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- genome sequences (3)
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The present phylogenetic analysis was conducted using mitochondrial genome sequences of plants to infer evolutionary relationship of bryophytes. Paraphyly of bryophytes was shown by reconstructed trees. Liverworts are the first to diverge therefore appeared as sister to land plants in nucleotide based trees. However protein sequences based tree show mosses and liverworts to form a joint clade. Hornworts formed sister relationship with vascular plants.
Combined data from chloroplast and mitochondrial genome sequences showed paraphyly of bryophytes
(2013)
The present study was conducted using chloroplast and mitochondrial genome sequences of plants to gain insight on evolutionary relationship of bryophytes. The representative taxa were selected considering the availability of both organelle genome sequences. Phylogenetic analysis using combined data from chloroplast and mitochondrial sequences infer paraphyly of bryophytes.
Microsatellites also known as simple sequence repeats (SSRs) are short repeat motifs (1-6 bp) found in DNA sequences Detection of microsatellites is important for the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. In the present study, chloroplast genome sequence of Anthoceros formosae, downloaded from the National Center for Biotechnology Information (NCBI) was mined with the help of MISA tool to detect SSRs in chloroplast genome (cpSSRs). A total of 67 SSRs were detected with a density of 1 SSR/2.4 kb in 161.162 kb sequence mined. Depending on the repeat units, the length of SSRs ranged from 12 to 18 bp for mono-, 14 to 46 bp for di-, 12 to 27 bp for tri-, 12 to 20 bp for tetra and 18 bp for hexa-nucleotide repeats. Mononucleotide repeats were the most frequent repeat type (35.82%) followed by dinucleotide repeats (25.37%). Penta-nucleotide repeats were not detected in chloroplast genome sequence of Anthoceros formosae.
Mining of simple sequence repeats in chloroplast genome of a parasitic liverwort: Aneura mirabilis
(2013)
Aneura mirabilis is a parasitic liverwort with a chloroplast genome size of 108007 bp. In this study simple sequence repeats (SSRs) were detected using bioinformatics approch in plastid genome of Aneura mirabilis. Due to its small genome size only 19 repeats were detected showing a density of 1 SSR/5.68 kb. The length of SSRs ranged from 12 to 20 bp. Mononucleotide repeats were the most frequent repeat type (36.84%) followed by tetranucleotide repeats (31.58%). Moreover hexanucleotide repeats were absent in chloroplast genome sequence of Aneura mirabilis.
The availability of organelle genome sequences in public databases facilitates the reconstruction of land plants phylogeny. Therefore the present phylogenetic analysis was conducted using chloroplast genome sequences of plants to study phylogenetic relationship of bryophytes. The representative taxa were selected considering the availability of organelle genome sequences in database. Inferred tree topologies showed paraphyly of bryophytes with sister relationship between hornworts and vascular plants irrespective of the method (Maximum Likelihood and Bayesian Inference) and type of sequences (Nucleotide and Protein) used. Among bryophytes liverworts are the first to diverge therefore appeared as sister to land plants. Moreover land plants formed a monophyletic group.