Chromosome Identification and Cytogenetic Map Construction of Zhikong Scallop (Chlamys farreri) Based on Fluorescence in situ Hybridization

Liping Hu,Qiang Zhao,Qiang Xing,Zhenmin Bao,Liming Jiang,Liyong Wang,Zujing Yang,Xiaoting Huang

doi:10.3389/fmars.2021.741230

Abstract

Zhikong scallop (Chlamys farreri) is a bivalve species with broad economic and biological value, and an essential species of aquaculture in North China. Recently, efforts have been made to improve knowledge of genome, genetics, and cytogenetics, which is devoted to develop the molecular breeding project for the scallop. In this study, we constructed a cytogenetic map and identified all chromosomes of C. farreri using fluorescence in situ hybridization (FISH). A total of 100 Bacterial Artificial Chromosome (BAC) clones and 27 fosmid clones, including 58 microsatellite marker-anchored BAC clones, 4 genes-anchored BAC clones, 38 random BAC clones, 22 repetitive sequences-anchored fosmid clones, and 5 gene-anchored fosmid clones, were tested as probes, and 69 of them produced specific and stable signal on one pair of chromosomes. Then, multiple co-hybridizations were conducted to distinguish all the submetacentric and subtelocentric chromosomes with similar morphology by the abovementioned chromosome-specific markers. On this basis, a cytogenetic map of C. farreri containing 69 clones was constructed by co-hybridization and karyotype analysis. The markers covered all 19 pairs of chromosomes, and the average number of markers on each chromosome was 3.6. The cytogenetic map provides a platform for genetic and genomic analysis of C. farreri, which facilitates the molecular breeding project of C. farreri and promotes the comparative studies of chromosome evolution in scallops and even bivalves.

Highlights

Chromosome identification is an important part of genome research, which provides a broad view of chromatin structure organization
The development of fluorescence in situ hybridization (FISH) is a significant step toward chromosome identification, and FISH is a well-established approach for determining the location and relative order of DNA sequences in chromosomes (Zhang et al, 2008a; Merlo et al, 2021)
Mapping using large-insert DNA genomic clones [e.g., P1, fosmid, and bacterial artificial chromosome (BAC)] as probes for FISH provided an alternative approach that has been successfully used in some shellfish species

Summary

INTRODUCTION

Chromosome identification is an important part of genome research, which provides a broad view of chromatin structure organization. The initial probes used as landmarks for chromosome distinguish were repetitive sequences, mainly including satellite sequences (Wang et al, 2001; Zhang et al, 2008a), ribosomal DNA (Zhang et al, 1999; Xu et al, 2001; Huang et al, 2007a,b), and histone genes (Eirín-López et al, 2002, 2004; Zhang et al, 2007a). Mapping using large-insert DNA genomic clones [e.g., P1, fosmid, and bacterial artificial chromosome (BAC)] as probes for FISH provided an alternative approach that has been successfully used in some shellfish species. Some chromosomes of C. farreri had been distinguished by FISH using repetitive sequences or large-insert DNA clones as probes (Huang et al, 2006, 2012; Zhang et al, 2007a, 2008b; Huan et al, 2009a,b; Feng et al, 2014). The integrated cytogenetic map will contribute to further characterization and application of the C. farreri genome

MATERIALS AND METHODS

RESULTS

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DATA AVAILABILITY STATEMENT