Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order

被引：60

作者：

Liu, H ^{[1
]}

Sachidanandam, R ^{[1
]}

Stein, L ^{[1
]}

机构：

[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

来源：

GENOME RESEARCH | 2001年 / 11卷 / 12期

关键词：

D O I：

10.1101/gr.194501

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We have investigated possible collinearity between the genomes of rice and Arabidopsis by comparing 126 annotated and mapped rice BAC Sequences (similar to 20 Mb of sequence) with the annotated and complete Arabidopsis genome (similar to 115 Mb). Although we were able to identify several re.-ions in which gene order is preserved, they are relatively small, and are interrupted by noncollinear genes. Computer simulation showed that these microscale collinearities are above the expectation for a random process. Oil the other hand, the order of exons within homolo.-ous.-enes (<2.5 kb) was preserved, as expected.

引用

页码：2020 / 2026

页数：7

共 18 条

[1] Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella [J].

Acarkan, A ;

Rossberg, M ;

Koch, M ;

Schmidt, R .

PLANT JOURNAL, 2000, 23 (01) :55-62

[2]

ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999

[3]

[Anonymous], 1999, GENOME

[4] Distribution of genes in the genome of Arabidopsis thaliana and its implications for the genome organization of plants [J].

Barakat, A ;

Matassi, G ;

Bernardi, G .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (17) :10044-10049

[5] The small, the large and the wild - the value of comparison in plant genomics [J].

Bevan, M ;

Murphy, G .

TRENDS IN GENETICS, 1999, 15 (06) :211-214

[6] Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes [J].

Chen, M ;

SanMiguel, P ;

deOliveira, AC ;

Woo, SS ;

Zhang, H ;

Wing, RA ;

Bennetzen, JL .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (07) :3431-3435

[7] Arabidopsis -: Rice:: Will colinearity allow gene prediction across the eudicot-monocot divide? [J].

Devos, KM ;

Beales, J ;

Nagamura, Y ;

Sasaki, T .

GENOME RESEARCH, 1999, 9 (09) :825-829

[8] Plant comparative genetics after 10 years [J].

Gale, MD ;

Devos, KM .

SCIENCE, 1998, 282 (5389) :656-659

[9] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[10] Colinearity and gene density in grass genomes [J].

Keller, B ;

Feuillet, C .

TRENDS IN PLANT SCIENCE, 2000, 5 (06) :246-251

← 1 2 →