High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences

Chengjun Zhang, Jun Wang, Nicholas C. Marowsky, Manyuan Long, Rod A Wing, Chuanzhu Fan

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which likely originated after O. sativa diverged from O. glaberrima. These genes account for around 1% (28/3,176) of all annotated genes on O. sativa's Chr3s. Among the28 newgenes, two recentlyduplicatedsegments contained eightgenes. Fourteen ofthe28 newgenes consist of chimeric gene structure derived from one or multiple parental genes and flanking targeting sequences. Although the majority of these 28 new genes were formed by single or segmental DNA-based gene duplication and recombination, we found two genes that were likely originated partially through exon shuffling. Sequence divergence tests between new genes and their putative progenitors indicated that new genes were most likely evolving under natural selection. We showed all 28 new genes appeared to be functional, as suggested by Ka/Ksanalysis and the presence of RNA-seq, cDNA, expressed sequence tag, massively parallel signature sequencing, and/or small RNA data. The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice's broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation

Original languageEnglish (US)
Pages (from-to)1038-1048
Number of pages11
JournalGenome Biology and Evolution
Volume5
Issue number5
DOIs
StatePublished - 2013

Fingerprint

Chromosomes, Human, Pair 3
chromosome
rice
genome
Genome
chromosomes
gene
Genes
genes
Oryza sativa
Surveys and Questionnaires
Oryza
RNA
High-Throughput Nucleotide Sequencing
Gene Duplication
Gene Targeting
DNA
Genetic Selection
Expressed Sequence Tags
domestication

Keywords

  • Chimera
  • Comparative genomics
  • Gene duplication
  • New gene
  • Oryza

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. / Zhang, Chengjun; Wang, Jun; Marowsky, Nicholas C.; Long, Manyuan; Wing, Rod A; Fan, Chuanzhu.

In: Genome Biology and Evolution, Vol. 5, No. 5, 2013, p. 1038-1048.

Research output: Contribution to journalArticle

Zhang, Chengjun ; Wang, Jun ; Marowsky, Nicholas C. ; Long, Manyuan ; Wing, Rod A ; Fan, Chuanzhu. / High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. In: Genome Biology and Evolution. 2013 ; Vol. 5, No. 5. pp. 1038-1048.
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