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

By

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

Type

Article

Date of Publication

2017

Original Publication

Comparative cytogenetics : international journal of plant & animal cytogenetics, karyosystematics and molecular systematics

Volume

11

Series / Issue

Issue: 2

Pages

405-420

Subjects

BAC , Cotton , draft genome assembly , Fish , physical map

Contributed by

Pensoft Publishers

Language

English

Published by

St. Petersburg, Russia [Published] with technical support of Zoological Institute RAS [2007]-

Identifiers

DOI: https://doi.org/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.