to bear different questions about their genetic composition, evolutionary survival, maintenance and functional role inside the cell. This study uncovers these phenomena in multiple species that we considered as representative organisms of both vertebrate and invertebrate models for B chromosome analysis. RESULTS We sequenced the genomes of three animal species including two fishes Astyanax mexicanus and Astyanax correntinus, and a grasshopper Abracris flavolineata, each with and without Bs, and identified their B-localized genes and repeat contents. We detected unique sequences occurring exclusively on Bs and discovered various evolutionary patterns of genomic rearrangements associated to Bs. In situ hybridization and quantitative polymerase chain reactions further validated our genomic approach confirming detection of sequences on Bs. The functional annotation of B sequences showed that the B chromosome comprises regions of gene fragments, novel genes, and intact genes, which encode a diverse set of functions related to important biological processes such as metabolism, morphogenesis, reproduction, transposition, recombination, cell cycle and chromosomes functions which might be important for their evolutionary success. CONCLUSIONS This study reveals the genomic structure, composition and function of Bs, which provide new insights for theories of B chromosome evolution. The selfish behavior of Bs seems to be favored by gained genes/sequences.
Collapse
Affiliation(s)
- Syed F Ahmad
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Ivan R Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Vladimir P Margarido
- Western Paraná State University (UNIOESTE), Center for Biology Science and Health, Cascavel, PR, Brazil
| | - Diogo C Cabral-de-Mello
- Department of General and Applied Biology, Institute of Biosciences, Sao Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Rachel O'Neill
- Department of Molecular and Cell Biology, University of Connecticut (UCONN), Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut (UCONN), Storrs, CT, USA
| | - Guilherme T Valente
- Bioprocess and Biotechnology Department, Agronomical Science Faculty, Sao Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| |
Collapse
|
33
|
Sember A, Pappová M, Forman M, Nguyen P, Marec F, Dalíková M, Divišová K, Doležálková-Kaštánková M, Zrzavá M, Sadílek D, Hrubá B, Král J. Patterns of Sex Chromosome Differentiation in Spiders: Insights from Comparative Genomic Hybridisation. Genes (Basel) 2020; 11:E849. [PMID: 32722348 PMCID: PMC7466014 DOI: 10.3390/genes11080849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023] Open
Abstract
Spiders are an intriguing model to analyse sex chromosome evolution because of their peculiar multiple X chromosome systems. Y chromosomes were considered rare in this group, arising after neo-sex chromosome formation by X chromosome-autosome rearrangements. However, recent findings suggest that Y chromosomes are more common in spiders than previously thought. Besides neo-sex chromosomes, they are also involved in the ancient X1X2Y system of haplogyne spiders, whose origin is unknown. Furthermore, spiders seem to exhibit obligatorily one or two pairs of cryptic homomorphic XY chromosomes (further cryptic sex chromosome pairs, CSCPs), which could represent the ancestral spider sex chromosomes. Here, we analyse the molecular differentiation of particular types of spider Y chromosomes in a representative set of ten species by comparative genomic hybridisation (CGH). We found a high Y chromosome differentiation in haplogyne species with X1X2Y system except for Loxosceles spp. CSCP chromosomes exhibited generally low differentiation. Possible mechanisms and factors behind the observed patterns are discussed. The presence of autosomal regions marked predominantly or exclusively with the male or female probe was also recorded. We attribute this pattern to intraspecific variability in the copy number and distribution of certain repetitive DNAs in spider genomes, pointing thus to the limits of CGH in this arachnid group. In addition, we confirmed nonrandom association of chromosomes belonging to particular CSCPs at spermatogonial mitosis and spermatocyte meiosis and their association with multiple Xs throughout meiosis. Taken together, our data suggest diverse evolutionary pathways of molecular differentiation in different types of spider Y chromosomes.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Michaela Pappová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Petr Nguyen
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Martina Dalíková
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Klára Divišová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Marie Doležálková-Kaštánková
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Magda Zrzavá
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic; (P.N.); (M.D.); (M.Z.)
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - David Sadílek
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Barbora Hrubá
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| | - Jiří Král
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic; (M.P.); (M.F.); (K.D.); (D.S.); (B.H.); (J.K.)
| |
Collapse
|
34
|
Yoshido A, Šíchová J, Pospíšilová K, Nguyen P, Voleníková A, Šafář J, Provazník J, Vila R, Marec F. Evolution of multiple sex-chromosomes associated with dynamic genome reshuffling in Leptidea wood-white butterflies. Heredity (Edinb) 2020; 125:138-154. [PMID: 32518391 PMCID: PMC7426936 DOI: 10.1038/s41437-020-0325-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Sex-chromosome systems tend to be highly conserved and knowledge about their evolution typically comes from macroevolutionary inference. Rapidly evolving complex sex-chromosome systems represent a rare opportunity to study the mechanisms of sex-chromosome evolution at unprecedented resolution. Three cryptic species of wood-white butterflies—Leptidea juvernica, L. sinapis and L. reali—have each a unique set of multiple sex-chromosomes with 3–4 W and 3–4 Z chromosomes. Using a transcriptome-based microarray for comparative genomic hybridisation (CGH) and a library of bacterial artificial chromosome (BAC) clones, both developed in L. juvernica, we identified Z-linked Leptidea orthologs of Bombyx mori genes and mapped them by fluorescence in situ hybridisation (FISH) with BAC probes on multiple Z chromosomes. In all three species, we determined synteny blocks of autosomal origin and reconstructed the evolution of multiple sex-chromosomes. In addition, we identified W homologues of Z-linked orthologs and characterised their molecular differentiation. Our results suggest that the multiple sex-chromosome system evolved in a common ancestor as a result of dynamic genome reshuffling through repeated rearrangements between the sex chromosomes and autosomes, including translocations, fusions and fissions. Thus, the initial formation of neo-sex chromosomes could not have played a role in reproductive isolation between these Leptidea species. However, the subsequent species-specific fissions of several neo-sex chromosomes could have contributed to their reproductive isolation. Then, significantly increased numbers of Z-linked genes and independent neo-W chromosome degeneration could accelerate the accumulation of genetic incompatibilities between populations and promote their divergence resulting in speciation.
Collapse
Affiliation(s)
- Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jindra Šíchová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Kristýna Pospíšilová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Anna Voleníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Jan Provazník
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| |
Collapse
|
35
|
Singh KS, Troczka BJ, Duarte A, Balabanidou V, Trissi N, Carabajal Paladino LZ, Nguyen P, Zimmer CT, Papapostolou KM, Randall E, Lueke B, Marec F, Mazzoni E, Williamson MS, Hayward A, Nauen R, Vontas J, Bass C. The genetic architecture of a host shift: An adaptive walk protected an aphid and its endosymbiont from plant chemical defenses. SCIENCE ADVANCES 2020; 6:eaba1070. [PMID: 32494722 PMCID: PMC7202869 DOI: 10.1126/sciadv.aba1070] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/18/2020] [Indexed: 05/05/2023]
Abstract
Host shifts can lead to ecological speciation and the emergence of new pests and pathogens. However, the mutational events that facilitate the exploitation of novel hosts are poorly understood. Here, we characterize an adaptive walk underpinning the host shift of the aphid Myzus persicae to tobacco, including evolution of mechanisms that overcame tobacco chemical defenses. A series of mutational events added as many as 1.5 million nucleotides to the genome of the tobacco-adapted subspecies, M. p. nicotianae, and yielded profound increases in expression of an enzyme that efficiently detoxifies nicotine, both in aphid gut tissue and in the bacteriocytes housing the obligate aphid symbiont Buchnera aphidicola. This dual evolutionary solution overcame the challenge of preserving fitness of a mutualistic symbiosis during adaptation to a toxic novel host. Our results reveal the intricate processes by which genetic novelty can arise and drive the evolution of key innovations required for ecological adaptation.
Collapse
Affiliation(s)
- Kumar Saurabh Singh
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Bartlomiej J. Troczka
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Ana Duarte
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Vasileia Balabanidou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece
| | - Nasser Trissi
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | | | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, 370 05 České Budějovice, Czech Republic
| | - Christoph T. Zimmer
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Kyriaki M. Papapostolou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece
| | - Emma Randall
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Bettina Lueke
- Bayer AG, Crop Science Division, R&D, Alfred Nobel-Strasse 50, 40789 Monheim, Germany
| | - Frantisek Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05 České Budějovice, Czech Republic
| | - Emanuele Mazzoni
- Department of Sustainable Crop Production, Section Sustainable Crop and Food Protection, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Martin S. Williamson
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Alex Hayward
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Alfred Nobel-Strasse 50, 40789 Monheim, Germany
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece
- Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
- Corresponding author.
| |
Collapse
|
36
|
Martin SH, Singh KS, Gordon IJ, Omufwoko KS, Collins S, Warren IA, Munby H, Brattström O, Traut W, Martins DJ, Smith DAS, Jiggins CD, Bass C, ffrench-Constant RH. Whole-chromosome hitchhiking driven by a male-killing endosymbiont. PLoS Biol 2020; 18:e3000610. [PMID: 32108180 PMCID: PMC7046192 DOI: 10.1371/journal.pbio.3000610] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022] Open
Abstract
Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences.
Collapse
Affiliation(s)
- Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Kumar Saurabh Singh
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | - Ian J. Gordon
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye, Rwanda
| | - Kennedy Saitoti Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Munby
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Walther Traut
- Institut für Biologie, Universität Lübeck, Lübeck, Germany
| | - Dino J. Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | | |
Collapse
|
37
|
Hejníčková M, Koutecký P, Potocký P, Provazníková I, Voleníková A, Dalíková M, Visser S, Marec F, Zrzavá M. Absence of W Chromosome in Psychidae Moths and Implications for the Theory of Sex Chromosome Evolution in Lepidoptera. Genes (Basel) 2019; 10:E1016. [PMID: 31817557 PMCID: PMC6947638 DOI: 10.3390/genes10121016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/17/2022] Open
Abstract
Moths and butterflies (Lepidoptera) are the largest group with heterogametic females. Although the ancestral sex chromosome system is probably Z0/ZZ, most lepidopteran species have the W chromosome. When and how the W chromosome arose remains elusive. Existing hypotheses place the W origin either at the common ancestor of Ditrysia and Tischeriidae, or prefer independent origins of W chromosomes in these two groups. Due to their phylogenetic position at the base of Ditrysia, bagworms (Psychidae) play an important role in investigating the W chromosome origin. Therefore, we examined the W chromosome status in three Psychidae species, namely Proutiabetulina, Taleporiatubulosa, and Diplodomalaichartingella, using both classical and molecular cytogenetic methods such as sex chromatin assay, comparative genomic hybridization (CGH), and male vs. female genome size comparison by flow cytometry. In females of all three species, no sex chromatin was found, no female-specific chromosome regions were revealed by CGH, and a Z-chromosome univalent was observed in pachytene oocytes. In addition, the genome size of females was significantly smaller than males. Overall, our study provides strong evidence for the absence of the W chromosome in Psychidae, thus supporting the hypothesis of two independent W chromosome origins in Tischeriidae and in advanced Ditrysia.
Collapse
Affiliation(s)
- Martina Hejníčková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Pavel Potocký
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
| | - Irena Provazníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anna Voleníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Martina Dalíková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Sander Visser
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| |
Collapse
|
38
|
Gokhman VE, Cioffi MDB, König C, Pollmann M, Gantert C, Krogmann L, Steidle JLM, Kosyakova N, Liehr T, Al-Rikabi A. Microdissection and whole chromosome painting confirm karyotype transformation in cryptic species of the Lariophagus distinguendus (Förster, 1841) complex (Hymenoptera: Pteromalidae). PLoS One 2019; 14:e0225257. [PMID: 31725808 PMCID: PMC6855445 DOI: 10.1371/journal.pone.0225257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/31/2019] [Indexed: 11/18/2022] Open
Abstract
Karyotypes of two cryptic species of parasitoid Hymenoptera with n = 5 and 6 belonging to the Lariophagus distinguendus (Förster, 1841) complex, which includes cosmopolitan parasitoids of coleopteran stored-product pests, were studied using glass-needle based microdissection, reverse and cross-species fluorescence in situ hybridisation (FISH). This experiment strongly indicates that the largest metacentric chromosome in the karyotype with n = 5 originated from a particular fusion between the only acrocentric and a smaller metacentric chromosome of the set with n = 6, therefore confirming our previous hypothesis based on the karyotypic analysis using chromosome morphometrics. This study represents the first successful application of both microdissection and whole chromosome painting for the reconstruction of karyotypic rearrangements in closely related species of parasitoids, as well as in the order Hymenoptera in general.
Collapse
Affiliation(s)
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Christian König
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
| | - Marie Pollmann
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
| | - Cornelia Gantert
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
| | - Lars Krogmann
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
- Department of Entomology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | | | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| |
Collapse
|
39
|
Gu L, Reilly PF, Lewis JJ, Reed RD, Andolfatto P, Walters JR. Dichotomy of Dosage Compensation along the Neo Z Chromosome of the Monarch Butterfly. Curr Biol 2019; 29:4071-4077.e3. [PMID: 31735674 DOI: 10.1016/j.cub.2019.09.056] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Mechanisms of sex chromosome dosage compensation (SCDC) differ strikingly among animals. In Drosophila flies, chromosome-wide transcription is doubled from the single X chromosome in hemizygous (XY) males, whereas in Caenorhabditis nematodes, expression is halved for both X copies in homozygous (XX) females [1, 2]. Unlike other female-heterogametic (WZ female and ZZ male) animals, moths and butterflies exhibit sex chromosome dosage compensation patterns typically seen only in male-heterogametic species [3]. The monarch butterfly carries a newly derived Z chromosome segment that arose from an autosomal fusion with the ancestral Z [4]. Using a highly contiguous genome assembly, we show that gene expression is balanced between sexes along the entire Z chromosome but with distinct modes of compensation on the two segments. On the ancestral Z segment, depletion of H4K16ac corresponds to nearly halving of biallelic transcription in males, a pattern convergent to nematodes. Conversely, the newly derived Z segment shows a Drosophila-like mode of compensation, with enriched H4K16ac levels corresponding to doubled monoallelic transcription in females. Our work reveals that, contrary to the expectation of co-opting regulatory mechanisms readily in place, the evolution of plural modes of dosage compensation is also possible along a single sex chromosome within a species.
Collapse
Affiliation(s)
- Liuqi Gu
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA.
| | - Patrick F Reilly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - James R Walters
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA.
| |
Collapse
|
40
|
Advances and Challenges of Using the Sterile Insect Technique for the Management of Pest Lepidoptera. INSECTS 2019; 10:insects10110371. [PMID: 31731445 PMCID: PMC6921062 DOI: 10.3390/insects10110371] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/20/2019] [Accepted: 10/23/2019] [Indexed: 11/24/2022]
Abstract
Over the past 30 years, the sterile insect technique (SIT) has become a regular component of area-wide integrated pest management (AW-IPM) programs against several major agricultural pests and vectors of severe diseases. The SIT-based programs have been especially successful against dipteran pests. However, the SIT applicability for controlling lepidopteran pests has been challenging, mainly due to their high resistance to the ionizing radiation that is used to induce sterility. Nevertheless, the results of extensive research and currently operating SIT programs show that most problems with the implementation of SIT against pest Lepidoptera have been successfully resolved. Here, we summarize the cytogenetic peculiarities of Lepidoptera that should be considered in the development and application of SIT for a particular pest species. We also discuss the high resistance of Lepidoptera to ionizing radiation, and present the principle of derived technology based on inherited sterility (IS). Furthermore, we present successful SIT/IS applications against five major lepidopteran pests, and summarize the results of research on the quality control of reared and released insects, which is of great importance for their field performance. In the light of new research findings, we also discuss options for the development of genetic sexing strains, which is a challenge to further improve the applicability of SIT/IS against selected lepidopteran pests.
Collapse
|
41
|
Wan F, Yin C, Tang R, Chen M, Wu Q, Huang C, Qian W, Rota-Stabelli O, Yang N, Wang S, Wang G, Zhang G, Guo J, Gu LA, Chen L, Xing L, Xi Y, Liu F, Lin K, Guo M, Liu W, He K, Tian R, Jacquin-Joly E, Franck P, Siegwart M, Ometto L, Anfora G, Blaxter M, Meslin C, Nguyen P, Dalíková M, Marec F, Olivares J, Maugin S, Shen J, Liu J, Guo J, Luo J, Liu B, Fan W, Feng L, Zhao X, Peng X, Wang K, Liu L, Zhan H, Liu W, Shi G, Jiang C, Jin J, Xian X, Lu S, Ye M, Li M, Yang M, Xiong R, Walters JR, Li F. A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance. Nat Commun 2019; 10:4237. [PMID: 31530873 PMCID: PMC6748993 DOI: 10.1038/s41467-019-12175-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/20/2019] [Indexed: 01/27/2023] Open
Abstract
The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion. The codling moth, Cydia pomonella, is one of the major pests of pome fruit (apples and pears) and walnuts. Here, the authors sequence and analyze its genome, providing insights on olfactory and detoxification processes that may underlie its worldwide expansion.
Collapse
Affiliation(s)
- Fanghao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Chuanlin Yin
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Rui Tang
- MARA-CABI Joint Laboratory for Bio-safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Maohua Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Qiang Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cong Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Wanqiang Qian
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-ecosystems and Bioresources, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Nianwan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Shuping Wang
- Technical Centre for Animal Plant and Food Inspection and Quarantine, Shanghai Custom, Shanghai, 200135, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guifen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianyang Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liuqi Aloy Gu
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66046, USA
| | - Longfei Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longsheng Xing
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yu Xi
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Feiling Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Kejian Lin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mengbo Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ruizheng Tian
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | | | - Pierre Franck
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Myriam Siegwart
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Lino Ometto
- Department of Sustainable Agro-ecosystems and Bioresources, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige (TN), Italy.,Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Gianfranco Anfora
- Department of Sustainable Agro-ecosystems and Bioresources, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige (TN), Italy.,Centre Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige (TN), Italy
| | - Mark Blaxter
- Edinburgh Genomics, and Institute of Evolutionary Biology, School of Biological Sciences, The King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Camille Meslin
- INRA, Institute of Ecology and Environmental Sciences of Paris, 78000, Versailles, France
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - Martina Dalíková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Jérôme Olivares
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Sandrine Maugin
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Jianru Shen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jinding Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinmeng Guo
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiapeng Luo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bo Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Likai Feng
- Institute of Plant Protection, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Xianxin Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiong Peng
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Kang Wang
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Lang Liu
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Haixia Zhan
- MARA-CABI Joint Laboratory for Bio-safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wanxue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guoliang Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chunyan Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jisu Jin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoqing Xian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Sha Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mingli Ye
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Meizhen Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Minglu Yang
- Xinjiang Production & Construction Corps Key Laboratory of Integrated Pest Management on Agriculture in South Xinjiang, Tarim University, Alar, 843300, China
| | - Renci Xiong
- Xinjiang Production & Construction Corps Key Laboratory of Integrated Pest Management on Agriculture in South Xinjiang, Tarim University, Alar, 843300, China
| | - James R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66046, USA.
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
42
|
Hora KH, Marec F, Roessingh P, Menken SBJ. Limited intrinsic postzygotic reproductive isolation despite chromosomal rearrangements between closely related sympatric species of small ermine moths (Lepidoptera: Yponomeutidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
In evolutionarily young species and sympatric host races of phytophagous insects, postzygotic incompatibility is often not yet fully developed, but reduced fitness of hybrids is thought to facilitate further divergence. However, empirical evidence supporting this hypothesis is limited. To assess the role of reduced hybrid fitness, we studied meiosis and fertility in hybrids of two closely related small ermine moths, Yponomeuta padella and Yponomeuta cagnagella, and determined the extent of intrinsic postzygotic reproductive isolation. We found extensive rearrangements between the karyotypes of the two species and irregularities in meiotic chromosome pairing in their hybrids. The fertility of reciprocal F1 and, surprisingly, also of backcrosses with both parental species was not significantly decreased compared with intraspecific offspring. The results indicate that intrinsic postzygotic reproductive isolation between these closely related species is limited. We conclude that the observed chromosomal rearrangements are probably not the result of an accumulation of postzygotic incompatibilities preventing hybridization. Alternative explanations, such as adaptation to new host plants, are discussed.
Collapse
Affiliation(s)
- Katerina H Hora
- Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Peter Roessingh
- Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Steph B J Menken
- Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
43
|
de Moraes RLR, Sember A, Bertollo LAC, de Oliveira EA, Ráb P, Hatanaka T, Marinho MMF, Liehr T, Al-Rikabi ABH, Feldberg E, Viana PF, Cioffi MDB. Comparative Cytogenetics and Neo-Y Formation in Small-Sized Fish Species of the Genus Pyrrhulina (Characiformes, Lebiasinidae). Front Genet 2019; 10:678. [PMID: 31428127 PMCID: PMC6689988 DOI: 10.3389/fgene.2019.00678] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
Although fishes have traditionally been the subject of comparative evolutionary studies, few reports have concentrated on the application of multipronged modern molecular cytogenetic techniques (such as comparative genomic hybridization = CGH and whole chromosome painting = WCP) to analyze deeper the karyotype evolution of specific groups, especially the historically neglected small-sized ones. Representatives of the family Lebiasinidae (Characiformes) are a notable example, where only a few cytogenetic investigations have been conducted thus far. Here, we aim to elucidate the evolutionary processes behind the karyotype differentiation of Pyrrhulina species on a finer-scale cytogenetic level. To achieve this, we applied C-banding, repetitive DNA mapping, CGH and WCP in Pyrrhulina semifasciata and P. brevis. Our results showed 2n = 42 in both sexes of P. brevis, while the difference in 2n between male and female in P. semifasciata (♂41/♀42) stands out due to the presence of a multiple X1X2Y sex chromosome system, until now undetected in this family. As a remarkable common feature, multiple 18S and 5S rDNA sites are present, with an occasional synteny or tandem-repeat amplification. Male-vs.-female CGH experiments in P. semifasciata highlighted the accumulation of male-enriched repetitive sequences in the pericentromeric region of the Y chromosome. Inter-specific CGH experiments evidenced a divergence between both species’ genomes based on the presence of several species-specific signals, highlighting their inner genomic diversity. WCP with the P. semifasciata-derived Y (PSEMI-Y) probe painted not only the entire metacentric Y chromosome in males but also the X1 and X2 chromosomes in both male and female chromosomes of P. semifasciata. In the cross-species experiments, the PSEMI-Y probe painted four acrocentric chromosomes in both males and females of the other tested Pyrrhulina species. In summary, our results show that both intra- and interchromosomal rearrangements together with the dynamics of repetitive DNA significantly contributed to the karyotype divergence among Pyrrhulina species, possibly promoted by specific populational and ecological traits and accompanied in one species by the origin of neo-sex chromosomes. The present results suggest how particular evolutionary scenarios found in fish species can help to clarify several issues related to genome organization and the karyotype evolution of vertebrates in general.
Collapse
Affiliation(s)
- Renata Luiza Rosa de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Luiz Antônio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Ezequiel Aguiar de Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Secretaria de Estado de Educação de Mato Grosso - SEDUC-MT, Cuiabá, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | | | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | | | - Eliana Feldberg
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Patrik F Viana
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Institute of Human Genetics, University Hospital Jena, Jena, Germany
| |
Collapse
|
44
|
Xu D, Sember A, Zhu Q, Oliveira EAD, Liehr T, Al-Rikabi ABH, Xiao Z, Song H, Cioffi MDB. Deciphering the Origin and Evolution of the X 1X 2Y System in Two Closely-Related Oplegnathus Species (Oplegnathidae and Centrarchiformes). Int J Mol Sci 2019; 20:E3571. [PMID: 31336568 PMCID: PMC6678977 DOI: 10.3390/ijms20143571] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 01/18/2023] Open
Abstract
Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X1X2Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of these sex chromosomes, with the aim to elucidate whether they had a single or convergent origin. To achieve this, conventional and molecular cytogenetic protocols, involving the mapping of repetitive DNA markers, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) were applied. Both species presented similar 2n, karyotype structure and hybridization patterns of repetitive DNA classes. 5S rDNA loci, besides being placed on the autosomal pair 22, resided in the terminal region of the long arms of both X1 chromosomes in females, and on the X1 and Y chromosomes in males. Furthermore, WCP experiments with a probe derived from the Y chromosome of O. fasciatus (OFAS-Y) entirely painted the X1 and X2 chromosomes in females and the X1, X2, and Y chromosomes in males of both species. CGH failed to reveal any sign of sequence differentiation on the Y chromosome in both species, thereby suggesting the shared early stage of neo-Y chromosome differentiation. Altogether, the present findings confirmed the origin of the X1X2Y sex chromosomes via Y-autosome centric fusion and strongly suggested their common origin.
Collapse
Affiliation(s)
- Dongdong Xu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Qihui Zhu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
| | - 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
- Secretaria de Estado de Educação de Mato Grosso-SEDUC-MT, Cuiabá MT 78049-909, Brazil
| | - Thomas Liehr
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany
| | | | - Zhizhong Xiao
- Laboratory for Marine Biology and Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Hongbin Song
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - 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.
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany.
| |
Collapse
|
45
|
Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome. Genome Biol Evol 2019; 11:1033-1044. [PMID: 30865260 PMCID: PMC6456005 DOI: 10.1093/gbe/evz053] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.
Collapse
Affiliation(s)
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| |
Collapse
|
46
|
Rovatsos M, Farkačová K, Altmanová M, Johnson Pokorná M, Kratochvíl L. The rise and fall of differentiated sex chromosomes in geckos. Mol Ecol 2019; 28:3042-3052. [DOI: 10.1111/mec.15126] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
| | - Klára Farkačová
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
- Institute of Animal Physiology and Genetics The Czech Academy of Sciences Liběchov Czech Republic
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
- Institute of Animal Physiology and Genetics The Czech Academy of Sciences Liběchov Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science Charles University Prague Czech Republic
| |
Collapse
|
47
|
Hill J, Rastas P, Hornett EA, Neethiraj R, Clark N, Morehouse N, de la Paz Celorio-Mancera M, Cols JC, Dircksen H, Meslin C, Keehnen N, Pruisscher P, Sikkink K, Vives M, Vogel H, Wiklund C, Woronik A, Boggs CL, Nylin S, Wheat CW. Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. SCIENCE ADVANCES 2019; 5:eaau3648. [PMID: 31206013 PMCID: PMC6561736 DOI: 10.1126/sciadv.aau3648] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 05/03/2019] [Indexed: 05/04/2023]
Abstract
Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.
Collapse
Affiliation(s)
- Jason Hill
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Corresponding author. (J.H.); (C.W.W.)
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Emily A. Hornett
- Department of Zoology, University of Cambridge, Cambridge, UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ramprasad Neethiraj
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nathan Clark
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nathan Morehouse
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Jofre Carnicer Cols
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- CREAF, Global Ecology Unit, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Heinrich Dircksen
- Functional Morphology, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Camille Meslin
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- INRA, Department of Sensory Ecology, Institute of Ecology and Environmental Sciences of Paris, Route de Saint-Cyr, 78026 Versailles Cedex, France
| | - Naomi Keehnen
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Peter Pruisscher
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Kristin Sikkink
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Maria Vives
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain
- CREAF, Global Ecology Unit, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Christer Wiklund
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Alyssa Woronik
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Center for Developmental Genetics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Carol L. Boggs
- Department of Biological Sciences University of South Carolina, Columbia, SC 29208, USA
| | - Sören Nylin
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Christopher W. Wheat
- Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
- Corresponding author. (J.H.); (C.W.W.)
| |
Collapse
|
48
|
Carabajal Paladino LZ, Provazníková I, Berger M, Bass C, Aratchige NS, López SN, Marec F, Nguyen P. Sex Chromosome Turnover in Moths of the Diverse Superfamily Gelechioidea. Genome Biol Evol 2019; 11:1307-1319. [PMID: 31028711 PMCID: PMC6486803 DOI: 10.1093/gbe/evz075] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 01/22/2023] Open
Abstract
Sex chromosomes play a central role in genetics of speciation and their turnover was suggested to promote divergence. In vertebrates, sex chromosome-autosome fusions resulting in neo-sex chromosomes occur frequently in male heterogametic taxa (XX/XY), but are rare in groups with female heterogamety (WZ/ZZ). We examined sex chromosomes of seven pests of the diverse lepidopteran superfamily Gelechioidea and confirmed the presence of neo-sex chromosomes in their karyotypes. Two synteny blocks, which correspond to autosomes 7 (LG7) and 27 (LG27) in the ancestral lepidopteran karyotype exemplified by the linkage map of Biston betularia (Geometridae), were identified as sex-linked in the tomato leafminer, Tuta absoluta (Gelechiidae). Testing for sex-linkage performed in other species revealed that while LG7 fused to sex chromosomes in a common ancestor of all Gelechioidea, the second fusion between the resulting neo-sex chromosome and the other autosome is confined to the tribe Gnoreschemini (Gelechiinae). Our data accentuate an emerging pattern of high incidence of neo-sex chromosomes in Lepidoptera, the largest clade with WZ/ZZ sex chromosome system, which suggest that the paucity of neo-sex chromosomes is not an intrinsic feature of female heterogamety. Furthermore, LG7 contains one of the major clusters of UDP-glucosyltransferases, which are involved in the detoxification of plant secondary metabolites. Sex chromosome evolution in Gelechioidea thus supports an earlier hypothesis postulating that lepidopteran sex chromosome-autosome fusions can be driven by selection for association of Z-linked preference or host-independent isolation genes with larval performance and thus can contribute to ecological specialization and speciation of moths.
Collapse
Affiliation(s)
- Leonela Z Carabajal Paladino
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- The Pirbright Institute, Surrey, United Kingdom
| | - Irena Provazníková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Madeleine Berger
- Rothamsted Research, Department of Biointeractions and Crop Protection, Herts, United Kingdom
| | - Chris Bass
- University of Exeter, College of Life and Environmental Sciences, Biosciences, Penryn, Cornwall, United Kingdom
| | - Nayanie S Aratchige
- Coconut Research Institute of Sri Lanka, Crop Protection Division, Bandirippuwa Estate, Lunuwila, Sri Lanka
| | - Silvia N López
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Microbiología y Zoología Agrícola, Hurlingham, Buenos Aires, Argentina
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| |
Collapse
|
49
|
Belousova I, Ershov N, Pavlushin S, Ilinsky Y, Martemyanov V. Molecular sexing of Lepidoptera. JOURNAL OF INSECT PHYSIOLOGY 2019; 114:53-56. [PMID: 30776424 DOI: 10.1016/j.jinsphys.2019.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
We developed a universal method of Lepidoptera molecular sexing. The method is based on comparing the number of copies of the same gene in different sexes. Males of the majority of lepidopteran species have two Z chromosomes, whereas females have only one Z chromosome. Correspondingly, the number of copies of each gene located on this chromosome differs by two times between males and females. For quantitative estimation, we used qPCR. Via multiple alignment of the kettin (a Z chromosome gene) nucleotide sequences, we detected the most conserved fragment and designed primers with broad interspecies specificity for Lepidoptera. Using these primers, we successfully determined the sex of three lepidopteran species belonging to different superfamilies. The developed method is a simple, cost-effective and high-throughput technique for routine sexing. The sex of lepidopteran individuals can be examined at any developmental stage.
Collapse
Affiliation(s)
- Irina Belousova
- Institute of Systematics and Ecology of Animals SB RAS, Frunze Str. 11, Novosibirsk 630091 Russia.
| | - Nikita Ershov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Sergey Pavlushin
- Institute of Systematics and Ecology of Animals SB RAS, Frunze Str. 11, Novosibirsk 630091 Russia
| | - Yury Ilinsky
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia; School of Life Sciences Immanuel Kant Baltic Federal University, Nevskogo Str. 14, Kaliningrad 236016, Russia
| | - Vyacheslav Martemyanov
- Institute of Systematics and Ecology of Animals SB RAS, Frunze Str. 11, Novosibirsk 630091 Russia; Biological Institute, National Research Tomsk State University, Lenin Ave. 36, Tomsk 634050, Russia
| |
Collapse
|
50
|
Uchibori-Asano M, Jouraku A, Uchiyama T, Yokoi K, Akiduki G, Suetsugu Y, Kobayashi T, Ozawa A, Minami S, Ishizuka C, Nakagawa Y, Daimon T, Shinoda T. Genome-wide Identification of Tebufenozide Resistant Genes in the smaller tea tortrix, Adoxophyes honmai (Lepidoptera: Tortricidae). Sci Rep 2019; 9:4203. [PMID: 30862839 PMCID: PMC6414682 DOI: 10.1038/s41598-019-40863-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/25/2019] [Indexed: 12/15/2022] Open
Abstract
The smaller tea tortrix, Adoxophyes honmai, has developed strong resistance to tebufenozide, a diacylhydrazine-type (DAH) insecticide. Here, we investigated its mechanism by identifying genes responsible for the tebufenozide resistance using various next generation sequencing techniques. First, double-digest restriction site-associated DNA sequencing (ddRAD-seq) identified two candidate loci. Then, synteny analyses using A. honmai draft genome sequences revealed that one locus contained the ecdysone receptor gene (EcR) and the other multiple CYP9A subfamily P450 genes. RNA-seq and direct sequencing of EcR cDNAs found a single nucleotide polymorphism (SNP), which was tightly linked to tebufenozide resistance and generated an amino acid substitution in the ligand-binding domain. The binding affinity to tebufenozide was about 4 times lower in in vitro translated EcR of the resistant strain than in the susceptible strain. RNA-seq analyses identified commonly up-regulated genes in resistant strains, including CYP9A and choline/carboxylesterase (CCE) genes. RT-qPCR analysis and bioassays showed that the expression levels of several CYP9A and CCE genes were moderately correlated with tebufenozide resistance. Collectively, these results suggest that the reduced binding affinity of EcR is the main factor and the enhanced detoxification activity by some CYP9As and CCEs plays a supplementary role in tebufenozide resistance in A. honmai.
Collapse
Affiliation(s)
- Miwa Uchibori-Asano
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Akiya Jouraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Toru Uchiyama
- Tea Research Center, Shizuoka Research Institute of Agriculture and Forestry, Kurasawa, Kikugawa, Shizuoka, 439-0002, Japan
| | - Kakeru Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Gaku Akiduki
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Kumamoto, 861-1192, Japan
| | - Yoshitaka Suetsugu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Tetsuya Kobayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Akihito Ozawa
- Tea Research Center, Shizuoka Research Institute of Agriculture and Forestry, Kurasawa, Kikugawa, Shizuoka, 439-0002, Japan
| | - Saki Minami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Chiharu Ishizuka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshiaki Nakagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takaaki Daimon
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan.,Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tetsuro Shinoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan.
| |
Collapse
|