1
|
Yang Z, Li X, Liao H, Hu L, Peng C, Wang S, Huang X, Bao Z. A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:731-742. [PMID: 31473865 DOI: 10.1007/s10126-019-09918-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
To consolidate the genetic, physical, and cytogenetic maps of scallop (Patinopecten yessoensis), we constructed a molecular cytogenetic map by localizing 84 fosmid clones that contain different SNP markers from 19 linkage groups (LGs) using fluorescence in situ hybridization (FISH). Among these 84 SNP-anchored clones, 56 clones produced specific and stable signals on one pair of chromosomes. Dual-color FISH assigned 19 LGs to their corresponding chromosomes with 38 SNP-anchored clones as probes. Among these 19 LGs, 17 LGs were assigned to their corresponding one pair of chromosomes, while two clones containing SNPs from LG10 and LG19 were located on two different pairs of chromosomes separately. The orientation of 7 LGs was corrected according to the chromosome location of SNPs within the same LG. In addition, a probe panel of SNP-anchored clones was developed to identify each chromosome of P. yessoensis. The molecular cytogenetic map will facilitate molecular breeding in scallop and enable comparative studies on chromosome evolution of bivalve mollusk.
Collapse
Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Liping Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Yantai Fisheries Research Institute, Yantai, China
| | - Cheng Peng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shenhai Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
2
|
Cross I, Portela-Bens S, García-Angulo A, Merlo MA, Rodríguez ME, Liehr T, Rebordinos L. A preliminary integrated genetic map distinguishes every chromosome pair and locates essential genes related to abiotic adaptation of Crassostrea angulata/gigas. BMC Genet 2018; 19:104. [PMID: 30442092 PMCID: PMC6238303 DOI: 10.1186/s12863-018-0689-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/30/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related to adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to the ability of this oyster to retain high concentrations of toxic heavy metals. There is, in addition, an unresolved controversy as to whether or not C. angulata and C. gigas are the same species or subspecies. Both oysters have 20 metacentric chromosomes of similar size that are morphologically indistinguishable. From a genomic perspective, as a result of the great variation and selection for heterozygotes in C. gigas, the assembly of its draft genome was difficult: it is fragmented in more than seven thousand scaffolds. RESULTS In this work sixty BAC sequences of C. gigas downloaded from NCBI were assembled in BAC-contigs and assigned to BACs that were used as probes for mFISH in C. angulata and C. gigas. In addition, probes of H3, H4 histone, 18S and 5S rDNA genes were also used. Hence we obtained markers identifying 8 out the 10 chromosomes constituting the karyotype. Chromosomes 1 and 9 can be distinguished morphologically. The bioinformatic analysis carried out with the BAC-contigs annotated 88 genes. As a result, genes associated with abiotic adaptation, such as metallothioneins, have been positioned in the genome. The gene ontology analysis has also shown many molecular functions related to metal ion binding, a phenomenon associated with detoxification processes that are characteristic in oysters. Hence the provisional integrated map obtained in this study is a useful complementary tool for the study of oyster genomes. CONCLUSIONS In this study 8 out of 10 chromosome pairs of Crassostrea angulata/gigas were identified using BAC clones as probes. As a result all chromosomes can now be distinguished. Moreover, FISH showed that H3 and H4 co-localized in two pairs of chromosomes different that those previously escribed. 88 genes were annotated in the BAC-contigs most of them related with Molecular Functions of protein binding, related to the resistance of the species to abiotic stress. An integrated genetic map anchored to the genome has been obtained in which the BAC-contigs structure were not concordant with the gene structure of the C. gigas scaffolds displayed in the Genomicus database.
Collapse
Affiliation(s)
- Ismael Cross
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Silvia Portela-Bens
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Aglaya García-Angulo
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Manuel A. Merlo
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - María E. Rodríguez
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Laureana Rebordinos
- Area de Genética. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Polígono Río San Pedro, 11510 Puerto Real, Cádiz, Spain
| |
Collapse
|
3
|
Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins. Nat Commun 2017; 8:1721. [PMID: 29167427 PMCID: PMC5700196 DOI: 10.1038/s41467-017-01927-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
Bivalve molluscs are descendants of an early-Cambrian lineage superbly adapted to benthic filter feeding. Adaptations in form and behavior are well recognized, but the underlying molecular mechanisms are largely unknown. Here, we investigate the genome, various transcriptomes, and proteomes of the scallop Chlamys farreri, a semi-sessile bivalve with well-developed adductor muscle, sophisticated eyes, and remarkable neurotoxin resistance. The scallop's large striated muscle is energy-dynamic but not fully differentiated from smooth muscle. Its eyes are supported by highly diverse, intronless opsins expanded by retroposition for broadened spectral sensitivity. Rapid byssal secretion is enabled by a specialized foot and multiple proteins including expanded tyrosinases. The scallop uses hepatopancreas to accumulate neurotoxins and kidney to transform to high-toxicity forms through expanded sulfotransferases, probably as deterrence against predation, while it achieves neurotoxin resistance through point mutations in sodium channels. These findings suggest that expansion and mutation of those genes may have profound effects on scallop's phenotype and adaptation.
Collapse
|
4
|
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
|
5
|
Feng D, Li Q, Yu H, Zhao X, Kong L. Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation. PLoS One 2015; 10:e0145257. [PMID: 26693729 PMCID: PMC4691203 DOI: 10.1371/journal.pone.0145257] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Shell color polymorphisms of Mollusca have contributed to development of evolutionary biology and population genetics, while the genetic bases and molecular mechanisms underlying shell pigmentation are poorly understood. The Pacific oyster (Crassostrea gigas) is one of the most important farmed oysters worldwide. Through successive family selection, four shell color variants (white, golden, black and partially pigmented) of C. gigas have been developed. To elucidate the genetic mechanisms of shell coloration in C. gigas and facilitate the selection of elite oyster lines with desired coloration patterns, differentially expressed genes (DEGs) were identified among the four shell color variants by RNA-seq. RESULTS Digital gene expression generated over fifteen million reads per sample, producing expression data for 28,027 genes. A total number of 2,645 DEGs were identified from pair-wise comparisons, of which 432, 91, 43 and 39 genes specially were up-regulated in white, black, golden and partially pigmented shell of C. gigas, respectively. Three genes of Abca1, Abca3 and Abcb1 which belong to the ATP-binding cassette (ABC) transporters super-families were significantly associated with white shell formation. A tyrosinase transcript (CGI_10008737) represented consistent up-regulated pattern with golden coloration. We proposed that white shell variant of C. gigas could employ "endocytosis" to down-regulate notch level and to prevent shell pigmentation. CONCLUSION This study discovered some potential shell coloration genes and related molecular mechanisms by the RNA-seq, which would provide foundational information to further study on shell coloration and assist in selective breeding in C. gigas.
Collapse
Affiliation(s)
- Dandan Feng
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Hong Yu
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Xuelin Zhao
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| |
Collapse
|