Consistent over-estimation of gene number in complex plant genomes

by: Jeffrey L Bennetzen, Craig Coleman, Renyi Liu, Jianxin Ma, Wusirika Ramakrishna

Current Opinion in Plant Biology, Vol. 7, No. 6. (December 2004), pp. 732-736.

View FullText article

DOI, ScienceDirect

Reviews [Write a review of this article]

There are no reviews of this article

Find related articles from these CiteULike users

sanchezbuelna

Find related articles with these CiteULike tags

gene, genome, genomics, over-estimation

Abstract

The first comprehensive comparison of gene content between higher plant species provided the unexpected conclusions that rice contained about twice as many genes as Arabidopsis, and that about half of the rice genes had no obvious homologs in any other organism. Our subsequent analyses indicate that most of these "extra, novel" rice genes are mis-annotated segments of transposable elements, especially retrotransposons. Aggressive annotation of a randomly selected subset of the rice genome suggests that the gene number is less than 40 000. The five fantasies of automated plant gene discovery are described and a protocol is provided to minimize (or at least predict) the inaccuracy of future plant genome annotations.

@article{citeulike:2803521, abstract = {The first comprehensive comparison of gene content between higher plant species provided the unexpected conclusions that rice contained about twice as many genes as Arabidopsis, and that about half of the rice genes had no obvious homologs in any other organism. Our subsequent analyses indicate that most of these "extra, novel" rice genes are mis-annotated segments of transposable elements, especially retrotransposons. Aggressive annotation of a randomly selected subset of the rice genome suggests that the gene number is less than 40 000. The five fantasies of automated plant gene discovery are described and a protocol is provided to minimize (or at least predict) the inaccuracy of future plant genome annotations.}, author = {Bennetzen, Jeffrey L. and Coleman, Craig and Liu, Renyi and Ma, Jianxin and Ramakrishna, Wusirika }, citeulike-article-id = {2803521}, doi = {10.1016/j.pbi.2004.09.003}, journal = {Current Opinion in Plant Biology}, keywords = {gene, genome, genomics, over-estimation}, month = {December}, number = {6}, pages = {732--736}, posted-at = {2008-05-16 02:44:02}, priority = {3}, title = {Consistent over-estimation of gene number in complex plant genomes}, url = {http://dx.doi.org/10.1016/j.pbi.2004.09.003}, volume = {7}, year = {2004} }

RIS record

TY - JOUR ID - citeulike:2803521 L3 - citeulike-article-id:2803521 TI - Consistent over-estimation of gene number in complex plant genomes JF - Current Opinion in Plant Biology VL - 7 IS - 6 SP - 732 EP - 736 N2 - The first comprehensive comparison of gene content between higher plant species provided the unexpected conclusions that rice contained about twice as many genes as Arabidopsis, and that about half of the rice genes had no obvious homologs in any other organism. Our subsequent analyses indicate that most of these "extra, novel" rice genes are mis-annotated segments of transposable elements, especially retrotransposons. Aggressive annotation of a randomly selected subset of the rice genome suggests that the gene number is less than 40 000. The five fantasies of automated plant gene discovery are described and a protocol is provided to minimize (or at least predict) the inaccuracy of future plant genome annotations. KW - gene KW - genome KW - genomics KW - over-estimation AU - Bennetzen, Jeffrey AU - Coleman, Craig AU - Liu, Renyi AU - Ma, Jianxin AU - Ramakrishna, Wusirika PY - 2004/12// UR - http://dx.doi.org/10.1016/j.pbi.2004.09.003 ER -

RIS BibTeX