title: Analyses of the complete genome and gene expression of chloroplast of sweet potato [Ipomoea batata].
abstract: Sweet potato [Ipomoea batatas (L.) Lam] ranks among the top seven most important food crops cultivated worldwide and is hexaploid plant (2n=6x=90) in the Convolvulaceae family with a genome size between 2,200 to 3,000 Mb. The genomic resources for this crop are deficient due to its complicated genetic structure. Here, we report the complete nucleotide sequence of the chloroplast (cp) genome of sweet potato, which is a circular molecule of 161,303 bp in the typical quadripartite structure with large (LSC) and small (SSC) single-copy regions separated by a pair of inverted repeats (IRs). The chloroplast DNA contains a total of 145 genes, including 94 protein-encoding genes of which there are 72 single-copy and 11 double-copy genes. The organization and structure of the chloroplast genome (gene content and order, IR expansion/contraction, random repeating sequences, structural rearrangement) of sweet potato were compared with those of Ipomoea (L.) species and some basal important angiosperms, respectively. Some boundary gene-flow and gene gain-and-loss events were identified at intra- and inter-species levels. In addition, by comparing with the transcriptome sequences of sweet potato, the RNA editing events and differential expressions of the chloroplast functional-genes were detected. Moreover, phylogenetic analysis was conducted based on 77 protein-coding genes from 33 taxa and the result may contribute to a better understanding of the evolution progress of the genus Ipomoea (L.), including phylogenetic relationships, intraspecific differentiation and interspecific introgression.
authors: College of Life Sciences, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, Chengdu, Sichuan, People's Republic of China.
authors: Lang
authors: L
authors: Yan
authors: Maize Research Institute of Sichuan Agriculture University, Key Laboratory of Crop Genetic Resource and Improvement, Ministry of Education, Wenjiang, Chengdu, People's Republic of China.
authors: Xianjun
authors: X
authors: Lai
authors: College of Life Sciences, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, Chengdu, Sichuan, People's Republic of China.
authors: Xuedan
authors: X
authors: Li
authors: College of Life Sciences, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, Chengdu, Sichuan, People's Republic of China.
authors: Changhe
authors: C
authors: Wei
authors: College of Life Sciences, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, Chengdu, Sichuan, People's Republic of China.
authors: Xuemei
authors: X
authors: Tan
authors: College of Life Sciences, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics, Chengdu, Sichuan, People's Republic of China.
authors: Yizheng
authors: Y
authors: Zhang
mesh_terms: D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics*; D002874:Chromosome Mapping; D018628:Gene Dosage; D018506:Gene Expression Regulation, Plant; D051456:Gene Flow; D017343:Genes, Plant; D054628:Genome, Chloroplast; D059014:High-Throughput Nucleotide Sequencing; D055029:Inverted Repeat Sequences; D027723:Ipomoea batatas / Q000145:classification / Q000235:genetics*; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011003:Ploidies; D017393:RNA Editing
chemical_list: D010940:Plant Proteins