Cytogenetic maps of homoeologous chromosomes A h01 and D h01 and their integration with the genome assembly in Gossypium hirsutum.

Yuling Liu,Xiaoyan Cai,Fang Liu,Yuhong Wang,Zhenmei Zhang,Zhen Liu,Zhongli Zhou,Xingxing Wang,Kunbo Wang,Renhai Peng

doi:10.3897/compcytogen.v11i2.12824

Abstract

Cytogenetic maps of Gossypium hirsutum (Linnaeus, 1753) homoeologous chromosomes Ah01 and Dh01 were constructed by fluorescence in situ hybridization (FISH), using eleven homoeologous-chromosomes-shared bacterial artificial chromosomes (BACs) clones and one chromosome-specific BAC clone respectively. We compared the cytogenetic maps with the genetic linkage and draft genome assembly maps based on a standardized map unit, relative map position (RMP), which allowed a global view of the relationship of genetic and physical distances along each chromosome, and assembly quality of the draft genome assembly map. By integration of cytogenetic maps with sequence maps of the two chromosomes (Ah01 and Dh01), we inferred the locations of two scaffolds and speculated that some homologous sequences belonging to homoeologous chromosomes were removed as repetitiveness during the sequence assembly. The result offers molecular tools for cotton genomics research and also provides valuable information for the improvement of the draft genome assembly.

Highlights

The genus Gossypium (Linnaeus, 1753) includes approximately 47 diploid species (2n = 2x = 26) that are divided into eight genome groups, named as A-G and K genome (Endrizzi et al 1985, Wendel et al 2012)
bacterial artificial chromosomes (BACs) used for fluorescence in situ hybridization (FISH) mapping were identified by screening two genomic BAC libraries derived from G. herbaceum (Linnaeus, 1753) var. africenum (Gao et al 2013) and G. barbadense (Linnaeus, 1753) Pima 90-53
To construct the cytogenetic maps of chromosomes Ah01 and Dh01 of G. hirsutum, an initial set of 47 simple sequence repeat (SSR) markers shared by both chromosomes of Ah01 and Dh01 from a whole genome marker map (WGMM) (Wang et al 2013, Rong et al 2004) and a genetic map (Yu et al 2011) were used to screen two BAC libraries of G. herbaceum var. africenum and G. barbadense Pima 90-53

Summary

Introduction

Ancient hybridization between A and D diploids resulted in a new allopolyploid (AD) (2n = 4x = 52) lineage approximately 1–2 million years ago (Wendel 1989, Li et al 2015, Zhang et al 2015, Liu et al 2015, Yuan et al 2015). At present, sequencing Gossypium species genomes is ongoing in full swing with successively draft maps of whole genome in wild and cultivated cotton species (Paterson et al 2012, Wang et al 2012, Li et al 2014, 2015, Zhang et al 2015, Liu et al 2015,Yuan et al 2015). It is necessary to carry out the relevant basic research work on cotton genome research to help for genome sequence assembly

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Discussion

Conclusion