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. 2017 Jun 19;11(2):405-420.
doi: 10.3897/CompCytogen.v11i2.12824. eCollection 2017.

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

Yuling Liu  1   2 , Zhen Liu  1 , Renhai Peng  1 , Yuhong Wang  2 , Zhongli Zhou  2 , Xiaoyan Cai  2 , Xingxing Wang  2 , Zhenmei Zhang  2 , Kunbo Wang  2 , Fang Liu  2
Affiliations

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

Yuling Liu et al. Comp Cytogenet. .

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.

Keywords: BAC; FISH; cotton; draft genome assembly; physical map.

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Figures

Figure 1.
Figure 1.
The order of two BACs on metaphase chromosome of G. hirsutum (AD1) TM-1 using Dual-color-FISH. a 305A19(green)/348I20(red) b 305A19 (green)/64M24(red) c 144E04 (red)/64M24(green) d 64M24 (red)/400N03(green) e 305A19 (red)/378J07(green) f 118G12(red)/164I24(green) g 423C18 (red)/400L15(green) h 85P13 (green)/400L15(red) i 85P13 (red)/421E24(green) j 85P13 (red)/164I24(green) k D1 (red)/118G12(green) l 378J07 (green)/ A1 (red). Bar = 5 µm.
Figure 2.
Figure 2.
Comparison of positions of BACs in cytogenetic maps of G. hirsutum Ah01/Dh01 with genetic positions of SSR markers a Positions of SSR markers based on WGMM; c, b Cytogenetic maps of G. hirsutum Ah01/Dh01.
Figure 3.
Figure 3.
Integrated cytogenetic /genome assembly maps of G. hirsutum Ah01/Dh01. a Relative map position of BACs mapping to Dh01 of the AD1-NBI draft genome b Cytogenetic map of G. hirsutum Chromosome Dh01 based on 12 BAC clones c Cytogenetic map of G. hirsutum Ah01 based on 12 BAC clones d Relative map position of BACs mapping to Ah01 of the AD1-NBI draft genome. Arrow-head in a and d represent the locations of scaffold3710_D01 and scaffold183_A01 in the draft genome (AD1-NBI) respectively.
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