A Comparative Study of the Chloroplast Genomes of Five Lepidium Medicinal Plants

Abstract Background Herb genomics is a rapidly developing field of medicinal plant research and development. Plant genomic studies demonstrate the unique advantage of employing plants in medicinal therapy. The genus Lepidium falls under the Brassicaceae family and it includes crucial medicinal plants. Herein, we sequenced the complete chloroplast (cp) genomes of Lepidium apetalum (LA) and Lepidium perfoliatum (LP) and assessed their genetic profiles against the reported profiles of Lepidium sativum (LS), Lepidium meyenii (LM), and Lepidium virginicum (LV). Results In particular, we examined genomic arrangement, gene number, type, and repeat sequences. Based on our annotation data, both LA and LP possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and 8 ribosomal RNA (rRNA) genes. Our repeat analyses revealed that LA harbored 20 forward repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas LP had 15 forward repeats, 20 palindrome repeats,4 reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium cp genomes and a remarkably high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium-specific gene fragments, particularly in the intergenic regions of the trnK-atpA, trnC-psbC, trnT-rbcL, ndhF-ndhH, ycf1-trnR, accD, ccsA, matK, ndhF, rpoB, rpoC2, and ycf1 genes. Moreover, following codon usage analysis, we observed that codon 14 was the most frequently used codon in the Lepidium CDS. In addition, correlation investigations revealed that the ENC (the effective number of codon) content was strongly associated with GC3, GC3s, and N. Conclusion Based on these data, LA and LP originate from very similar genetic backgrounds. Furthermore, neutrality, ENC, and PR2-plots analyses demonstrated that the CUB (the codon usage bias) of Lepidium cp genome was strongly influenced by mutation and natural selection. Our analysis of the cp genomic sequences of LA and LP will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.

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Large-scale de novo transcriptome analysis reveals specific gene expression and novel simple sequence repeats markers in salinized roots of the euhalophyte Salicornia europaea

Acta Physiologiae Plantarum ◽

10.1007/s11738-018-2702-z ◽

2018 ◽

Vol 40 (8) ◽

Cited By ~ 1

Author(s):

Jinbiao Ma ◽

Xinlong Xiao ◽

Li Li ◽

Albino Maggio ◽

Dayong Zhang ◽

...

Keyword(s):

Gene Expression ◽

Transcriptome Analysis ◽

Simple Sequence Repeats ◽

Large Scale ◽

De Novo ◽

Specific Gene ◽

Salicornia Europaea ◽

De Novo Transcriptome ◽

Specific Gene Expression ◽

Simple Sequence

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Lineage-Specific Tandem Repeats Riding on a Transposable Element of MITE in Xenopus Evolution: A New Mechanism for Creating Simple Sequence Repeats

Journal of Molecular Evolution ◽

10.1007/s00239-004-2664-1 ◽

2004 ◽

Vol 59 (6) ◽

pp. 738-746 ◽

Cited By ~ 15

Author(s):

Akira Hikosaka ◽

Akira Kawahara

Keyword(s):

Transposable Element ◽

Simple Sequence Repeats ◽

Tandem Repeats ◽

Simple Sequence

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Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea

Scientific Reports ◽

10.1038/s41598-020-80431-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hukam C. Rawal ◽

Sangeeta Borchetia ◽

Biswajit Bera ◽

S. Soundararajan ◽

R. Victor J. Ilango ◽

...

Keyword(s):

Comparative Analysis ◽

Codon Usage ◽

Simple Sequence Repeats ◽

Morphological Characteristics ◽

Distribution Patterns ◽

Chloroplast Genomes ◽

Cp Genome ◽

Different Origins ◽

Indian Tea ◽

Simple Sequence

AbstractBased upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.

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Polymorphism revealed by simple sequence repeats

Trends in Plant Science ◽

10.1016/s1360-1385(96)86898-0 ◽

1996 ◽

Vol 1 (7) ◽

pp. 215-222 ◽

Cited By ~ 528

Author(s):

W POWELL ◽

G MACHRAY ◽

J PROVAN

Keyword(s):

Simple Sequence Repeats ◽

Simple Sequence

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DNA Fingerprinting and Characterization of some Egyptian Date Palm Cultivars Using Simple Sequence Repeats (SSRs)

Journal of Plant Production Sciences ◽

10.21608/jpps.2015.7402 ◽

2015 ◽

Vol 3 (1) ◽

pp. 31-41

Author(s):

Mohammed Hussein ◽

Samah Sabry ◽

Manal Eid

Keyword(s):

Dna Fingerprinting ◽

Simple Sequence Repeats ◽

Date Palm ◽

Simple Sequence

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The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽

10.3390/plants10081517 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1517

Author(s):

Se-Hwan Cheon ◽

Min-Ah Woo ◽

Sangjin Jo ◽

Young-Kee Kim ◽

Ki-Joong Kim

Keyword(s):

Northeast Asia ◽

Single Copy ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Protein Coding ◽

Tropical Regions ◽

Relationship Of ◽

The Relationship ◽

Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

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Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae

Non-Coding RNA ◽

10.3390/ncrna7030041 ◽

2021 ◽

Vol 7 (3) ◽

pp. 41

Author(s):

Emma Lesage ◽

Jorge Perez-Fernandez ◽

Sophie Queille ◽

Christophe Dez ◽

Olivier Gadal ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Tandem Repeats ◽

Chromatin State ◽

Rrna Genes ◽

Rdna Genes ◽

Regulatory Pathways ◽

Chromatin States ◽

Non Coding Rnas ◽

Pervasive Transcription

Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.

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