Plastid Genes Research Articles

Molecular phylogenetic analysis of Tulipa (Liliaceae) from Aksu-Zhabagly Nature Reserve

Barcodes are conserved sequences of genomic, plastid and mitochondrial DNA that can be utilized to uniquely identify an unidentified specimen to its species when conventional identification methods are inapplicable. Among prokaryotic and eukaryotic species, nuclear ribosomal internal transcribed spacer (ITS) sections are one of the most often utilized DNA markers in DNA barcoding and phylogenetic research. In addition to the ribosomal genes, the plastid genes are the most suitable for identifying plant species. The Aksu-Zhabagly Nature Reserve is the oldest nature reserve in Central Asia and is home to 1,312 vascular plant species, 44 of which are categorized as threatened or endangered in Kazakhstan's red data book. In this study, a collection of specimens of uncommon tulip species was compiled, along with their morphological identification and DNA barcoding. The ITS region and parts of the matK and ycf1b genes of tulip plastid DNA were sequenced. The evolutionary link between species of tulips was investigated. Phylogenetic study predicted two Tulipa subclades. Tulipa species have substantially preserved MatK genes. Tulips' ycf1b gene has evolved more slowly than other Liliaceae family members. Nuclear and plastid DNA sequences investigated Tulipa species evolutionary relationships. The findings about the ITS region of nuclear DNA were more definite. Overall, our work shows that genetic data will be important in determining species concepts in this genus, however, even with a molecular perspective pulling apart closely related taxa can be extremely challenging.

Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades

Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale.

Saxifragales is a 15-family order of early-divergent Eudicots with a rich morphological diversity and an ancient rapid radiation. Codon usage bias (CUB) analyses have emerged as an essential tool for understanding the evolutionary dynamics in genes. Thus far, the codon utilization patterns had only been reported in four separate genera within Saxifragales. This study provides a comprehensive assessment of the codon manipulation based on 50 plastid genes, covering 11 constituent families at a larger sampling scale. Our results first showed a high preference for AT bases and AT-ending codons. We then used effective number of codons (ENC) to assess a range of codon bias levels in the plastid genes. We also detected high-informative intrafamilial differences of ENC in three families. Subsequently, parity rule 2 (PR2) plot analyses revealed both family-unique and order-shared bias patterns. Most importantly, the ENC plots and neutrality analyses collectively supported the dominant roles of selection in the CUB of Saxifragales plastid genes. Notably, the phylogenetic affinities inferred by both ML and BI methods were consistent with each other, and they all comprised two primary clades and four subclades. These findings significantly enhance our understanding of the evolutionary processes of the Saxifrage order, and could potentially inspire more CUB analyses at higher taxonomic levels.

The allopolyploid origin(s) and diversification of New Caledonian Grevillea (Proteaceae)

ABSTRACT The assembly of island plant communities is the result of a number of processes: immigration (dispersal), speciation, and extinction. Using four plastid genes and one low-copy nuclear gene, we investigated the origin of the New Caledonian Grevillea (Proteaceae), an otherwise largely Australian genus. In the combined plastid analysis, the species form two distinct clades, the exul (four species) and gillivrayi groups (six species), within group 3 of Grevillea. All New Caledonian Grevillea display two distinct copies of PHYA, one copy in group 3, and another in group 4. Previously published chromosome counts for G. meisneri and two new genome size estimates of G. gillivrayi and G. rubiginosa suggest that these plants are tetraploids. Altogether, the current data available suggest that New Caledonian Grevillea are allotetraploids, resulting from one or two hybridisation events between two or three distinct parents. A possible scenario is that modern Grevillea has descended from a hybrid swarm that formed 9–13 Mya between multiple immigrants (now extinct) that reached the island. Grevillea can be added to the list of island plant radiations with an early history of hybridisation and polyploidy. The relative importance, location and timing of these two mechanisms remain to be elucidated. The two groups of New Caledonian Grevillea may be easily distinguished by their inflorescences, flowers and fruits, with the gillivrayi group displaying greater ecological and morphological diversity. The seed characteristics of New Caledonian Grevillea are consistent with their pioneer behavior.

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events.

Our previous study was the first to confirm that the predominant conformation of mitochondrial genome (mitogenome) sequence of Salvia species contains two circular chromosomes. To further understand the organization, variation, and evolution of Salvia mitogenomes, we characterized the mitogenome of Salvia officinalis. The mitogenome of S. officinalis was sequenced using Illumina short reads and Nanopore long reads and assembled using a hybrid assembly strategy. We found that the predominant conformation of the S. officinalis mitogenome also had two circular chromosomes that were 268,341 bp (MC1) and 39,827 bp (MC2) in length. The S. officinalis mitogenome encoded an angiosperm-typical set of 24 core genes, 9 variable genes, 3 rRNA genes, and 16 tRNA genes. We found many rearrangements of the Salvia mitogenome through inter- and intra-specific comparisons. A phylogenetic analysis of the coding sequences (CDs) of 26 common protein-coding genes (PCGs) of 11 Lamiales species and 2 outgroup taxa strongly indicated that the S. officinalis was a sister taxon to S. miltiorrhiza, consistent with the results obtained using concatenated CDs of common plastid genes. The mapping of RNA-seq data to the CDs of PCGs led to the identification of 451 C-to-U RNA editing sites from 31 PCGs of the S. officinalis mitogenome. Using PCR amplification and Sanger sequencing methods, we successfully validated 113 of the 126 RNA editing sites from 11 PCGs. The results of this study suggest that the predominant conformation of the S. officinalis mitogenome are two circular chromosomes, and the stop gain of rpl5 was found through RNA editing events of the Salvia mitogenome.

Light-dependent signal transduction in the marine diatom Phaeodactylum tricornutum

Unlike most higher plants, unicellular algae can acclimate to changes in irradiance on time scales of hours to a few days. The process involves an enigmatic signaling pathway originating in the plastid that leads to coordinated changes in plastid and nuclear gene expression. To deepen our understanding of this process, we conducted functional studies to examine how the model diatom, Phaeodactylum tricornutum, acclimates to low light and sought to identify the molecules responsible for the phenomenon. We show that two transformants withaltered expressionof twoputativesignal transduction molecules,a light-specific soluble kinase and a plastid transmembrane protein, that appears to be regulated by a long noncoding natural antisense transcript, arising from the opposite strand, are physiologically incapable of photoacclimation. Based on these results, we propose a working model of the retrograde feedback in the signaling and regulation of photoacclimation in a marine diatom.

Limiting etioplast gene expression induces apical hook twisting during skotomorphogenesis of Arabidopsis seedlings.

When covered by a layer of soil, seedling development follows a dark-specific program (skotomorphogenesis). In the dark, seedlings consist of small, non-green cotyledons, a long hypocotyl, and an apical hook to protect meristematic cells. We recently highlighted the role played by mitochondria in the high energy-consuming reprogramming of Arabidopsis skotomorphogenesis. Here, the role played by plastids, another energy-supplying organelle, in skotomorphogenesis is investigated. This study was conducted in dark conditions to exclude light signals so as to better focus on those produced by plastids. It was found that limitation of plastid gene expression (PGE) induced an exaggerated apical hook bending. Inhibition of PGE was obtained at the levels of transcription and translation using the antibiotics rifampicin (RIF) and spectinomycin, respectively, as well as plastid RPOTp RNA polymerase mutants. RIF-treated seedlings also showed expression induction of marker nuclear genes for mitochondrial stress, perturbation of mitochondrial metabolism, increased ROS levels, and an augmented capacity of oxygen consumption by mitochondrial alternative oxidases (AOXs). AOXs act to prevent overreduction of the mitochondrial electron transport chain. Previously, we reported that AOX1A, the main AOX isoform, is a key component in the developmental response to mitochondrial respiration deficiency. In this work, we suggest the involvement of AOX1A in the response to PGE dysfunction and propose the importance of signaling between plastids and mitochondria. Finally, it was found that seedling architecture reprogramming in response to RIF was independent of canonical organelle retrograde pathways and the ethylene signaling pathway.

Plastid DNA sequences and oospore characters of some European taxa of Tolypella section Tolypella (Characeae) identify five clusters, including one new cryptic Tolypella taxon from Sardinia, but they do not coincide with current morphological descriptions.

In Europe, the genus Tolypella (Characeae) comprises four to eight Tolypella taxa in sections Rothia and Tolypella that have been distinguished by vegetative morphology and gametangial characters such as antheridial size and oospore wall ornamentation. However, morphological differentiation is difficult in some cases due to overlapping and variable vegetative features, which in many cases are difficult to observe clearly. To clarify the taxonomic status of the five European taxa of Tolypella in section Tolypella, sequence data of the plastid genes atpB, rbcL and psbC for Tolypella glomerata (Desv.) Leonh., Tolypella hispanica Allen, Tolypella nidifica (O.F. Müll.) A. Braun, Tolypella normaniana (Nordst.) Nordst. and Tolypella salina Cor. were combined with data on oospore morphology, including oospore wall ornamentation. Gene sequence data identified five distinct clusters, but they were not consistent with the morphologically identified five taxa. T. glomerata consisted of some of the samples morphologically identified as T. glomerata and seven samples of T. normaniana, while the remaining T. glomerata samples clustered with specimens of unclear affiliation (Tolypella sp.). We identified two clusters of T. hispanica within the European material: cluster T. hispanica I consisted of samples from various locations, whereas the second cluster (T. hispanica II) consisted of samples of T. hispanica from Sardinia Island. The remaining cluster consisted of all the specimens that had been determined as T. salina or T. nidifica in addition to two specimens of T. normaniana. Oospore morphology was most clearly distinguishable for T. glomerata. Oospore characteristics for all other taxa were not as informative but showed some geographical and/or environmentally influenced differences, especially for T. nidifica and T. salina. Our results suggest the need to further check the different taxonomy of Tolypella sect. Tolypella in which specimens normally identified as T. glomerata might be two different taxa, T. glomerata and an unidentified taxon; T. nidifica and T. salina are not separate taxa; T. normaniana is a diminutive variant of two different Tolypella taxa; and T. hispanica comprises two different taxa, one from the Mediterranean island Sardinia.

A comparative study across the parasitic plants of Cuscuta subgenus Grammica (Convolvulaceae) reveals a possible loss of the plastid genome in its section Subulatae

Most species in Cuscuta subgenus Grammica retain many photosynthesis-related plastid genes, generally under purifying selection. A group of holoparasitic species in section Subulatae may have lost their plastid genomes entirely. The c. 153 species of plants belonging to Cuscuta subgenus Grammica are all obligate stem parasites. However, some have completely lost the ability to conduct photosynthesis while others retain photosynthetic machinery and genes. The plastid genome that primarily encodes key photosynthesis genes functions as a bellwether for how reliant plants are on primary production. This research assembles and analyses 17 plastomes across Cuscuta subgenus Grammica with the aim of characterizing the state of the plastome in each of its sections. By comparing the structure and content of plastid genomes across the subgenus, as well as by quantifying the selection acting upon each gene, we reconstructed the patterns of plastome change within the phylogenetic context for this group. We found that species in 13 of the 15 sections that comprise Grammica retain the bulk of plastid photosynthesis genes and are thus hemiparasitic. The complete loss of photosynthesis can be traced to two clades: the entire section Subulatae and a complex of three species within section Ceratophorae. We were unable to recover any significant plastome sequences from section Subulatae, suggesting that plastomes in these species are either drastically reduced or lost entirely.

Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins.

In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.

A taxonomic revision of Keraunea, including three new species and its phylogenetic realignment with Ehretiaceae (Boraginales).

Keraunea is an enigmatic genus of lianescent shrubs endemic to Brazil and found within the Caatinga and Mata Atlântica phytogeographic regions. When first published, Keraunea was included in the Convolvulaceae and there has been considerable recent disagreement about its true family placement on the Angiosperm tree of life. Based on further assessment of morphology and a new comprehensively-sampled combined phylogenetic analysis of nuclear and plastid genes from recently published DNA sequence data, we settle the position of the genus within the Ehretiaceae as sister to the Australian genus Halgania Gaudich. and provide an expanded family description. We recognize five species within Keraunea, three of them newly described here: K.brasiliensis Cheek & Simão-Bianchini, K.bullata Moonlight & D.B.O.S.Cardoso, sp. nov., K.capixaba Lombardi, K.confusa Moonlight & D.B.O.S.Cardoso, sp. nov. and K.velutina Moonlight & D.B.O.S.Cardoso, sp. nov. We also provide a full taxonomic revision of the genus, including a key, descriptions, map of geographical distribution and provisional IUCN threat assessments for all species.

Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae

Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.

Understanding parasitism in Loranthaceae: Insights from plastome and mitogenome of Helicanthes elastica

Loranthaceae is the largest family of the order Santalales and includes root and stem hemiparasites. The parasites are known to exhibit reductions in the genomic features as well as relaxed or intensified selection shifts. In this study, we report plastome and mitogenome sequence of Helicanthes elastica (subtribe Amyeminae, tribe Lorantheae), an endemic, monotypic genus of Western Ghats, India growing on remarkably diverse host range. The length of plastome sequence was 1,28,805 bp while that of mitogenome was 1,65,273 bp. This is the smallest mitogenome from Loranthaceae reported till date. The plastome of Helicanthes exhibited loss of ndh genes (ψndhB), ψinfA, rps15, rps16, rpl32, trnK-UUU, trnG-UCC, trnV-UAC and trnA-UGC while mitogenome exhibited pseudogenized cox2, nad1 and nad4 genes. The comparative study of Loranthaceae plastomes revealed that the pseudogenization or loss of genes was not specific to any genus or tribe and variation was noted in the number of introns of clpP gene in the family. Several photosynthetic genes have undergone relaxed selection supporting lower photosynthetic rates in parasitic plants while some respiratory genes exhibited intensified selection supporting the idea of host-parasite arm race in Loranthaceae. The plastome gene content was found conserved in root hemiparasites compared to stem hemiparasites. The atp1 gene of mitogenome was chimeric and part of it exhibited similarities with Lamiales members. The phylogenetic analysis based on plastid genes placed Helicanthes sister to the members of subtribe Dendrophthoinae.

An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data.

A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s. l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene while dispersal into South America likely occurred during the Neogene. Diversification within the Northern Hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following the PhyloCode. Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names. This article is protected by copyright. All rights reserved.

О роде Oncophorus (Rhabdoweisiaceae, Bryophyta) в России

Revision of the genus Oncophorus s. str. in Russia based on throughout study of extensive materials kept in LE, MAG, MHA, MW, IRK, KRABG, NSK, PTZ and UUH was carried out. The genus is represented in Russia by two species, O. integerrimus and O. virens. New subspecies, O. virens subsp. minor has been revealed and described based on integrative morphological and molecular (plastid rps4 gene with trnS-rps4 spacer, plastid, trnL-trnF region and nuclear ITS1-2 region) studies. It differs from O. virens subsp. virens in very dense (vs. loose) tufts, smaller plant size (1–3 cm vs. (2)5–8 cm), smaller leaves [(1.3)1.7–2.1 × (0.4)0.6–0.7 mm vs. 2.4–4.0 × 0.6–1.0 mm)] and smaller mid-leaf cells [(4.3)5.0–9.5(15.0) × (7.6)8.9–11.4(13.0) µm vs. 8–17(20) × 6–10 µm]. Descriptions of O. integerrimus and both subspecies of O. virens together with their photomicrographs, graphic illustrations and a key for their differentiation are provided. Their distribution in Russia is discussed and mapped.

Control of plastid inheritance by environmental and genetic factors

The genomes of cytoplasmic organelles (mitochondria and plastids) are maternally inherited in most eukaryotes, thus excluding organellar genomes from the benefits of sexual reproduction and recombination. The mechanisms underlying maternal inheritance are largely unknown. Here we demonstrate that two independently acting mechanisms ensure maternal inheritance of the plastid (chloroplast) genome. Conducting large-scale genetic screens for paternal plastid transmission, we discovered that mild chilling stress during male gametogenesis leads to increased entry of paternal plastids into sperm cells and strongly increased paternal plastid transmission. We further show that the inheritance of paternal plastid genomes is controlled by the activity of a genome-degrading exonuclease during pollen maturation. Our data reveal that (1) maternal inheritance breaks down under specific environmental conditions, (2) an organelle exclusion mechanism and a genome degradation mechanism act in concert to prevent paternal transmission of plastid genes and (3) plastid inheritance is determined by complex gene–environment interactions.

Loss of plastid ndh genes in an autotrophic desert plant

Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.

<i>Trans</i>-Factor PTF1 Participates in the Response to Salinity but Does Not Regulate Expression of the <i>psbD</i> Gene in <i>Arabidopsis thaliana</i>

The existing data on the role of PTF1/TCP13 belonging to the TCP family of transcription factors in regulating expression of a psbD plastid gene encoding a D2 protein of PSII are controversial. To analyze biological functions of PTF1/TCP13, transformed plants expressing PTF1/TCP13 under a -estradiolinducible promoter were used. PTF1/TCP13 overexpression did not provide the expected increase in the accumulation of psbD transcripts transcribed from BLRP (Blue Light Responsive Promoter), though their level significantly increased under exposure to light or abscisic acid (ABA). PTF1/TCP13 was up-regulated by ABA; moreover, genes of the canonic pathway of the ABA signal transduction were involved in the regulation of PTF1/TCP13 expression. In addition, PTF1/TCP13 was induced in response to salt stress However, in the overexpressing line, salt tolerance and expression of salt stress markers, as well as a number of genes for the synthesis and signaling of ABA, were reduced compared to plants with the normal level of expression of this transcription factor, that is, PTF1/TCP13 acted as a negative regulator of salt stress Thus, PTF1 does not belong to plastid transcription factors. Nevertheless, it represents one of the components of the ABA-dependent regulatory chain capable of modifying expression of nuclear and chloroplast genes in response to changes in homeostasis.

Taxonomic novelties in the Asteraceae–Inuleae with the description of a new genus, Galgera separate from Laggera

Phylogenetic analyses of DNA sequences from the plastid gene ndhF from a large number of species of the Asteraceae tribe Inuleae reveal the need for some taxonomic and nomenclatural changes. The genera Laggera, Pentanema and Pluchea as presently understood are all polyphyletic. It is concluded that the old name Vicoa should be used for three species of Pentanema, and a new species of the genus is described. Two species of Cyathocline (previously recognized as a genus in the tribe Astereae) are confirmed to be close to Blumea of the Inuleae–Inulinae and are included here in the latter genus, requiring a new combination. The new genus Galgera, sister to Antiphiona, is described for a former Laggera species. Citation: Anderberg A. A. & Bengtson A. 2022: Taxonomic novelties in the Asteraceae–Inuleae with the description of a new genus, Galgera separate from Laggera. – Willdenowia 52: 373–386. Version of record first published online on 27 December 2022 ahead of inclusion in December 2022 issue.

Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat (Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers.

Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into "rounded" and "nearly elongated". Estimates of heritability (H2) for these morphological characters ranged from 4.93 to 100%. The highest H2 values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H2 value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.