scholarly journals Complete Chloroplast Genomes and Comparative Analyses of L. chinensis, L. anhuiensis, and L. aurea (Amaryllidaceae)

2020 ◽  
Vol 21 (16) ◽  
pp. 5729
Author(s):  
Fengjiao Zhang ◽  
Tao Wang ◽  
Xiaochun Shu ◽  
Ning Wang ◽  
Weibing Zhuang ◽  
...  
Keyword(s):  
Native Species ◽  
Ornamental Plants ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Germplasm Identification ◽  
Gene Expansion ◽  
Phylogeny Analysis ◽  
Chloroplast Genomes ◽  
Simple Sequence

The genus Lycoris (about 20 species) includes important medicinal and ornamental plants. Due to the similar morphological features and insufficient genomic resources, germplasm identification and molecular phylogeny analysis are very limited. Here, we sequenced the complete chloroplast genomes of L. chinensis, L. anhuiensis, and L. aurea; they have very similar morphological traits that make it difficult to identify. The full length of their cp genomes was nearly 158k bp with the same guanine-cytosine content of 37.8%. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNAs, and eight rRNAs. A comparative analysis revealed the conservation in sequence size, GC content, and gene content. Some variations were observed in repeat structures, gene expansion on the IR-SC (Inverted Repeat-Single-Copy) boundary regions. Together with the cpSSR (chloroplast simple sequence repeats), these genetic variations are useful to develop molecular markers for germplasm identification. Phylogenetic analysis showed that seven Lycoris species were clustered into a monophyletic group, and closed to Narcissus in Amaryllidaceae. L. chinensis, L. anhuiensis, and L. longituba were clustered together, suggesting that they were very likely to be derived from one species, and had the same ancestor with L. squamigera. Our results provided information on the study of genetic diversity, origins or relatedness of native species, and the identification of cultivars.

scholarly journals Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2137 ◽  
Author(s):  
Xiang-Xiao Meng ◽  
Yan-Fang Xian ◽  
Li Xiang ◽  
Dong Zhang ◽  
Yu-Hua Shi ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Future Studies ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
Cp Genome ◽  
Sanguisorba Officinalis

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

scholarly journals Structural and Comparative Analysis of the Complete Chloroplast Genome of Pyrus hopeiensis—“Wild Plants with a Tiny Population”—and Three Other Pyrus Species

2018 ◽  
Vol 19 (10) ◽  
pp. 3262 ◽  
Author(s):  
Yongtan Li ◽  
Jun Zhang ◽  
Longfei Li ◽  
Lijuan Gao ◽  
Jintao Xu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Population Decline ◽  
Gc Content ◽  
Single Copy ◽  
Wild Plants ◽  
Similar Degree ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
History Of

Pyrus hopeiensis is a valuable wild resource of Pyrus in the Rosaceae. Due to its limited distribution and population decline, it has been listed as one of the “wild plants with a tiny population” in China. To date, few studies have been conducted on P. hopeiensis. This paper offers a systematic review of P. hopeiensis, providing a basis for the conservation and restoration of P. hopeiensis resources. In this study, the chloroplast genomes of two different genotypes of P. hopeiensis, P. ussuriensis Maxin. cv. Jingbaili, P. communis L. cv. Early Red Comice, and P. betulifolia were sequenced, compared and analyzed. The two P. hopeiensis genotypes showed a typical tetrad chloroplast genome, including a pair of inverted repeats encoding the same but opposite direction sequences, a large single copy (LSC) region, and a small single copy (SSC) region. The length of the chloroplast genome of P. hopeiensis HB-1 was 159,935 bp, 46 bp longer than that of the chloroplast genome of P. hopeiensis HB-2. The lengths of the SSC and IR regions of the two Pyrus genotypes were identical, with the only difference present in the LSC region. The GC content was only 0.02% higher in P. hopeiensis HB-1. The structure and size of the chloroplast genome, the gene species, gene number, and GC content of P. hopeiensis were similar to those of the other three Pyrus species. The IR boundary of the two genotypes of P. hopeiensis showed a similar degree of expansion. To determine the evolutionary history of P. hopeiensis within the genus Pyrus and the Rosaceae, 57 common protein-coding genes from 36 Rosaceae species were analyzed. The phylogenetic tree showed a close relationship between the genera Pyrus and Malus, and the relationship between P. hopeiensis HB-1 and P. hopeiensis HB-2 was the closest.

scholarly journals Chloroplast Genome of Phyllanthus Emblica and Leptopus Cordifolius: Comparative Analysis and Phylogenetic within Family Phyllanthaceae

2021 ◽  
Author(s):  
Umar Rehman ◽  
Nighat Sultana ◽  
Abdullah . ◽  
Abbas Jamal ◽  
Maryam Muzaffar ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Gc Content ◽  
Single Copy ◽  
Phyllanthus Emblica ◽  
Protein Coding ◽  
Coding Sequences ◽  
Tropical Regions ◽  
Chloroplast Genomes ◽  
The Family

Family Phyllanthaceae is one of the largest segregates of the eudicot order Malpighiales and its species are herb, shrub, and tree, which are mostly distributed in tropical regions. Certain taxonomic discrepancies exist at genus and family level. Here, we report chloroplast genomes of three Phyllanthaceae species—Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius— and compare them with six others previously reported Phyllanthaceae chloroplast genomes. The species of Phyllanthaceae displayed quadripartite structure, comprising inverted repeat regions (IRa and IRb) that separate large single copy (LSC) and small single copy (SSC) regions. The length of complete chloroplast genome ranged from 154,707 bp to 161,093 bp; LSC from 83,627 bp to 89,932 bp; IRs from 23,921 bp to 27,128 bp; and SSC from 17,424 bp to 19,441 bp. Chloroplast genomes contained 111 to 112 unique genes, including 77 to 78 protein-coding, 30 transfer RNA (tRNA), and 4 ribosomal RNA (rRNA) that showed similarities in arrangement. The number of protein-coding genes varied due to deletion/pseudogenization of rps16 genes in Baccaurea ramiflora and Leptopus cordifolius. High variability was seen in number of oligonucleotide repeats while analysis of guanine-cytosine (GC) content, codon usage, amino acid frequency, simple sequence repeats analysis, synonymous and non-synonymous substitutions, and transition and transversion substitutions showed similarities in all Phyllanthaceae species. We detected a higher number of transition substitutions in the coding sequences than non-coding sequences. Moreover, the high number of transition substitutions was determined among the distantly related species in comparison to closely related species. Phylogenetic analysis shows the polyphyletic nature of the genus Phyllanthus which requires further verification. We also determined suitable polymorphic coding genes, including rpl22, ycf1, matK, ndhF, and rps15 which may be helpful for the reconstruction of the high-resolution phylogenetic tree of the family Phyllanthaceae using a large number of species in the future. Overall, the current study provides insight into chloroplast genome evolution in Phyllanthaceae.

scholarly journals Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae

2021 ◽  
Vol 11 ◽  
Author(s):  
Yongtan Li ◽  
Yan Dong ◽  
Yichao Liu ◽  
Xiaoyue Yu ◽  
Minsheng Yang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Chloroplast Genome ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Evolutionary Relationships ◽  
Trna Genes ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Cp Genome

In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.

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.

scholarly journals The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽  
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.

scholarly journals Draft Genome Sequence of Bacillus sp. Strain IGA-FME-2, Isolated from the Bulk Soil of Soybean (Glycine max L.) in Northeast China

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
Zhenhua Yu ◽  
Sergio de los Santos-Villalobos ◽  
Yansheng Li ◽  
Jian Jin ◽  
Fannie Isela Parra Cota ◽  
...  
Keyword(s):  
Glycine Max ◽  
Draft Genome ◽  
Gc Content ◽  
Single Copy ◽  
Bulk Soil ◽  
23S Rrna ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Glycine Max L

ABSTRACT Here, we present the draft genome of Bacillus sp. strain IGA-FME-2. This strain was isolated from the bulk soil of soybean (Glycine max L.). Its genome consists of 3,810 protein-coding genes, 44 tRNAs, two 16S rRNAs, and a single copy of 23S rRNA, with a GC content of 46.4%.

scholarly journals Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8450 ◽  
Author(s):  
Sunan Huang ◽  
Xuejun Ge ◽  
Asunción Cano ◽  
Betty Gaby Millán Salazar ◽  
Yunfei Deng
Keyword(s):  
Adaptive Evolution ◽  
Phylogenetic Relationships ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Variable Regions ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

scholarly journals The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 261 ◽  
Author(s):  
Yongfu Li ◽  
Steven Paul Sylvester ◽  
Meng Li ◽  
Cheng Zhang ◽  
Xuan Li ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Sequence Data ◽  
Genome Structure ◽  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Critically Endangered Species ◽  
Genomic Study

Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.

scholarly journals The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

2019 ◽  
Vol 42 (4) ◽  
pp. 601-611 ◽  
Author(s):  
Yan Li ◽  
Liukun Jia ◽  
Zhihua Wang ◽  
Rui Xing ◽  
Xiaofeng Chi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Single Copy ◽  
Bootstrap Support ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

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