Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

Abstract Background Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca ‘Greizy’, Pilea peperomioides and Pilea serpyllacea ‘Globosa’) and performed comprehensive comparative analysis. Results The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. Conclusion Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

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Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea

10.21203/rs.3.rs-49270/v3 ◽

2020 ◽

Author(s):

Jingling Li ◽

Jianmin Tang ◽

Siyuan Zeng ◽

Fang Han ◽

Jing Yuan ◽

...

Keyword(s):

Comparative Analysis ◽

Plastid Genome ◽

Dna Barcode ◽

Sequence Divergence ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Hypervariable Regions ◽

Plastid Genomes ◽

Insight Into

Abstract Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

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Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea

10.21203/rs.3.rs-49270/v4 ◽

2020 ◽

Author(s):

Jingling Li ◽

Jianmin Tang ◽

Siyuan Zeng ◽

Fang Han ◽

Jing Yuan ◽

...

Keyword(s):

Comparative Analysis ◽

Plastid Genome ◽

Dna Barcode ◽

Sequence Divergence ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Hypervariable Regions ◽

Plastid Genomes ◽

Insight Into

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Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea

10.21203/rs.3.rs-49270/v2 ◽

2020 ◽

Author(s):

Jingling Li ◽

Jianmin Tang ◽

Siyuan Zeng ◽

Fang Han ◽

Jing Yuan ◽

...

Keyword(s):

Comparative Analysis ◽

Plastid Genome ◽

Dna Barcode ◽

Sequence Divergence ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Hypervariable Regions ◽

Plastid Genomes ◽

Insight Into

Abstract Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis Wedd., Pilea glauca 'Greizy', Pilea peperomioides Diels. and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified, petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1, which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

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Title: The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species

10.21203/rs.3.rs-290026/v1 ◽

2021 ◽

Author(s):

Mahtab Moghaddam ◽

Atsushi Ohta ◽

Motoki Shimizu ◽

Ryohei Terauchi ◽

Shahrokh Kazempour-Osaloo

Keyword(s):

Comparative Analysis ◽

Plastid Genome ◽

Phylogenetic Analyses ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Plastid Genomes ◽

Chloroplast Genomes ◽

Paired End Sequencing

Abstract Plastid genome sequences provide valuable markers for surveying the evolutionary relationships and population genetics of plant species. In the present study, the complete plastid genome of Onobrychis gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes. The O. gaubae plastid genome was 123,645 bp in length and included a large single-copy (LSC) region of 81,034 bp, a small single-copy (SSC) region of 13,788 bp and one copy of the inverted repeat (IRb) of 28,823 bp. The genome encoded 110 genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes and possessed 89 simple sequence repeats (SSRs) and 28 repeated structures with the highest proportion in the LSC. Comparative analysis of the chloroplast genomes across IRLC revealed three hotspot genes (ycf1, ycf2, clpP) which could be used as molecular markers for resolving phylogenetic relationships and species identification. IRLC plastid genomes also showed multiple gene losses and inversions. Phylogenetic analyses revealed that O. gaubae is closely related to Hedysarum. The complete O. gaubae genome is a valuable resource for investigating evolution of Onobrychis species and can be used to identify related species.

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Comparative Survey of Morphological Variations and Plastid Genome Sequencing Reveals Phylogenetic Divergence between Four Endemic Ilex Species

Forests ◽

10.3390/f11090964 ◽

2020 ◽

Vol 11 (9) ◽

pp. 964

Author(s):

Tao Su ◽

Mengru Zhang ◽

Zhenyu Shan ◽

Xiaodong Li ◽

Biyao Zhou ◽

...

Keyword(s):

Plastid Genome ◽

Strong Association ◽

Nuclear Genome ◽

Image Cytometry ◽

Single Copy ◽

Reproductive Organs ◽

Rrna Genes ◽

Phenotypic Traits ◽

Trna Genes ◽

Plastid Genomes

Holly (Ilex L.), from the monogeneric Aquifoliaceae, is a woody dioecious genus cultivated as pharmaceutical and culinary plants, ornamentals, and industrial materials. With distinctive leaf morphology and growth habitats, but uniform reproductive organs (flowers and fruits), the evolutionary relationships of Ilex remain an enigma. To date, few contrast analyses have been conducted on morphology and molecular patterns in Ilex. Here, the different phenotypic traits of four endemic Ilex species (I. latifolia, I. suaveolens, I. viridis, and I. micrococca) on Mount Huangshan, China, were surveyed through an anatomic assay and DNA image cytometry, showing the unspecified link between the examined morphology and the estimated nuclear genome size. Concurrently, the newly-assembled plastid genomes in four Ilex have lengths ranging from 157,601 bp to 157,857 bp, containing a large single-copy (LSC, 87,020–87,255 bp), a small single-copy (SSC, 18,394–18,434 bp), and a pair of inverted repeats (IRs, 26,065–26,102 bp) regions. The plastid genome annotation suggested the presence of numerable protein-encoding genes (89–95), transfer RNA (tRNA) genes (37–40), and ribosomal RNA (rRNA) genes (8). A comprehensive comparison of plastomes within eight Ilex implicated the conserved features in coding regions, but variability in the junctions of IRs/SSC and the divergent hotspot regions potentially used as the DNA marker. The Ilex topology of phylogenies revealed the incongruence with the traditional taxonomy, whereas it informed a strong association between clades and geographic distribution. Our work herein provided novel insight into the variations in the morphology and phylogeography in Aquifoliaceae. These data contribute to the understanding of genetic diversity and conservation in the medicinal Ilex of Mount Huangshan.

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The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis

Science Progress ◽

10.1177/00368504211059973 ◽

2021 ◽

Vol 104 (4) ◽

pp. 003685042110599

Author(s):

Dhafer Alzahrani ◽

Enas Albokhari ◽

Abidina Abba ◽

Samaila Yaradua

Keyword(s):

Plastid Genome ◽

High Throughput Sequencing ◽

Genome Structure ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Plastid Genomes ◽

Small Single Copy

Caylusea hexagyna and Ochradenus baccatus are two species in the Resedaceae family. In this study, we analysed the complete plastid genomes of these two species using high-throughput sequencing technology and compared their genomic data. The length of the plastid genome of C. hexagyna was 154,390 bp while that of O. baccatus was 153,380 bp. The lengths of the inverted repeats (IR) regions were 26,526 bp and 26,558 bp, those of the large single copy (LSC) regions were 83,870 bp and 83,023 bp; and those of the small single copy (SSC) regions were 17,468 bp and 17,241 bp in C. hexagyna and O. baccatus, respectively. Both genomes consisted of 113 genes: 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Repeat analysis showed that the plastid genome included all types of repeats, with more frequent occurrences of palindromic sequences. Comparative studies of SSR markers showed that there were 256 markers in C. hexagyna and 255 in O. baccatus; the majority of the SSRs in these plastid genomes were mononucleotide repeats (A/T). All the clusters in the phylogenetic tree had high support. This study reported the first complete plastid genomes of the genera Caylusea and Ochradenus and the first for the Resedaceae family.

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Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj18.390 ◽

2018 ◽

Vol 22 (5) ◽

pp. 524-530 ◽

Cited By ~ 1

Author(s):

M. A. Filyushin ◽

A. M. Mazur ◽

A. V. Shchennikova ◽

Е. Z. Kochieva

Keyword(s):

Comparative Analysis ◽

Rrna Genes ◽

Trna Genes ◽

Vegetable Crops ◽

Structural Elements ◽

Protein Coding ◽

Plastid Genomes ◽

Plastome Evolution ◽

Taxonomic Studies

Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genusAlliumL. (family Amaryllidaceae) incorporates more than 900 species, includes economically significant vegetable crops such as garlicA. sativum, onionA. cepa, leekA. porrum, etc. In this work, the plastome of garlicA. sativumhas been completely sequenced. TheA. sativumplastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis ofA. sativumandA. cepaplastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat boundaries. The total numbers of genes inA. sativumandA. cepaare the same, but the gene composition is different: therpl22gene is functional inA. sativum, being a pseudogene inA. cepa; conversely, therps16gene is a pseudogene inA. sativumand a protein-coding gene inA. cepa. In theA. sativumandA. cepaplastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species.

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The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, IR expansions and phylogenomic implications

10.21203/rs.3.rs-373541/v1 ◽

2021 ◽

Author(s):

Qiulin Qin ◽

Jingling Li ◽

Siyuan Zeng ◽

Yiceng Xu ◽

Fang Han ◽

...

Keyword(s):

Comparative Analysis ◽

Food Industry ◽

Rrna Genes ◽

Trna Genes ◽

Dna Barcodes ◽

Protein Coding ◽

Hypervariable Regions ◽

The Family ◽

Perennial Shrub ◽

Intron Region

Abstract Background: Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandiflorus and S. validus, and carried out a comprehensive comparative analysis.Results: The four Selenicereus plastomes all have a typical quartile structure. The plastome size ranged from 133,146 bp to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the IR regions had undergone a dramatic expansion and formed a previously unreported SC/IR border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Phylogenetic analysis indicated that Hylocereus was nested in Selenicereus.Conclusion: Our study enriches the plastomic resources in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.

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Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

10.21203/rs.3.rs-49270/v1 ◽

2020 ◽

Author(s):

Jingling Li ◽

Jianmin Tang ◽

Siyuan Zeng ◽

Fang Han ◽

Jing Yuan ◽

...

Keyword(s):

Comparative Analysis ◽

Dna Barcode ◽

Morphological Characteristics ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Coding Regions ◽

Chloroplast Genomes ◽

Interspecific Diversity

Abstract Background Pilea is a genus of perennial herbs from the family Urticaceae, which are used for courtyard ornamental. For some species, they are used as medicinal plants in traditional Chinese medicine as well. The morphological characteristics of medicinal species from Pilea are similar, and it is difficult to accurately distinguish them based only on morphological characteristics. Besides, the species classification of Pilea are still controversial. The classification of many species are still in an unresolved state. At present, there is no information about the chloroplast genomes of Pilea, which limits our further understanding of this genus. Here, we first reported 4 chloroplast genomes of Pilea taxa (P. mollis, P. glauca, P. peperomioides and P. serpyllacea), and performed comprehensive comparative analysis. Results The four chloroplast genomes have similar structural characteristics and gene order with other angiosperms. These genomes all have a typical quartile structure, which contains 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Besides, we detected SSRs and repeat sequences, and analyzed the expansion/contraction of IR regions. In particular, the comparative analysis showed a rather level of sequence divergence in the non-coding regions, even in the protein-coding regions of the four genome sequences, suggesting a high level of genetic diversity in Pilea. Moreover, we identified eight hypervariable regions, including petN-psbM; psbZ-trnG-GCC; trnT-UGU-trnL-UAA; accD-psbI; ndhF-rpl32; rpl32-trnL-UAG; ndhA-intron and ycf1, are proposed for use as DNA barcode regions. Phylogenetic analysis showed that four Pilea species form a monophyletic cluster with a 100% bootstrap value. Conclusion The results obtained here could provide abundant information for the phylogenetic position of Pilea and further species identification. High levels of sequences divergence promote our understanding of the interspecific diversity of this genus, also provide reference for the rational classification of unsolved species in the future.

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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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