scholarly journals Comparison and Phylogenetic Analyses of Nine Complete Chloroplast Genomes of Zingibereae

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 710
Author(s):  
Heng Liang ◽  
Juan Chen
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
The Family ◽  
Phylogenomic Analyses ◽  
Close Relatives ◽  
Rna Genes ◽  
Insight Into ◽  
Simple Sequence

Zingibereae is a large tribe in the family Zingiberaceae, which contains plants with important medicinal, edible, and ornamental values. Although tribes of Zingiberaceae are well circumscribed, the circumscription of many genera within Zingibereae and the relationships among them remain elusive, especially for the genera of Boesenbergia, Curcuma, Kaempferia and Pyrgophyllum. In this study, we investigated the plastome variation in nine species representing five genera of Zingibereae. All plastomes showed a typical quadripartite structure with lengths ranging from 162,042 bp to 163,539 bp and contained 132–134 genes, consisting of 86–88 coding genes, 38 transfer RNA genes and eight ribosomal RNA genes. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were detected. In addition, we conducted phylogenomic analyses of the Zingibereae and related taxa with plastomes data from additional 32 species from Genbank. Our results confirmed that Stahlianthus is closely related to Curcuma, supporting the idea of merging it into Curcuma. Kaempferia, Boesenbergia and Zingiber were confirmed as close relatives and grouped together as the Kaempferia group. Pyrgophyllum is not allied with the Curcuma clade but instead is embedded within the Hedychium clade. Our results demonstrate the power of plastid phylogenomics in improving the phylogenetic relationships within Zingibereae and provide a new insight into plastome evolution in Zingibereceae.

scholarly journals Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1143 ◽  
Author(s):  
Hang Ran ◽  
Yanyan Liu ◽  
Cui Wu ◽  
Yanan Cao
Keyword(s):  
Genomic Structure ◽  
Phylogenetic Analyses ◽  
Sister Relationship ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Flora Of China ◽  
Phylogenetic Resolution ◽  
Sister Relationships ◽  
Phylogenomic Analyses ◽  
Cp Genome

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

scholarly journals The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Wenbin Xu ◽  
Boshun Xia ◽  
Xinwei Li
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Noncoding Sequences ◽  
Chloroplast Genomes ◽  
Rna Genes

AbstractThe six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

scholarly journals Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenpan Dong ◽  
Yanlei Liu ◽  
Chao Xu ◽  
Yongwei Gao ◽  
Qingjun Yuan ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Ribosomal Rna ◽  
Leaf Size ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Chloroplast Genomes ◽  
Conserved Gene ◽  
Rna Genes ◽  
Simple Sequence

Abstract Background Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary tremendously making it difficult to use those characters to identify most species and a significant challenge to address the taxonomy of Distylium. To infer robust relationships and develop variable markers to identify Distylium species, we sequenced most of the Distylium species chloroplast genomes. Results The Distylium chloroplast genome size was 159,041–159,127 bp and encoded 80 protein-coding, 30 transfer RNAs, and 4 ribosomal RNA genes. There was a conserved gene order and a typical quadripartite structure. Phylogenomic analysis based on whole chloroplast genome sequences yielded a highly resolved phylogenetic tree and formed a monophyletic group containing four Distylium clades. A dating analysis suggested that Distylium originated in the Oligocene (34.39 Ma) and diversified within approximately 1 Ma. The evidence shows that Distylium is a rapidly radiating group. Four highly variable markers, matK-trnK, ndhC-trnV, ycf1, and trnT-trnL, and 74 polymorphic simple sequence repeats were discovered in the Distylium plastomes. Conclusions The plastome sequences had sufficient polymorphic information to resolve phylogenetic relationships and identify Distylium species accurately.

scholarly journals Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

scholarly journals Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1185
Author(s):  
Wenqian Wang ◽  
Huan Zhang ◽  
Jérôme Constant ◽  
Charles R. Bartlett ◽  
Daozheng Qin
Keyword(s):  
Control Region ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Start Codon ◽  
Rrna Genes ◽  
Rich Region ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Rna Genes ◽  
Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

scholarly journals Three redescriptions in Tintinnopsis (Protista: Ciliophora: Tintinnina) from coastal waters of China, with cytology and phylogenetic analyses based on ribosomal RNA genes

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yang Bai ◽  
Rui Wang ◽  
Wen Song ◽  
Lifang Li ◽  
Luciana F. Santoferrara ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Coastal Waters ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Middle Portion ◽  
Closely Related Species ◽  
Molecular Information ◽  
Ciliary Tuft ◽  
Rna Genes ◽  
Rrna Sequences

Abstract Background The taxonomy of tintinnine ciliates is vastly unresolved because it has traditionally been based on the lorica (a secreted shell) and it has only recently incorporated cytological and molecular information. Tintinnopsis, the most speciose tintinnine genus, is also the most problematic: it is known to be non-monophyletic, but it cannot be revised until more of its species are studied with modern methods. Results Here, T. hemispiralis Yin, 1956, T. kiaochowensis Yin, 1956, and T. uruguayensis Balech, 1948, from coastal waters of China, were studied. Lorica and cell features were morphometrically investigated in living and protargol-stained specimens, and sequences of three ribosomal RNA (rRNA) loci were phylogenetically analyzed. The three species show a complex ciliary pattern (with ventral, dorsal, and posterior kineties and right, left, and lateral ciliary fields), but differ in lorica morphology, details of the somatic ciliature and rRNA gene sequences. Tintinnopsis hemispiralis is further distinguished by a ciliary tuft (a ribbon of very long cilia originated from the middle portion of the ventral kinety and extending out of the lorica) and multiple macronuclear nodules. Both T. kiaochowensis and T. uruguayensis have two macronuclear nodules, but differ in the number of somatic kineties and the position of the posterior kinety. Two neotypes are fixed for T. hemispiralis and T. kiaochowensis to stabilize the species names objectively, mainly because of the previous unavailability of type materials. By phylogenetic analysis and comparison with closely-related species, we infer that the ciliary tuft and details such as the commencement of the rightmost kinety in the lateral ciliary field are synapomorphies that may help clarify the systematics of Tintinnopsis-like taxa. Conclusion The redescriptions of three poorly known Tintinnopsis species, namely T. hemispiralis, T. kiaochowensis, and T. uruguayensis firstly revealed their ciliary patterns and rRNA sequences. This study expands knowledge and database of tintinnines and helps in identifying potential synapomorphies for future taxonomic rearrangements.

scholarly journals The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 181
Author(s):  
Zhenya Li ◽  
Xinxin Li ◽  
Nan Song ◽  
Huiji Tang ◽  
Xinming Yin
Keyword(s):  
Ribosomal Rna ◽  
Mitochondrial Protein ◽  
Carabid Beetles ◽  
Protein Coding ◽  
Sequencing Method ◽  
The Family ◽  
Outgroup Species ◽  
Complete Mitogenome ◽  
Rna Genes ◽  
Generation Sequencing

Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.

Chloroplast genomes of seven species of Coryloideae (Betulaceae): structures and comparative analysis

Genome ◽  
2020 ◽  
Vol 63 (7) ◽  
pp. 337-348
Author(s):  
Guanglong Hu ◽  
Lili Cheng ◽  
Wugang Huang ◽  
Qingchang Cao ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Information ◽  
Molecular Breeding ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Mutational Hotspots ◽  
The Family ◽  
Identification Of Species

Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera: Carpinus, Corylus, Ostrya, and Ostryopsis. We sequenced the plastomes of six species of Corylus and one species of Ostryopsis for comparative and phylogenetic analyses. The plastomes are 159–160 kb long and possess typical quadripartite cp architecture. The plastomes show moderate divergence and conserved arrangement. Five mutational hotspots were identified by comparing the plastomes of seven species of Coryloideae: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1. We assembled the most complete phylogenomic tree for the family Betulaceae using 68 plastomes. Our cp genomic sequence phylogenetic analyses placed Carpinus, Ostrya, and Ostryopsis in a clade together and left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the existence of five subclades reflecting the phylogeographical relationships among the species. The data offer significant genetic information for the identification of species of the Coryloideae, taxonomic and phylogenetic studies, and molecular breeding.

scholarly journals Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

2015 ◽  
Vol 82 (4) ◽  
pp. 1215-1226 ◽  
Author(s):  
Francy Jimenez-Infante ◽  
David Kamanda Ngugi ◽  
Manikandan Vinu ◽  
Intikhab Alam ◽  
Allan Anthony Kamau ◽  
...  
Keyword(s):  
Red Sea ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Niche Differentiation ◽  
Content Type ◽  
Nadh:Quinone Oxidoreductase ◽  
Distinct Cluster ◽  
The Family ◽  
Phylogenomic Analyses ◽  
Cultivation Techniques

ABSTRACTThe OM43 clade within the familyMethylophilaceaeofBetaproteobacteriarepresents a group of methylotrophs that play important roles in the metabolism of C1compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields.

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