scholarly journals Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10964
Author(s):  
Danmei Su ◽  
Fumin Xie ◽  
Haiying Liu ◽  
Dengfeng Xie ◽  
Juan Li ◽  
...  
Keyword(s):  
Related Species ◽  
Gene Tree ◽  
Population Level ◽  
Hybrid Breeding ◽  
Tibet Plateau ◽  
Variable Regions ◽  
Morphological Studies ◽  
Plastid Genomes ◽  
Close Phylogenetic Relationship ◽  
Nuclear Its

Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei, L. stewartianum, L. matangense, L. lophophorum, and L. nanum. However, molecular markers still lack sufficient signals for population-level research of the genus Lilium. We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions (trnC-petN and rpl32-trnL) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium.

scholarly journals High Genetic Differentiation among European White Oak Species (Quercus spp.) at a Dehydrin Gene

2015 ◽  
Vol 43 (2) ◽  
pp. 582-588 ◽  
Author(s):  
Iacob CRĂCIUNESC ◽  
Barbara VORNAM ◽  
Ludger LEINEMANN ◽  
Reiner FINKELDEY ◽  
Neculae ȘOFLETEA ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Related Species ◽  
Population Level ◽  
Quercus Petraea ◽  
White Oak ◽  
Closely Related Species ◽  
Significant Differentiation ◽  
Dehydrin Gene ◽  
First Time ◽  
Two Populations

Dehydryn genes are involved in plant response to environmental stress and may be useful to examine functional diversity in relation to adaptive variation. Recently, a dehydrin gene (DHN3) was isolated in Quercus petraea and showed little differentiation between populations of the same species in an altitudinal transect. In the present study, inter- and intraspecific differentiation patterns in closely related and interfertile oaks were investigated for the first time at the DHN3 locus. A four-oak-species stand (Quercus frainetto Ten., Q. petraea (Matt.) Liebl., Q. pubescens Willd., Q. robur L.) and two populations for each of five white oak species (Q. frainetto Ten., Q. petraea (Matt.) Liebl., Q. pubescens Willd., Q. robur L. and Q. pedunculiflora K. Koch) were analyzed. Three alleles shared by all five oak species were observed. However, only two alleles were present in each population, but with different frequencies according to the species. At population level, all interspecific pairs of populations showed significant differentiation, except for pure Q. robur and Q. pedunculiflora populations. In contrast, no significant differentiation (p > 0.05) was found among conspecific populations. The DHN3 locus proved to be very useful to differentiate Q. frainetto and Q. pubescens from Q. pedunculiflora (FST = 0.914 and 0.660, respectively) and Q. robur (FST = 0.858 and 0.633, respectively). As expected, the lowest level of differentiation was detected between the most closely related species, Q. robur and Q. pedunculiflora (FST = 0.020). Our results suggest that DHN3 can be an important genetic marker for differentiating among European white oak species.

scholarly journals Rhamnella intermedia (Rhamnaceae), a new evergreen species from southwest Guangxi

PhytoKeys ◽  
2020 ◽  
Vol 159 ◽  
pp. 115-126
Author(s):  
Zhiqiang Lu ◽  
Yongshuai Sun
Keyword(s):  
New Species ◽  
Related Species ◽  
Principal Component ◽  
Phenotypic Traits ◽  
Evergreen Species ◽  
Closely Related Species ◽  
Field Investigations ◽  
Sequence Variations ◽  
Dried Fruit ◽  
Nuclear Its

Rhamnella intermedia, a new evergreen species from southwest Guangxi, is described and illustrated in this study. This species is similar to R. brachycarpa by the size and ratio of length to width of dried fruit and seeds, by which it differs from R. rubrinervis and R. tonkinensis. However, it differs from R. brachycarpa by rarely mucronate seed apices, larger ratio of length to width of leaves, leaf apices acuminate to long acuminate, shorter leaf petioles, and longer fruiting pedicels. Principal component analysis based on phenotypic traits further recognised three separated groups. Rhamnella rubrinervis and R. tonkinensis were clustered into one group; the other two groups represented R. brachycarpa and two Guangxi populations, respectively. Furthermore, phylogenetic analysis of nuclear ITS sequence variations highly supported that the two Guangxi populations represented an independent evolutionary lineage and were closest to R. rubrinervis. Four fixed nucleotide sites were found and were different from R. rubrinervis. However, besides the differentiated traits in seeds and fruit, densely pilose young branches also separated them from R. rubrinervis. In addition, during our field investigations, none of the three closely related species were found at locations where this new species was distributed. Therefore, this new species, based on the two Guangxi populations, is named R. intermedia. The key to four closely related species is also presented.

scholarly journals DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Tai Wang ◽  
Yan-ping Zhang ◽  
Zhuo-yu Yang ◽  
Zhe Liu ◽  
Yan-yan Du
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Related Species ◽  
Native Species ◽  
Molecular Methods ◽  
Tibet Plateau ◽  
Closely Related Species ◽  
Northeastern Part ◽  
Qinghai Tibet Plateau

Abstract Background The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions. Conclusions The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.

Molecules match morphology: mitochondrial DNA supports Bayer's Lytreia - Bebryce - Heterogorgia (Alcyonacea : Octocorallia) clade hypothesis

2010 ◽  
Vol 24 (1) ◽  
pp. 23 ◽  
Author(s):  
Sergio Vargas ◽  
Michael Eitel ◽  
Odalisca Breedy ◽  
Bernd Schierwater
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationship ◽  
Morphological Variation ◽  
Mitochondrial Marker ◽  
Morphological Studies ◽  
Close Phylogenetic Relationship ◽  
Morphological Assessment ◽  
Molecular Characters

Several studies attempting to clarify the taxonomy and systematics of Octocorallia have highlighted the important role of molecular characters in corroborating or rejecting previous hypotheses based on morphological variation. One such hypothesis is that of a close phylogenetic relationship between the genera Lytreia, Bebryce and Heterogorgia proposed by Bayer based on morphological studies of the genera. Herein, we tested Bayer’s hypothesis using the mitochondrial marker mshI. We deduced a molecular phylogeny including members of the families Gorgoniidae and ‘Paramuriceidae’ that corroborated the existence of Bayer’s Lytreia–Bebryce–Heterogorgia clade. In addition, we provide a morphological assessment of the three genera as well as diagnoses for each of them. We also discuss, based on the phylogenetic results obtained, the evolution of sclerite morphology within Bayer’s Lytreia–Bebyce–Heterogorgia clade. Finally, we propose a Tethyan origin for the Lytreia–Bebryce–Heterogorgia clade.

scholarly journals DNA Barcoding Reveals Cryptic Diversity in the Genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the Northeastern Qinghai-Tibet Plateau

2020 ◽  
Author(s):  
tai wang ◽  
Yanping Zhang ◽  
Zhuoyu Yang ◽  
Zhe Liu ◽  
Yanyan Du
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Related Species ◽  
Native Species ◽  
Molecular Methods ◽  
Tibet Plateau ◽  
Ecological Value ◽  
Closely Related Species ◽  
Qinghai Tibet Plateau

Abstract Background: The northeastern part of the Qinghai-Tibet Plateau (QTP) is one of the areas where the number of species of plateau loach is the largest. As one of the three major groups of fishes distributed on the QTP, plateau loach have very important ecological value. However, their taxonomy and systematics are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and there are many cryptic species. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the taxonomic characteristics of the plateau loach by means of morphology, DNA barcoding and multiple species demarcation methods to accurately describe species and allocate taxonomic units to unknown specimens. Results: After careful identification and comparison of the morphology and DNA barcoding of 1,630 specimens, 22 species were identified, 20 of which were considered valid local species and two of which were new species that had not been described. Based on the combination of morphological and molecular methods, a total of 24 native species have been found, two of which are cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes, which allow them to be reliably identified. The remaining cases involved 10 closely related species, some of which were rapidly differentiated, had a disputed taxonomic status, or showed introgressions.Conclusions: The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially in closely related species such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.

scholarly journals Stachys babylonica (Lamiaceae), a new species from Iraq

2019 ◽  
Vol 29 (4) ◽  
pp. 14
Author(s):  
Modhafer A. Hamodie
Keyword(s):  
New Species ◽  
Related Species ◽  
Morphological Characters ◽  
Pollen Grain ◽  
Closely Related Species ◽  
Morphological Studies ◽  
A New Species

Stachys babylonica (Lamiaceae). A new species from the mountainous, Kurdistan Iraq, is described and illustrated. Its distinguishing characters are discussed. It is distinguished from the closely related species S. kotschyi by having elliptic-rhombic (vs. ovate or oval- elliptic) leaves, (30-35 x 10-16 mm) (vs. 25-47 x 14-21mm), lower leaves petioles longer ± 16mm (vs. C.7mm), the median leaves petiole ± 7mm (vs. subsessile – sessile), calyx is narrowly tubular appressed (vs. infundibular – campanulate ± spreading), bracteoles are well developed as long as or longer than calyx (vs. shorter than calyx or absent), teeth of calyx are narrowly lanceolate (vs. broadly lanceolate and spreading). This new species to science is represented only by two specimens: the holotype & the isotype #12125.Specimen #12125 has been mistakenly identified as S. tomentosa Rech.f. by Rechinger [1]. Rechinger used only morphological characters in his identification. To clear the ambiguity, Pollen grain study was done and the results of this study were tabulated in Hamodie's work [2] .Specimen #50059 mentioned by Al –Zubaedy [3] as collected by Ali Halob in 2010 from Piera Magron Mt. was also mistakenly identified as S.babylonica. The consideration of specimens belong to S. kotschyi Boiss. as S. babylonica Hamodie & Wilcock made errors on conclusions by Al-Zubaedy [3] on molecular & P.G and morphological studies and reconsideration on these issues are needed. All the indicators so far gathered, approve that plants of this new species were most likely vanished from Piera Magron Mt. in Sulaimaniya sometime after 1948.

scholarly journals Response of Lamiophlomis rotata (Benth.) Kudo to degradation of alpine grasslands in the western Sichuan plateau, China

2020 ◽  
Author(s):  
Tong Niu ◽  
Hui Sun ◽  
Rui Gu ◽  
Shihong Zhong ◽  
Lin Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Alpine Grassland ◽  
Tibetan Medicine ◽  
Tibet Plateau ◽  
Adaptation Mechanism ◽  
Submicroscopic Structure ◽  
Western Sichuan ◽  
Morphological Studies ◽  
Degraded Grassland ◽  
Artificial Cultivation

Abstract Background: Lamiophlomis rotata (Benth.)Kudo, also known as Duyiwei in China, is considered to be one of the most common Tibetan medicine. It is famous for the significant effects on improving blood circulation and relieving pain. Due to the environmental deterioration and excessive consumption, the wild resources of L.rotata is decreasing year by year. However, its artificial cultivation has not been realized. This study aimed to initially explore the adaptation mechanism of L.rotata to degraded alpine grassland, and provide reference for its wild tending and artificial cultivation.Methods: In this study, we used a sample method to conduct a population ecological survey of plants and collect plant leaf samples from mildly, moderately, and extremely degraded grassland. The content of SOD, POD, CAT, PRO, MDA, SS, SP, carotene, chlorophyll A and chlorophyll B in different sample leaves was measured by colorimetry. Microscopic characteristics of the cross-section, epidermis and submicroscopic structure of the leaves were observed and compared.Results: The density of L. rotata in moderately degraded grassland was the highest，where L. rotata had the strongest resistance. And the analysis of seven physiological indicators combined with stress resistance showed that the average content of MDA, SOD, POD, CAT and SS is the highest in L. rotata of the moderately degraded grassland. The microscopic observation showed that, by increasing the thickness of the epidermis, the density of the glandular scales, the proportion of palisade tissue and the number of gland scales, L. rotata was able to adapt to the degraded grassland. Meanwhile, morphological studies have shown that L. rotata could enhance root growth in the degraded grassland. Furthermore, in response to the degradation of alpine grassland on the Qinghai-Tibet Plateau, L. rotata population and biomass distribution in the underground parts have increased. However, L. rotata does not have a competitive advantage in mildly degraded grassland. Compare with the mildly and moderately habitat, the population of L. rotata is small in the extremely degraded habitat.Conclusion: The results showed that among the 3 levels of degraded grassland, L. rotata in the moderately degraded grassland shows the strongest resistance. This study can provide a reference for breeding and ecological planting of L. rotata, suggests that in the nursery stage, the medium degraded grassland should be chosen for ecological breeding to enhance the survival rate of seedlings. While after large-scale planting, reasonable community interventions, like the P. fruticosa+F. rubra community, should be built to simulate the yield of medicinal materials.

scholarly journals Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Jeffrey P. Rose ◽  
Ricardo Kriebel ◽  
Larissa Kahan ◽  
Alexa DiNicola ◽  
Jesús G. González-Gallegos ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Divergence Time ◽  
Time Estimation ◽  
Single Copy ◽  
Lineage Sorting ◽  
Divergence Time Estimation ◽  
Sequencing Technologies ◽  
Plastid Genomes ◽  
Gene Tree Discordance

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

scholarly journals Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes

2018 ◽  
Vol 123 (5) ◽  
pp. 857-865 ◽  
Author(s):  
Jacqueline Heckenhauer ◽  
Ovidiu Paun ◽  
Mark W Chase ◽  
Peter S Ashton ◽  
A S Kamariah ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Gc Content ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Plastid Genomes ◽  
Snp Data ◽  
Phylogenomic Analyses

Abstract Background and Aims Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. Methods A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Key Results Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Conclusions Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

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