Chloroplast genomic comparison of two sister species Allium macranthum and A. fasciculatum provides valuable insights into adaptive evolution.

Genes & Genomics
Hao LiXing-Jin He

Abstract

Allium macranthum and Allium fasciculatum are two sister species and their natural populations are separated by high mountains and deep valleys with exact opposite habitat. The chloroplast genome in angiosperms has showed useful for investigating plant evolution and systematic studies. Comparative analysis of these genomes revealed potential markers and phylogenetic analysis, and discuss the influence of positive selected sites on adaptive evolution. Here, we sequenced the complete chloroplast genomes of these two species and analyzed the repeat sequences components, nucleotide diversity, selection pressure and the phylogeny relationships with related species. A typical quadripartite structure was detected with a genome size changed from 152,148 to 152,931 bp. We identified 67 and 79 simple sequence repeats in A. macranthum and A. fasciculatum, in which the mono-nucleotide repeats A/T possess the highest percentage. Three mutational hotspots (rpl32, rps16 and matK) at the SSC and LSC regions were observed, which showed remarkably higher Pi value (> 0.03). Additionally, eight genes (rpoA, atpF, cemA, rps4, ccsA, rpoC2, rpl14 and clpP) exhibited elevated pairwise Ka/Ks ratios in alpine species. Phylogenetic analyses based on the ...Continue Reading

References

Aug 15, 1995·Proceedings of the National Academy of Sciences of the United States of America·W PowellJ A Rafalski
Aug 5, 1998·Proceedings of the National Academy of Sciences of the United States of America·W Makalowski, M S Boguski
Jul 27, 1999·The Plant Journal : for Cell and Molecular Biology·G De Santis-MacIossekR G Herrmann
Dec 15, 2000·Trends in Ecology & Evolution·Z Yang, J P Bielawski
Aug 15, 2002·Trends in Genetics : TIG·Laurence D Hurst
Feb 18, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·T ThielA Graner
Oct 7, 2003·Annual Review of Genomics and Human Genetics·Justin C Fay, Chung-I Wu
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
Oct 27, 2004·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Ki-Joong Kim, Hae-Lim Lee
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Robert K JansenJeffrey L Boore
Apr 18, 2008·Briefings in Bioinformatics·Sudhir KumarKoichiro Tamura
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jul 29, 2011·Genome Génome / Conseil National De Recherches Canada·Dai-Yong KuangLu Lu
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Jun 25, 2016·Genome Biology·Henry DaniellWan-Jung Chang
Oct 24, 2017·Frontiers in Plant Science·Su-Young HongYul-Ho Kim
Feb 10, 2018·International Journal of Molecular Sciences·Cuihua GuZhiqiang Wu
Jun 5, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Hai-Ying LiuSong-Dong Zhou

❮ Previous
Next ❯

Citations

Oct 9, 2020·Scientific Reports·Jeremy R ShearmanWirulda Pootakham

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.