Dataset Information

Characterization of the complete chloroplast genome of Phleum pratense L. cv. Minshan.

ABSTRACT: Severe seed degradation of Phleum pratense L. cv. Minshan restricts its productivity and promotion, the chloroplast genome and evolutionary relationship analysis of Minshan could provide inheritance reasons on seed degradation and fundamental genetic reference for its molecular breeding and biological research. Its chloroplast genome was 134,973 bp in length, containing a pair of inverted repeated regions (42,726 bp) which were separated by a large single copy region of 79,473 bp, and a small single copy region of 12,774 bp. Moreover, a total of 114 functional genes were annotated, including 79 mRNA, 32 tRNA genes, and 5 rRNA genes. The phylogenetic relationships of 25 species indicated that Minshan was closely related to Avena damascene.

SUBMITTER: Cui G

PROVIDER: S-EPMC7707759 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Characterization of the complete chloroplast genome of <i>Phleum pratense</i> L. cv. Minshan.

Cui Guangxin G Lu Yuan Y Wei Xiaoxing X Wang Xiaoli X Wang Chunmei C Gao Yaqin Y Duan Huirong H

Mitochondrial DNA. Part B, Resources 20191121 2

Severe seed degradation of <i>Phleum pratense</i> L. cv. Minshan restricts its productivity and promotion, the chloroplast genome and evolutionary relationship analysis of Minshan could provide inheritance reasons on seed degradation and fundamental genetic reference for its molecular breeding and biological research. Its chloroplast genome was 134,973 bp in length, containing a pair of inverted repeated regions (42,726 bp) which were separated by a large single copy region of 79,473 bp, and a s ...[more]

PMID: 33366372

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Project description:BackgroundSeveral bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar 'Tombul' with multiple annotation tools.ResultsThree different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales.ConclusionIn this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.

Dataset Information

Characterization of the complete chloroplast genome of Phleum pratense L. cv. Minshan.

Publications

Characterization of the complete chloroplast genome of <i>Phleum pratense</i> L. cv. Minshan.

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