一个来自水牛基因组序列组装的水牛1号染色体有序支架的框架辐射杂种图谱。

A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly.

作者信息

Stafuzza N B, Naressi B C M, Yang E, Cai J J, Amaral-Trusty M E J

机构信息

Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil.

Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.

出版信息

Genet Mol Res. 2015 Oct 27;14(4):13096-104. doi: 10.4238/2015.October.26.5.

DOI:10.4238/2015.October.26.5

PMID:26535622

Abstract

River buffalo chromosome 1 (BBU1) is a sub-metacentric chromosome homologous to bovine chromosomes 1 and 27. In this study, we constructed a new framework radiation hybrid (RH) map from BBU1 using BBURH5000 panel adding nine new genes (ADRB3, ATP2C1, COPB2, CRYGS, P2RY1, SLC5A3, SLC20A2, SST, and ZDHHC2) and one microsatellite (CSSM043) to the set of markers previously mapped on BBU1. The new framework RH map of BBU1 contained 141 markers (55 genes, 2 ESTs, 10 microsatellites, and 74 SNPs) distributed within one linkage group spanning 2832.62 centirays. Comparison of the RH map to sequences from bovine chromosomes 1 and 27 revealed an inversion close to the telomeric region. In addition, we ordered a set of 34 scaffolds from the buffalo genome assembly UMD_CASPUR_WB_2.0. The RH map could provide a valuable tool to order scaffolds from the buffalo genome sequence, contributing to its annotation.

摘要

河流型水牛1号染色体（BBU1）是一条亚中着丝粒染色体，与牛的1号和27号染色体同源。在本研究中，我们利用BBURH5000板构建了一个新的BBU1框架辐射杂种（RH）图谱，在先前定位在BBU1上的标记集中增加了9个新基因（ADRB3、ATP2C1、COPB2、CRYGS、P2RY1、SLC5A3、SLC20A2、SST和ZDHHC2）和一个微卫星（CSSM043）。新的BBU1框架RH图谱包含141个标记（55个基因、2个EST、10个微卫星和74个SNP），分布在一个跨度为2832.62厘镭的连锁群内。将该RH图谱与牛1号和27号染色体的序列进行比较，发现靠近端粒区域存在一个倒位。此外，我们对来自水牛基因组组装UMD_CASPUR_WB_2.0的一组34个支架进行了排序。该RH图谱可为从水牛基因组序列中排序支架提供有价值的工具，有助于其注释。