Ontology highlight
ABSTRACT:
PROVIDER: PRJNA692662 | ENA |
REPOSITORIES: ENA
Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| SRR13449797_1.fastq.gz | Fastqsanger.gz | |||
| SRR13449797_2.fastq.gz | Fastqsanger.gz |
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Project description:Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.
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Project description:<i>Artemisia selengensis</i> Turcz (Louhao in Chinese) is a widely used health food and a well-known traditional Chinese medicine. However, only a small part of the chloroplast genome data of <i>Artemisia</i> has been reported and there was no report for <i>A. selengensis</i>. In this study, we presented the complete chloroplast genome of <i>A. selengensis</i> and analysed its phylogenetic relationship with other 28 related species belonging to the <i>Asteraceae</i> family. The result showed that the whole genome was 151 215?bp in length with a typical conserved quadripartite structure. The total GC content of whole genome, LSC, SSC, and IRa/IRb regions was 37.46, 35.55, 30.81, and 43.09%, respectively. A total of 133 genes were identified, including 88 protein-coding, 37 transfer RNA, and eight ribosome RNA genes. Among these genes, nineteen genes contained a single intron and two genes contained two introns. The phylogenetic relationship showed that <i>A. selengensis</i> was similar to <i>A. gmelinii</i>. The complete chloroplast genome presented here will enrich the genetic resources of medicinal plant and promote our understanding of the phylogeny of <i>Artemisia</i> within the Asteraceae family.
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Project description:Artemisia selengenesis is not only a health food, but also a well-known traditional Chinese medicine. Only a fraction of the chloroplast (cp) genome data of Artemisia has been reported and chloroplast genomic materials have been widely used in genomic evolution studies, molecular marker development, and phylogenetic analysis of the genus Artemisia, which makes evolutionary studies, genetic improvement, and phylogenetic identification very difficult. In this study, the complete chloroplast genome of A. selengensis was compared with that of other species within Artemisia and phylogenetic analyses was conducted with other genera in the Asteraceae family. The results showed that A. selengensis is an AT-rich species and has a typical quadripartite structure that is 151,215 bp in length. Comparative genome analyses demonstrated that the available chloroplast genomes of species of Artemisia were well conserved in terms of genomic length, GC contents, and gene organization and order. However, some differences, which may indicate evolutionary events, were found, such as a re-inversion event within the Artemisia genus, an unequal duplicate phenomenon of the ycf1 gene because of the expansion and contraction of the IR region, and the fast-evolving regions. Repeated sequences analysis showed that Artemisia chloroplast genomes presented a highly similar pattern of SSR or LDR distribution. A total of 257 SSRs and 42 LDRs were identified in the A. selengensis chloroplast genome. The phylogenetic analysis showed that A. selengensis was sister to A. gmelinii. The findings of this study will be valuable in further studies to understand the genetic diversity and evolutionary history of Asteraceae.
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Project description:Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three <i>Salix</i> species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus <i>Populus</i>, which most likely results from homoplasy. By comparing three <i>Salix</i> chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of <i>P. trichocarpa</i> at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs) and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in Salicaceae provide resources to better understand the successful adaptation of Salicaceae species.
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Project description:In this study, the complete chloroplast genome of <i>Chenopodium</i> sp. were sequenced and annotated. The complete chloroplast genome of <i>Chenopodium</i> sp. was composed of circular DNA molecules with a total length of 152,068?bp. The base composition of this chloroplast genome is as follows: A (31.16%), T (31.58%), G (18.27%), and C (18.99%). The chloroplast genome contains 84 protein-coding genes, 8 ribosomal RNA genes (rRNA), and 37 transfer RNA (tRNA) genes. The taxonomic status of the <i>Chenopodium</i> sp. chloroplast genome exhibits a closest relationship with Chenopodium quinoa.
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2016-01-01 | S-EPMC5104525 | BioStudies