scholarly journals Mining and analysis of simple sequence repeats in the chloroplast genomes of genus Vigna

2018 ◽  
Vol 2 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Nidhi Shukla ◽  
Himani Kuntal ◽  
Asheesh Shanker ◽  
Satyendra Nath Sharma
Keyword(s):  
Simple Sequence Repeats ◽  
Chloroplast Genomes ◽  
Simple Sequence ◽  
Genus Vigna

scholarly journals The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 299 ◽  
Author(s):  
Jakub Sawicki ◽  
Alina Bączkiewicz ◽  
Katarzyna Buczkowska ◽  
Piotr Górski ◽  
Katarzyna Krawczyk ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Land Plant ◽  
Stable Structure ◽  
Inverted Repeats ◽  
Phylogenomic Analysis ◽  
Dinucleotide Repeats ◽  
Early Land Plant ◽  
Chloroplast Genomes ◽  
Early Land ◽  
Simple Sequence

The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.

scholarly journals In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

2009 ◽  
Vol 9 (4) ◽  
pp. 344-352 ◽  
Author(s):  
E.V. Tambarussi ◽  
D.M. Melotto-Passarin ◽  
S.G. Gonzalez ◽  
J.B. Brigati ◽  
F.A. Jesus ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
In Silico ◽  
In Silico Analysis ◽  
Chloroplast Genomes ◽  
Solanaceae Species ◽  
Silico Analysis ◽  
Simple Sequence

scholarly journals Characterization of a New Natural Periclinal Navel–Satsuma Chimera of Citrus: ‘Zaohong’ Navel Orange

2007 ◽  
Vol 132 (3) ◽  
pp. 374-380 ◽  
Author(s):  
Min Zhang ◽  
Xiuxin Deng ◽  
Changping Qin ◽  
Chunli Chen ◽  
Hongyan Zhang ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Cell Layer ◽  
Fruit Shape ◽  
Navel Orange ◽  
Fresh Market ◽  
Satsuma Mandarin ◽  
Chloroplast Genomes ◽  
Predominant Component ◽  
Simple Sequence ◽  
Juice Sacs

‘Zaohong’ navel orange [Citrus sinensis (L.) Osbeck + C. unshiu Marc.], a new strain of citrus from a graft chimera, was discovered in China. It was diploid and arose at the junction where a ‘Robertson’ navel orange scion was top-worked onto a Satsuma mandarin (C. unshiu). Some characteristics determined by the L1 cell layer, such as juice sacs of fruit and stoma length, were similar to those of Satsuma mandarin, while others, including leaf index, fruit shape, navel, and color and aroma of the rind, were determined by the L2 cell layer, were similar to ‘Robertson’ navel orange. High-performance liquid chromatography analysis of the carotenoid extracts of the flesh of ‘Zaohong’ navel orange indicated that it had the carotenoids profile of Satsuma mandarin with β-cryptoxanthin as the predominant component in the juice sacs in mature fruit. Simple sequence repeats (SSR) and chloroplast simple sequence repeats (cpSSR) analysis showed that both nuclear and chloroplast genomes of ‘Zaohong’ navel orange were composed of both donor plants. On the basis of these facts, ‘Zaohong’ navel orange was found to be a periclinal chimera consisting of L1 derived from Satsuma mandarin and L2/L3 from ‘Robertson’ navel orange. It combined the valuable traits of both donor plants, matured ≈1 month earlier than the present navel orange cultivars, and therefore had good potential in citrus fresh market.

scholarly journals The Complete Chloroplast Genome Sequence of Four Plant Species, Their SSR Identification and Phylogenetic Analysis

2021 ◽  
Author(s):  
Yueyi Zhu ◽  
Xianwen Zhang ◽  
Guopeng Li ◽  
Jiqian Xiang ◽  
Jinghua Su ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Markers ◽  
Chloroplast Genome ◽  
Simple Sequence Repeats ◽  
Genetic Information ◽  
Phylogenetic Trees ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Chloroplast Genome Sequence ◽  
Simple Sequence

The chloroplast genome is conservative and stable, which can be employed to resolve genotypes. Currently, published nuclear sequences and molecular markers failed to differentiate the species from taxa robustly, including Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. In this study, the four chloroplast genomes were characterized, and then their simple sequence repeats (SSRs) and phylogenetic positions were analyzed. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. Moreover, the chloroplast genomes contained typical four regions. Six classes of SSR were identified from the four chloroplast genomes, in which mononucleotide was the class with the most members. The types of the repeats were various within individual classes of SSR. Phylogenetic trees indicated that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed under family Ocimeae. Additionally, R. bambusarum and R. henryi were clustered together, whereas they did not belong to the same species due to the differing SSR features. This research would provide evidence for resolving the species and contributed new genetic information for further study.

scholarly journals Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

2021 ◽  
Author(s):  
Ming Zhu ◽  
Peipei Feng ◽  
Jingyao Ping ◽  
Jinye Li ◽  
Ying-juan Su ◽  
...  
Keyword(s):  
Relative Density ◽  
Relative Abundance ◽  
Simple Sequence Repeats ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Gene ◽  
Large Single Copy ◽  
Genus Level ◽  
Chloroplast Genomes ◽  
Simple Sequence

Recent taxonomic and molecular phylogenetic studies have shown that Gymnosphaera should be recognized as an independent taxonomic unit at the genus level under the family Cyatheaceae. In this study, the complete chloroplast genomes of the eight species of Cyatheaceae were sequenced, and their phylogenetic relationships were reconstructed using the maximum likelihood, Bayesian inference, maximum parsimony, and neighbor-joining methods, and the characteristics of their simple sequence repeats (SSRs) were compared and analyzed for the first time. The results showed that when Cyatheaceae was divided into three genera,the number, relative abundance, relative density, and GC content of all SSRs and of SSRs of certain unit lengths in the chloroplast genomes of the eight species of Cyatheaceae were genus specific in the whole chloroplast genomes and in their different regions (large single-copy, small single-copy, inverted repeat, intergenic spacer, intron, rRNA gene, and coding sequence regions). The SSRs overall and the single-nucleotide SSRs had significant differences in number, relative abundance, relative density, and GC content between the chloroplast genomes, their intergenic regions, and large single-copy regions. When Cyatheaceae was divided into two genera, only the difference in GC content was significant. Therefore, our results support the restoration of the hierarchical status of Gymnosphaera. This study provides an important basis for the identification of the phylogenetic relationship of Cyatheaceae plants.

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