Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species

• Published in: PloS one Vol. 9; no. 11; p. e113657
• Main Authors: Ye, Chu-Yu, Lin, Zhangxiang, Li, Gengmi, Wang, Ying-Ying, Qiu, Jie, Fu, Fei, Zhang, Haiqiang, Chen, Li, Ye, Sisi, Song, Weijie, Jin, Gulei, Zhu, Jinwen, Lu, Yongliang, Guo, Longbiao, Fan, Longjiang
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 26-11-2014; Public Library of Science (PLoS)
• Subjects: Agricultural production; Agriculture; Agronomy; Asclepias syriaca; Barley; Base pairs; Base Sequence; Bioinformatics; Biological evolution; Biology; Biology and Life Sciences; Biotechnology; Chloroplasts; Crop yield; Deoxyribonucleic acid; Divergence; DNA; DNA sequencing; DNA, Plant - genetics; Echinochloa; Echinochloa - classification; Echinochloa - genetics; Echinochloa crus-galli; Echinochloa oryzicola; Evolution; Evolution, Molecular; Gene sequencing; Genes; Genome, Chloroplast; Genomes; Genomics; INDEL Mutation; Laboratories; Next-generation sequencing; Nucleotide sequence; Oryza; Phylogenetics; Phylogeny; Plant Leaves - genetics; Poaceae; Population; Rice; Sequence Alignment; Setaria italica; Species; Studies; Taxonomy
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0113657

The genus Echinochloa (Poaceae) includes numerous problematic weeds that cause the reduction of crop yield worldwide. To date, DNA sequence information is still limited in the genus Echinochloa. In this study, we completed the entire chloroplast genomes of two Echinochloa species (Echinochloa oryzicola and Echinochloa crus-galli) based on high-throughput sequencing data from their fresh green leaves. The two Echinochloa chloroplast genomes are 139,891 and 139,800 base pairs in length, respectively, and contain 131 protein-coding genes, 79 indels and 466 substitutions helpful for discrimination of the two species. The divergence between the genus Echinochloa and Panicum occurred about 21.6 million years ago, whereas the divergence between E. oryzicola and E. crus-galli chloroplast genes occurred about 3.3 million years ago. The two reported Echinochloa chloroplast genome sequences contribute to better understanding of the diversification of this genus.