1
|
Zeng Q, Liu J, Wang C, Wang H, Zhang L, Hu J, Bao L, Wang S. High-quality reannotation of the king scallop genome reveals no 'gene-rich' feature and evolution of toxin resistance. Comput Struct Biotechnol J 2021; 19:4954-4960. [PMID: 34527199 PMCID: PMC8437780 DOI: 10.1016/j.csbj.2021.08.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/14/2021] [Accepted: 08/25/2021] [Indexed: 11/27/2022] Open
Abstract
The king scallop, Pecten maximus is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recently been published for P. maximus, however, it is suspicious that over 67,700 genes are annotated in this genome, which is unexpectedly larger than its close relatives of pectinids. Herein, we provide an improved high-quality chromosome-level reference genome assembly and annotation for the king scallop P. maximus. A final set of 26,995 genes is annotated after carefully checking and curation of the predicted gene models, which significantly improves the accuracy of gene structure information. The large number of gene duplicates in the previous genome is mainly distorted by the fragmented annotation. Through integrated genomic, evolutionary and transcriptomic analyses, we reveal that the Phi subfamily of ionotropic glutamate receptors (iGluRs) are well preserved in molluscs, and P. maximus experienced the rapid expansion of the Phi class of iGluR (GluF) gene family. The GluF genes exhibit ubiquitously high expression and altered sequence characteristics for ligand selectivity, which may contribute to the remarkable tolerance to neurotoxins in P. maximus. Taken together, our study disapproves the previous claim of the 'gene-rich' genome of this species and provides a high-quality genome assembly for further understanding of its biology and evolution of toxin resistance.
Collapse
Affiliation(s)
- Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Chunde Wang
- Yantai Institute of Coastal Zone Research and Center for Ocean Mega-Science, Chinese Academy of Sciences, Yantai, 264003, China
- Qingdao Agricultural University, Qingdao 266109, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Lisui Bao
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| |
Collapse
|
2
|
Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST. The gene-rich genome of the scallop Pecten maximus. Gigascience 2020; 9:giaa037. [PMID: 32352532 PMCID: PMC7191990 DOI: 10.1093/gigascience/giaa037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/26/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
Collapse
Affiliation(s)
- Nathan J Kenny
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | - Shane A McCarthy
- University of Cambridge, Department of Genetics,Cambridge CB2 3EH, UK
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Katherine James
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | | | - Craig Corton
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jale Dolucan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Dan Mead
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Pelan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Yan Ryan
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Institute of Infection and Global Health, Liverpool University, iC2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | | | | | | | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Erez L Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
- School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Kerstin Howe
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Suzanne T Williams
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| |
Collapse
|
3
|
Fernández-Pérez J, Nantón A, Méndez J. Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae). BMC Genet 2018; 19:97. [PMID: 30367592 PMCID: PMC6204057 DOI: 10.1186/s12863-018-0684-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/11/2018] [Indexed: 01/04/2023] Open
Abstract
Background The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated. Results The length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170–210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies. Conclusions This is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources. Electronic supplementary material The online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain.
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
| |
Collapse
|
4
|
Hu L, Jiang L, Bi K, Liao H, Yang Z, Huang X, Bao Z. Genomic in situ hybridization in interspecific hybrids of scallops (Bivalvia, Pectinidae) and localization of the satellite DNA Cf303, and the vertebrate telomeric sequences (TTAGGG)n on chromosomes of scallop Chlamys farreri (Jones & Preston, 1904). COMPARATIVE CYTOGENETICS 2018; 12:83-95. [PMID: 29675138 PMCID: PMC5904364 DOI: 10.3897/compcytogen.v12i1.14995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/27/2017] [Indexed: 06/08/2023]
Abstract
Mitotic chromosome preparations of the interspecific hybrids Chlamys farreri (Jones & Preston, 1904) × Patinopecten yessoensis (Jay, 1857), C. farreri × Argopecten irradians (Lamarck, 1819) and C. farreri × Mimachlamys nobilis (Reeve, 1852) were used to compare two different scallop genomes in a single slide. Although genomic in situ hybridization (GISH) using genomic DNA from each scallop species as probe painted mitotic chromosomes of the interspecific hybrids, the painting results were not uniform; instead it showed species-specific distribution patterns of fluorescent signals among the chromosomes. The most prominent GISH-bands were mainly located at centromeric or telomeric regions of scallop chromosomes. In order to illustrate the sequence constitution of the GISH-bands, the satellite Cf303 sequences of C. farreri and the vertebrate telomeric (TTAGGG)n sequences were used to map mitotic chromosomes of C. farreri by fluorescence in situ hybridization (FISH). The results indicated that the GISH-banding pattern presented by the chromosomes of C. farreri is mainly due to the distribution of the satellite Cf303 DNA, therefore suggesting that the GISH-banding patterns found in the other three scallops could also be the result of the chromosomal distribution of other species-specific satellite DNAs.
Collapse
Affiliation(s)
- Liping Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Yantai Fisheries Research Institute, Yantai 264003, China
| | - Liming Jiang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA
| | - Huan Liao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zujing Yang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiaoting Huang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
5
|
Li X, Yang Z, Liao H, Zhang Z, Huang X, Bao Z. Chromosomal mapping of tandem repeats in the Yesso Scallop, Patinopecten yessoensis (Jay, 1857), utilizing fluorescence in situ hybridization. COMPARATIVE CYTOGENETICS 2016; 10:157-169. [PMID: 27186345 PMCID: PMC4856933 DOI: 10.3897/compcytogen.v10i1.7391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/26/2016] [Indexed: 05/29/2023]
Abstract
Construction of cytogenetic maps can provide important information for chromosome identification, chromosome evolution and genomic research. However, it hasn't been conducted in many scallop species yet. In the present study, we attempted to map 12 fosmid clones containing tandem repeats by fluorescence in situ hybridization (FISH) in the Yesso scallop Patinopecten yessoensis (Jay, 1857). The results showed 6 fosmid clones were successfully mapped and distributed in 6 different pairs of chromosomes. Three clones were respectively assigned to a pair of metacentric chromosomes, a pair of submetacentric chromosomes and a pair of telocentric chromosomes and the remaining 3 clones showed their loci on three different pairs of subtelocentric chromosomes by co-hybridization. In summary, totally 8 pairs of chromosomes of the Yesso scallop were identified by 6 fosmid clones and two rDNA probes. Furthermore, 6 tandem repeats of 5 clones were sequenced and could be developed as chromosome specific markers for the Yesso scallop. The successful localization of fosmid clones will undoubtedly facilitate the integration of linkage groups with cytogenetic map and genomic research for the Yesso scallop.
Collapse
Affiliation(s)
- Xuan Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Zujing Yang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Huan Liao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Zhengrui Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| |
Collapse
|
6
|
Feng L, Hu L, Fu X, Liao H, Li X, Zhan A, Zhang L, Wang S, Huang X, Bao Z. An integrated genetic and cytogenetic map for Zhikong scallop, Chlamys farreri, based on microsatellite markers. PLoS One 2014; 9:e92567. [PMID: 24705086 PMCID: PMC3976258 DOI: 10.1371/journal.pone.0092567] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 02/24/2014] [Indexed: 11/18/2022] Open
Abstract
The reliability of genome analysis and proficiency of genetic manipulation requires knowledge of the correspondence between the genetic and cytogenetic maps. In the present study, we integrated cytogenetic and microsatellite-based linkage maps for Zhikong scallop, Chlamys farreri. Thirty-eight marker-anchored BAC clones standing for the 19 linkage groups were used to be FISH probes. Of 38 BAC clones, 30 were successfully located on single chromosome by FISH and used to integrate the genetic and cytogenetic map. Among the 19 linkage groups, 12 linkage groups were physically anchored by 2 markers, 6 linkage groups were anchored by 1 marker, and one linkage group was not anchored any makers by FISH. In addition, using two-color FISH, six linkage groups were distinguished by different chromosomal location; linkage groups LG6 and LG16 were placed on chromosome 10, LG8 and LG18 on chromosome 14. As a result, 18 of 19 linkage groups were localized to 17 pairs of chromosomes of C. farreri. We first integrated genetic and cytogenetic map for C. farreri. These 30 chromosome specific BAC clones in the cytogenetic map could be used to identify chromosomes of C. farreri. The integrated map will greatly facilitate molecular genetic studies that will be helpful for breeding applications in C. farreri and the upcoming genome projects of this species.
Collapse
Affiliation(s)
- Liying Feng
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Liping Hu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Yantai Fisheries Research Institute, Yantai, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huan Liao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuan Li
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Lingling Zhang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shi Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail: (XH); (ZB)
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail: (XH); (ZB)
| |
Collapse
|
7
|
Gokhman VE, Yefremova ZA, Yegorenkova EN. Karyotypes of parasitic wasps of the family Eulophidae (Hymenoptera) attacking leaf-mining Lepidoptera (Gracillariidae, Gelechiidae). COMPARATIVE CYTOGENETICS 2014; 8:31-41. [PMID: 24744832 PMCID: PMC3978241 DOI: 10.3897/compcytogen.v8i1.6537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/19/2014] [Indexed: 05/22/2023]
Abstract
Karyotypes of eleven parasitoid species of the family Eulophidae were examined, namely, Chrysocharis laomedon (Walker, 1839) (2n = 10), Chrysocharis sp. aff. laomedon (n = 5, 2n = 10), Chrysocharis sp. aff. albipes (Ashmead, 1904) (2n = 12), Mischotetrastichus petiolatus (Erdös, 1961) (n = 6, 2n = 12), Minotetrastichus frontalis (Nees, 1834) (n = 5, 2n = 10), Cirrospilus pictus (Nees, 1834) (2n = 12), Hyssopus geniculatus (Hartig, 1838) (2n = 16), Sympiesis gordius (Walker, 1839) (2n = 12), S. sericeicornis (Nees, 1834) (2n = 12), Pnigalio agraules (Walker, 1839) (2n = 12 + 0-2B) and Pnigalio gyamiensis Myartseva & Kurashev, 1990 (2n = 12 + 0-6B) reared from Phyllonorycter acerifoliella (Zeller, 1839), Ph. apparella (Herrich-Schäffer, 1855), Ph. issikii (Kumata, 1963) (Gracillariidae) and Chrysoesthia sexguttella (Thunberg, 1794) (Gelechiidae). Chromosome sets of all species except P. agraules and P. gyamiensis were studied for the first time. B chromosomes were detected in the two latter species; in P. gyamiensis, the maximum number of B chromosomes represents the highest value known for parasitic wasps to date.
Collapse
Affiliation(s)
| | - Zoya A. Yefremova
- Department of Zoology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | | |
Collapse
|
8
|
Gebiola M, Giorgini M, Navone P, Bernardo U. A karyological study of the genus Pnigalio Schrank (Hymenoptera: Eulophidae): assessing the taxonomic utility of chromosomes at the species level. BULLETIN OF ENTOMOLOGICAL RESEARCH 2012; 102:43-50. [PMID: 21736855 DOI: 10.1017/s0007485311000356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We provide a karyological study of 12 species of the genus Pnigalio in an attempt to evaluate the taxonomic utility of karyotypes at the species level. For all species of Pnigalio examined the number of chromosome was 2n=12. Karyotype formulae presented mainly metacentric and submetacentric chromosomes, although a pair of acrocentrics or subtelocentrics, shorter than biarmed chromosomes, was present in some species. The analysis of karyotypes of Pnigalio showed frequent but not general interspecific variability of the chromosome traits. Although most of the studied species revealed concordance between morphological and karyological characters (centromeric index and relative length), two other categories have been identified: morphologically distinct species without reciprocal differences in karyotype structure, and morphologically similar species that strongly differ in chromosomal characters.
Collapse
Affiliation(s)
- M Gebiola
- Dipartimento di Entomologia e Zoologia Agraria F. Silvestri, Università degli Studi di Napoli Federico II, via Università 100, Portici, Naples, Italy.
| | | | | | | |
Collapse
|
9
|
Comparative Cytogenetics Analysis of Chlamys farreri, Patinopecten yessoensis, and Argopecten irradians with Ct-1 DNA by Fluorescence In Situ Hybridization. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2011; 2011:785831. [PMID: 21845202 PMCID: PMC3138726 DOI: 10.1155/2011/785831] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 05/16/2011] [Indexed: 11/17/2022]
Abstract
The chromosomes of
Chlamys farreri,
Patinopecten yessoensis, and
Argopecten irradians were
studied by FISH using C. farreri C0t-1 DNA probes. The results showed that C0t-1 DNA signals spread on all chromosomes in the three scallops, whereas signal density and intensity were different strikingly. Clustering brighter signals presented in the centromeric and telomeric regions of most C. farreri chromosomes, and in the centromeric or pericentromeric regions of several P. yessoensis chromosomes. Comparative analysis of the mapping indicated a relatively higher homology in the repetitive DNA sequences of the genome between C. farreri and P. yessoensis than that between C. farreri and A. irradians. In addition, FISH showed that the distribution of C0t-1 DNA clustering signals in C. farreri displayed completely similar signal bands between homologous chromosomes. Based on the C0t-1 DNA fluorescent bands, a more exact karyotype of C. farreri has been obtained. In this study, the comparative analysis based on C0t-1 DNA provides a new insight into
the chromosomal reconstructions during the evolution process, and
it is helpful for understanding an important source of genomic
diversity, species relationships, and genome
evolution.
Collapse
|
10
|
Cytogenetic characterization and mapping of rDNAs, core histone genes and telomeric sequences in Venerupis aurea and Tapes rhomboides (Bivalvia: Veneridae). Genetica 2011; 139:823-31. [PMID: 21670988 DOI: 10.1007/s10709-011-9587-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 05/31/2011] [Indexed: 10/18/2022]
Abstract
We describe the chromosomal location of GC-rich regions, 28S and 5S rDNA, core histone genes, and telomeric sequences in the veneroid bivalve species Venerupis aurea and Tapes (Venerupis) rhomboides, using fluorochrome staining with propidium iodide, DAPI and chromomycin A3 (CMA) and fluorescent in situ hybridization (FISH). DAPI dull/CMA bright bands were coincident with the chromosomal location of 28S rDNA in both species. The major rDNA was interstitially clustered at a single locus on the short arms of the metacentric chromosome pair 5 in V. aurea, whereas in T. rhomboides it was subtelomerically clustered on the long arms of the subtelocentric chromosome pair 17. 5S rDNA also was a single subtelomeric cluster on the long arms of subtelocentric pair 17 in V. aurea and on the short arms of the metacentric pair 9 in T. rhomboides. Furthermore, V. aurea showed four telomeric histone gene clusters on three metacentric pairs, at both ends of chromosome 2 and on the long arms of chromosomes 3 and 8, whereas histone genes in T. rhomboides clustered interstitially on the long arms of the metacentric pair 5 and proximally on the long arms of the subtelocentric pair 12. Double and triple FISH experiments demonstrated that rDNA and H3 histone genes localized on different chromosome pairs in the two clam species. Telomeric signals were found at both ends of every single chromosome in both species. Chromosomal location of these three gene families in two species of Veneridae provides a clue to karyotype evolution in this commercially important bivalve family.
Collapse
|
11
|
Pérez-García C, Guerra-Varela J, Morán P, Pasantes JJ. Chromosomal mapping of rRNA genes, core histone genes and telomeric sequences in Brachidontes puniceus and Brachidontes rodriguezi (Bivalvia, Mytilidae). BMC Genet 2010; 11:109. [PMID: 21143946 PMCID: PMC3003622 DOI: 10.1186/1471-2156-11-109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 12/10/2010] [Indexed: 11/25/2022] Open
Abstract
Background Chromosome rearrangements are an important part of the speciation process in many taxa. The study of chromosome evolution in bivalves is hampered by the absence of clear chromosomal banding patterns and the similarity in both chromosome size and morphology. For this reason, obtaining good chromosome markers is essential for reliable karyotypic comparisons. To begin this task, the chromosomes of the mussels Brachidontes puniceus and B. rodriguezi were studied by means of fluorochrome staining and fluorescent in situ hybridization (FISH). Results Brachidontes puniceus and B. rodriguezi both have 2n = 32 chromosomes but differing karyotype composition. Vertebrate-type telomeric sequences appear at both ends of every single chromosome. B. puniceus presents a single terminal major rRNA gene cluster on a chromosome pair while B. rodriguezi shows two. Both mussels present two 5S rDNA and two core histone gene clusters intercalary located on the long arms of two chromosome pairs. Double and triple-FISH experiments demonstrated that one of the 5S rDNA and one of the major rDNA clusters appear on the same chromosome pair in B. rodriguezi but not in B. puniceus. On the other hand, the second 5S rDNA cluster is located in one of the chromosome pairs also bearing one of the core histone gene clusters in the two mussel species. Conclusion Knowledge of the chromosomal distribution of these sequences in the two species of Brachidontes is a first step in the understanding of the role of chromosome changes on bivalve evolution.
Collapse
|
12
|
Chromosomal mapping of repetitive DNAs in the beetle Dichotomius geminatus provides the first evidence for an association of 5S rRNA and histone H3 genes in insects, and repetitive DNA similarity between the B chromosome and A complement. Heredity (Edinb) 2009; 104:393-400. [PMID: 19756039 DOI: 10.1038/hdy.2009.126] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
|
13
|
José López-Piñón M, Freire R, Insua A, Méndez J. Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in some scallops (Bivalvia: Pectinidae). Hereditas 2008; 145:9-19. [DOI: 10.1111/j.0018-0661.2008.2034.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
14
|
José López-Piñón M, Freire R, Insua A, Méndez J. Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in some scallops (Bivalvia: Pectinidae). Hereditas 2008. [DOI: 10.1111/j.2007.0018-0661.02034x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
15
|
Huang X, Hu J, Hu X, Zhang C, Zhang L, Wang S, Lu W, Bao Z. Cytogenetic characterization of the bay scallop, Argopecten irradians irradians, by multiple staining techniques and fluorescence in situ hybridization. Genes Genet Syst 2007; 82:257-63. [PMID: 17660696 DOI: 10.1266/ggs.82.257] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The chromosomes of Argopecten irradians irradians were studied by various cytogenetic approaches. Conventional chromosome characterization built on C-banding, DAPI-staining, and silver staining was complemented by the physical mapping of ribosomal DNA and telomeric sequence (TTAGGG)n by FISH. Results showed that the constitutive heterochromatin revealed by C-banding was mainly distributed at telomeric and centromeric regions. However, interstitial C-bands were also observed. The pattern of DAPI banding was almost consistent with that of C-banding. Silver staining revealed that NORs were located on the short arms of chromosome 3 and 10, and this was further confirmed by FISH using 18S-28S rDNA. 5S rDNA was mapped as two distinguishable loci on the long arm of chromosome 11. 18S-28S and 5S rDNA were located on different chromosomes by sequential FISH. FISH also showed that the vertebrate telomeric sequence (TTAGGG)n was located on both ends of each chromosome and no interstitial signals were detected. Sequential 18S-28S rDNA and (TTAGGG)n FISH demonstrated that repeated units of the two multicopy families were closely associated on the same chromosome pair.
Collapse
Affiliation(s)
- Xiaoting Huang
- Laboratory of Marine Genetics and Breeding (MGB), Division of the Life Science and Technology, Ocean University of China, Qingdao, China
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Biscotti MA, Canapa A, Olmo E, Barucca M, Teo CH, Schwarzacher T, Dennerlein S, Richter R, Heslop-Harrison JSP. Repetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus). Gene 2007; 406:91-8. [PMID: 17706376 DOI: 10.1016/j.gene.2007.06.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 06/15/2007] [Accepted: 06/25/2007] [Indexed: 11/26/2022]
Abstract
We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.
Collapse
|