Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics.
BACKGROUND
Long-established protein-coding genes may lose their coding potential during evolution ("unitary gene loss"). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated and remain largely elusive.


RESULTS
Using a locally developed pipeline, we identified 129 unitary gene loss events for long-established protein-coding genes from four representative species of Poaceae, i.e. brachypodium, rice, sorghum and maize. Functional annotation suggested that the lost genes in all or most of Poaceae species are enriched for genes involved in development and response to endogenous stimulus. We also found that 44 mutated genomic loci of lost genes, which we referred as relics, were still actively transcribed, and of which 84% (37 of 44) showed significantly differential expression across different tissues. More interestingly, we found that there were totally five expressed relics may function as competitive endogenous RNA in brachypodium, rice and sorghum genome.


CONCLUSIONS
Based on comparative genomics and transcriptome data, we firstly compiled a comprehensive catalogue of unitary gene loss events in Poaceae species and characterized a statistically significant functional preference for these lost genes as well showed the potential of relics functioning as competitive endogenous RNAs in Poaceae genomes.
State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China. zhaoy@mail.cbi.pku.edu.cn.
Yi
Y
Zhao
State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China. ecologytang@aliyun.com.|Current address: College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, People's Republic of China. ecologytang@aliyun.com.
Liang
L
Tang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China. lizhe@ibcas.ac.cn.
Zhe
Z
Li
State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China. jinjp@mail.cbi.pku.edu.cn.
Jinpu
J
Jin
State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China. luojc@mail.cbi.pku.edu.cn.
Jingchu
J
Luo
State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China. gaog@mail.cbi.pku.edu.cn.
Ge
G
Gao
D019143:Evolution, Molecular; D017343:Genes, Plant; D023281:Genomics; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D014158:Transcription, Genetic; D059467:Transcriptome