Intrageneric Classification Research Articles

Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae.

Sargassum hemiphyllum var. chinense, a prevalent seaweed along the Chinese coast, has economic and ecological significance. However, systematic positions within Sargassum and among the three orders of Phaeophyceae, Fucales, Ectocarpales, and Laminariales are in debate. Here, we reported the organellar genomes of S. hemiphyllum var. chinense (34,686-bp mitogenome with 65 genes and 124,323 bp plastome with 173 genes) and the investigation of comparative genomics and systematics of 37 mitogenomes and 22 plastomes of Fucales (including S. hemiphyllum var. chinense), Ectocarpales, and Laminariales in Phaeophyceae. Whole genome collinearity analysis showed gene number, type, and arrangement were consistent in organellar genomes of Sargassum with 360 SNP loci identified as S. hemiphyllum var. chinense and two genes (rps7 and cox2) identified as intrageneric classifications of Sargassum. Comparative genomics of the three orders of Phaeophyceae exhibited the same content and different types (petL was only found in plastomes of the order Fucales and Ectocarpales) and arrangements (most plastomes were rearranged, but trnA and trnD in the mitogenome represented different orders) in genes. We quantified the frequency of RNA-editing (canonical C-to-U) in both organellar genomes; the proportion of edited sites corresponded to 0.02% of the plastome and 0.23% of the mitogenome (in reference to the total genome) of S. hemiphyllum var. chinense. The repetition ratio of Fucales was relatively low, with scattered and tandem repeats (nine tandem repeats of 14-24 bp) dominating, while most protein-coding genes underwent negative selection (Ka/Ks < 1). Collectively, these findings provide valuable insights to guide future species identification and evolutionary status of three important Phaeophyceae order species.

Comparative genomics on chloroplasts of Rubus (Rosaceae)

Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.

Three Newly Described Species of Ziziphus from Maharashtra, India Based on Morphological and Molecular Evidence

Abstract— Three new species of Ziziphus (Rhamnaceae) from Maharashtra, India, Z. bhandarii, Z. naikii, and Z. bhansalii are described here. These species occur in isolated fragments of the Deccan thorn scrub forest ecoregion on the Deccan plateau. Their placement in Ziziphus is confirmed by molecular analyses combining nrITS and trnL-F spacer regions. Given this phylogeny is the most robust to date of Ziziphus, a previously proposed intrageneric classification was tested, and the classification was not supported suggesting a need for additional investigations in this genus. The new species are most closely related to three Indian species, Z. horrida, Z. xylopyrus, and Z. caracutta, respectively, which are morphologically similar and sympatric, and are distinguishable from known species based on several vegetative and reproductive characteristics presented here. A diagnostic key to the Ziziphus species known to occur in Maharashtra is provided.

Phylogenetic relationships of the North American catfishes (Ictaluridae, Siluriformes): Investigating the origins and parallel evolution of the troglobitic species

Insular habitats have played an important role in developing evolutionary theory, including natural selection and island biogeography. Caves are insular habitats that place extreme selective pressures on organisms due to the absence of light and food scarcity. Therefore, cave organisms present an excellent opportunity for studying colonization and speciation in response to the unique abiotic conditions that require extreme adaptations. One vertebrate family, the North American catfishes (Ictaluridae), includes four troglobitic species that inhabit the karst region bordering the western Gulf of Mexico. The phylogenetic relationships of these species have been contentious, and conflicting hypotheses have been proposed to explain their origins. The purpose of our study was to construct a time-calibrated phylogeny of Ictaluridae using first-occurrence fossil data and the largest molecular dataset on the group to date. We test the hypothesis that troglobitic ictalurids have evolved in parallel, thus resulting from repeated cave colonization events. We found that Prietella lundbergi is sister to surface-dwelling Ictalurus and that Prietella phreatophila + Trogloglanis pattersoni are sister to surface-dwelling Ameiurus, suggesting that ictalurids colonized subterranean habitats at least twice in evolutionary history. The sister relationship between Prietella phreatophila and Trogloglanis pattersoni may indicate that these two species diverged from a common ancestor following a subterranean dispersal event between Texas and Coahuila aquifers. We recovered Prietella as a polyphyletic genus and recommend P. lundbergi be removed from this genus. With respect to Ameiurus, we found evidence for a potentially undescribed species sister to A. platycephalus, which warrants further investigation of Atlantic and Gulf slope Ameiurus species. In Ictalurus, we identified shallow divergence between I. dugesii and I. ochoterenai, I. australis and I. mexicanus, and I. furcatus and I. meridionalis, indicating a need to reexamine the validity of each species. Lastly, we propose minor revisions to the intrageneric classification of Noturus including the restriction of subgenus Schilbeodes to N. gyrinus (type species), N. lachneri, N. leptacanthus, and N. nocturnus.

The taxonomic status of the kukri snake Oligodon arenarius Vassilieva, 2015 with a redescription of Oligodon macrurus (Angel, 1927) (Squamata, Serpentes, Colubridae)

We investigated the taxonomic status of the recently described kukri snakeOligodon arenariusVassilieva, 2015 and the morphologically similarOligodon macrurus(Angel, 1927), two species endemic to the southern coast of Vietnam. Based on phylogenetic analyses using three mitochondrial genes (12S–16S rRNA, cytochromeb), we recoveredO. arenariusandO. macrurusin a clade within theO. cyclurus-taeniatusspecies group, agreeing with previous intrageneric classifications. Genetic distances betweenO. arenariusandO. macrurusare extremely low (less than 0.5% based on 12S–16S) and renderO. arenariusparaphyletic. All preserved specimens ofO. arenariusandO. macrurusconvey little to no differences in color pattern, hemipenial morphology and osteological features; the latter of which is based on three dimensional micro computer tomography (µCT) scans of one specimen per species. Contrasting these results, univariate and multivariate analyses revealed significant differences in relative tail length, and the number of ventral and subcaudal scales between both species. Although the molecular and morphological datasets present conflicting results, integrating the evidence leads us to synonymizeO. arenariuswithO. macrurus. We provide a formal redescription ofO. macrurus, designate a neotype specimen to avoid future taxonomic confusion, and provide the first detailed osteological description of this species.Oligodon macrurussensu stricto is endemic to coastal dunefields and adjacent forest habitats in southern Vietnam, where ongoing human development, tourism and road mortality pose significant threats to its conservation. Consequently, we suggest thatO. macrurusshould be listed as “Vulnerable” based on the assessment criteria of the International Union for Conservation of Nature (IUCN).

The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species.

Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.

Species Identification and Phylogenetic Reconstruction in Acer Linn. by Restriction Site-Associated DNA Sequencing

Acer Linn. is a genus with high variation in species morphology in Sapindaceae, its phylogeny and intrageneric classification remain undefined. Here, 93 samples including 1 Dipteronia species and 52 Acer species were used for restriction site-associated DNA sequencing (RAD-seq). The basic characteristics were evaluated, and the high-quality single nucleotide polymorphism (SNP) data were used for genotyping, clustering and phylogenetic tree construction. The results showed that 12 sections of Acer was monophyletic except section Lithocarpa; it was supported to classify A. wardii into section Macrantha and become one series; it was supported to combine section Pentaphylla and section Trifoliata. It was not supported to revise A. yangjuechi and A. olivaceum into A. miaotaiense and A. elegantulum, respectively. The systematic relationships of some taxa of Acer was clarified based on population genetic structure analysis, PCA clustering and phylogenetic tree analysis, and the origin, evolution and distribution of some taxa of Acer were also discussed in combination with data such as morphological characteristics, fossil evidence, and distribution information of Acer. The results confirmed that SNP data generated by RAD-seq can be used for species identification and phylogenetic analysis of Acer. It also indicated that it is feasible in complex group classification and phylogenetic studies.

Systematics of Afrotropical Eristalinae (Diptera: Syrphidae) using mitochondrial phylogenomics

AbstractWe examined the phylogeny and intrageneric classification of eristaline hoverfly genera from the Afrotropical Region using mitochondrial genomes. Genome skimming was used to obtain (nearly) full mtDNA and nuclear rDNA (18S, 28S) genomes of 120 museum vouchers from eight genera and 98 species. Phylogenetic reconstructions of mitogenomes and mitogenomes + nuclear rDNA yielded comparable phylogenies while that of rDNA only resulted in poorly resolved phylogenies. Phylogenetic analyses focused on six genera and supported the monophyly of the genera Chasmomma Bezzi, Eristalinus Rondani, Mesembrius Rondani and Syritta Le Peletier &amp; Serville, whereas Simoides Loew was not monophyletic and rendered Phytomia Guérin‐Méneville paraphyletic. We therefore synonymize Simoides with Phytomia. Within Chasmomma, two species‐groups that differ in the colour and the shape of the hind femora (Chasmomma femoratum and Chasmomma nigrum species‐groups) were supported. Within Eristalinus, the monophyly of the subgenera Merodonoides Curran and Eristalodes Mik was supported, but not of the subgenus Eristalinus Rondani. Within Syritta, the monophyly of three out of the five species‐groups tested was rejected. This approach illustrates the importance of integrative and iterative approaches in taxonomy and shows that genomic data may not only clarify the systematic relationships among hoverfly genera and species, but also offer perspectives into the evolution of morphological and ecological variation within the family.

СИСТЕМАТИЧЕСКИЙ АНАЛИЗ ВИДОВ РОДА QUERCUS L. В ДЕНДРОЛОГИЧЕСКОМ ГЕРБАРИИ ВУЗА

The results of the analysis of Quercus L. species stored in the herbarium of the Department of Botany and Plant Physiology of Federal State Budget Educational Institution of Higher Education VSUFT (Voronezh) are presented. This herbarium of historical plant collections of the genus Quercus L. is critical for tracking changes in the genus, including the introduction and distribution of species. We examined the belonging of the species to systematic units – subgenus, section, subsection, row, using the traditional classification and the updated intrageneric classification of oaks. Information about the life form, plant height, date and place of collection of the specimen was recorded. We entered information into the database, which will further simplify the work on registration, revision of the herbarium fund and when replenishing herbarium specimens. Conclusions were drawn based on the results of the workabout changes in the taxonomic nature and phylogenetic relationships of species in Quercus L. genus

Comparative Osteology, Phylogeny and Classification of the Eastern South American Catfish Genus Trichomycterus (Siluriformes: Trichomycteridae)

Trichomycterus has been considered for a long time to be the most problematic genus of the diverse neotropical subfamily Trichomycterinae. Recently, Trichomycterus was restricted to a clade from eastern South America supported by molecular data, but no unique morphological character state was found to distinguish it, making it difficult to allocate new species based on morphology alone. The objectives of this study were to conduct an osteological comparative analysis comprising a large sample of valid species of Trichomycterus, to conduct a total evidence phylogenetic analysis, combining osteological characters and a multigene database, and to propose an intrageneric classification based on the results of the phylogenetic analysis. Fifty-two osteological characters were combined with a multigene molecular data set of 2974 bp for 44 species of Trichomycterus, and 21 outgroups generated a well-supported phylogenetic tree, making it possible to delimit and diagnose intrageneric lineages, of which six subgenera are recognized. The high morphological diversity of osteological structures herein first reported for Trichomycterus from eastern South America is possibly related to some ecological specializations. This study shows that osteological characters combined with molecular data may be useful to consistently delimit and distinguish between trichomycterines, shedding light on the still persistent problems in trichomycterine systematics.

Comparative chloroplast genome analysis of medicinally important Veratrum (Melanthiaceae) in China: Insights into genomic characterization and phylogenetic relationships

Members of Veratrum are perennial herbs widely used in traditional Chinese medicine to induce vomiting, resolve blood stasis and relieve pain. However, the intrageneric classification and phylogenetic relationships within Veratrum have long been controversial due to the complexity of morphological variations and lack of high-resolution molecular markers. In this study, we reevaluated the infrageneric relationships with the genus Veratrum using complete chloroplast genome sequence data. Herein, the complete cp genomes of ten species of Veratrum were newly sequenced and characterized. The complete cp genomes of ten species of Veratrum had the typical quadripartite structure, ranging from 151,597 bp to 153,711 bp in size and comprising a total of 135 genes. The structure of Veratrum cp genomes (i.e., gene order, content, and genome components) was highly similar across species. The number of simple sequence repeats (SSRs) ranged from 63 to 78, and of long repeats ranged from 31 to 35. Eight highly divergent regions (ndhF, psbC-psbZ, psbK-psbI, rpoB-trnC_GCA, trnK_UUU-trnQ_UUG, trnS_GCU-trnG_UCC, trnT_UGU-trnL_UAA and ycf1) were identified and are potentially useful for the DNA barcoding of Veratrum. Phylogenetic analysis among 29 taxa based on cp genomes, total genes, protein-coding genes and intergenic regions strongly supported the monophyly of Veratrum. The circumscription and relationships of the infrageneric taxa of Veratrum were well-presented with great resolution. These results will facilitate the identification, taxonomy, and utilization of Veratrum plants as well as the evolutionary studies of Melanthiaceae.

Evaluation of seed morphology characteristics of Alnus taxa in Iran

Alnus Mill. is a problematic genus of Betulaceae, and there are several intrageneric classifications for the genus. Alnus species are widely distributed in the Hyrcanian forest of Iran, and different species with some intraspecific taxonomic ranks including subspecies and varieties have been reported from this country. We evaluate seed micromorphology characteristics of ten taxa using scanning electron microscopy and light microscopy in the current study. The data were analyzed using SPSS and MVSP software. Results revealed that qualitative characteristics such as seed shape, surface sculpturing pattern, presence of indumentum, and its type vary among the studied taxa and have diagnostic value. However, seed color was nearly stable among the taxa. Besides, quantitative variables highly differed among the taxa. In the UPGMA tree, Alnus taxa were clustered into three groups, and these groups were supported by PCA and PCO plots. According to the PCA bi-plot, some taxa were characterized by the particular characteristic(s) that was useful for their identification. In some cases taxa clustering was similar to those of previous phylogenetic and morphological studies. Our findings revealed that seed morphology characteristics are a valuable taxonomical tool in identifying most Alnus taxa, except for A. glutinosa subspecies, which have similar seed morphology features in common.

Reevaluation of species richness in Winnertzia (Diptera, Cecidomyiidae, Winnertziinae), with descriptions of 37 new species from Sweden, Peru and Australia

Tentative studies of Malaise trap samples from different geographic regions and habitats indicate unanimously that Winnertzia, a genus of mycophagous gall midges (Cecidomyiidae), is exceptionally speciose, but hard data in proof of that were previously unavailable. A taxonomic inventory of mycophagous cecidomyiids in Sweden has now revealed that, of 751 species found in total, 93 are Winnertzia. A preliminary census in 2013 had identified only 26 different Winnertzia in Sweden. Two factors are responsible for this increment: the inclusion of large amounts of fresh material to study and the application of a narrower species concept. The latter results from the reevaluation of male morphological characters in the light of COI sequence (DNA barcoding) data. With the inclusion of 37 new Winnertzia described here, the genus now contains 136 extant species. New Winnertzia discovered in Sweden are described here under the following names: W. acutistylus sp. nov., W. angustistylus sp. nov., W. arctostylus sp. nov., W. bicolor sp. nov., W. brachytarsus sp. nov., W. dentata sp. nov., W. egregia sp. nov., W. ekdalensis sp. nov., W. fraxinophila sp. nov., W. grytsjoenensis sp. nov., W. hamatula sp. nov., W. hemisphaerica sp. nov., W. imbecilla sp. nov., W. incisa sp. nov., W. inornata sp. nov., W. lapponica sp. nov., W. lobata sp. nov., W. longicoxa sp. nov., W. normalis sp. nov., W. oelandica sp. nov., W. ombergensis sp. nov., W. parvidens sp. nov., W. pilosistylus sp. nov., W. pratensis sp. nov., W. pustulatula sp. nov., W. quercinophila sp. nov., W. rickebasta sp. nov., W. ruliki sp. nov., W. serri sp. nov., W. setosa sp. nov., W. silvestris sp. nov., W. smalandensis sp. nov., W. sundini sp. nov., W. tumidoides sp. nov., and W. upplandensis sp. nov. Additionally, W. panguana sp. nov. is the first Winnertzia described from the Neotropical region (Peru), and W. warraensis sp. nov. is the first member of the genus described from the Australasian region (Tasmania). Parwinnertzia Felt, 1920 syn. nov. is revealed to be a junior synonym of Winnertzia Rondani, 1860, implying the recombinations of Winnertzia notmani (Felt) comb. nov. and Winnertzia italiana (Mamaev Zaitzev) comb. nov. The intrageneric classification of Winnertzia is reviewed and developed further, with the W. setosa group introduced for species whose gonostylar claw is conspicuously long and exposed, and whose gonocoxal emargination is bordered by dense, large setae. Winnertzia feralis Mamaev, revived here from synonymy with W. tridens Panelius, and W. fusca Kieffer are new faunistic records in Sweden. Swedish records published in the past of W. brachypalpa Mamaev and W. pravdini Mamaeva Mamaev rest on misidentifications, and both species are deleted from the Swedish checklist.

&lt;p&gt;&lt;strong&gt;A new variety of &lt;em&gt;Erythroxylum ulei &lt;/em&gt;from the Cordillera Escalera of Peru (&lt;em&gt;Archerythroxylum&lt;/em&gt;, Erythroxylaceae)&lt;/strong&gt;&lt;/p&gt;

Erythroxylum ulei var. escalerense is a new variety described from a single collection made in a remote region of the Cordillera Escalera in Loreto, Peru. It is an understory shrub exhibiting the erect lateral setae on the stipules and ovoid fruits characteristic of E. ulei, but with much smaller, narrowly elliptic to lanceolate leaves without bifacial coloration. Morphological comparison and phylogenetic relationships with similar Erythroxylum are presented and discussed, as well as implications for the current intrageneric classification system.

Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species).

This investigation establishes the first DNA-sequence-based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa. We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. We show that neotropical Erythroxylum are monophyletic within the paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense, but relationships within this "coca" clade remain equivocal. Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify E. gracilipes and E. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.

An early Oligocene fossil acorn, associated leaves and pollen of the ring‐cupped oaks (Quercus subg. Cyclobalanopsis) from Maoming Basin, South China

AbstractThe ring‐cupped oaks (Quercus subg. Cyclobalanopsis) characterized by united and concentric ring‐cupped acorns, are mainly distributed in broad‐leaved evergreen forests in tropical and subtropical regions of East and Southeast Asia. Their geological history has been traced from the middle Eocene to Pleistocene. Most reports of the subgenus have been on the basis of leaves, whereas the acorns or cupules, more valuable evidence for the inter‐ and intrageneric classifications, have been relatively poorly documented. Here, we describe a new species, Quercus shangcunensis sp. nov., based on a ring‐cupped fossil acorn and pollen on the acorn, as well as Quercus sp. associated leaves, recovered from the early Oligocene Shangcun Formation of Maoming Basin, Guangdong Province, South China. The morphological and anatomical structures of these fossils confirm their attribution to the subg. Cyclobalanopsis. Quercus shangcunensis sp. nov. represents the world's first Oligocene fossil acorn and the earliest fossil acorn in China for the subgenus, indicating that the subg. Cyclobalanopsis arrived in the low latitude area of South China at least by the early Oligocene. Our fossil provides evidence that the subgenus was present in one of its modern distribution centers in the Oligocene, suggesting that the modern distribution patterns of the subg. Cyclobalanopsis most likely originated during or prior to the Oligocene.

Phylogeny and biogeography of the pantropical genus Zanthoxylum and its closest relatives in the proto-Rutaceae group (Rutaceae)

Zanthoxylum L. (prickly ash) is the only genus in the Citrus L. family (Rutaceae) with a pantropical distribution. We present the first detailed phylogenetic and biogeographic study of the genus and its close relatives in the proto-Rutaceae group. Our phylogenetic analyses based on two plastid and two nuclear markers show that the genus Toddalia Juss. is nested within Zanthoxylum, that earlier generic and intrageneric classifications need revision, and that the homochlamydeous flowers of the temperate species of Zanthoxylum are the result of a reduction from heterochlamydeous flowers. The biogeographic analyses reveal a Eurasian origin of Zanthoxylum in the Paleocene or Eocene with successive intercontinental or long-range migrations. Zanthoxylum likely crossed the North Atlantic Land Bridges to colonize the Americas in the Eocene, and migrated back to the Old World probably via the Bering Land Bridge in the Oligocene or Miocene. Zanthoxylum also colonized several Pacific Islands and the Hawaiian clade shows phylogenetic incongruence between the plastid and nuclear datasets, suggesting hybridization. The Hawaiian species are one of the rare examples of endemic Hawaiian lineages that are older than the current main islands.

Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species.

Ziziphus Mill. (Rhamnaceae) is comprised of about 170 species that are mainly distributed in tropical to subtropical regions, with few in the temperate zone. Several Ziziphus fruit tree species are important energy, nutrient, and medicinal resources for human populations, particularly for those living in rural regions. To date, limited genomic information is available for this genus. Here, we assembled the complete chloroplast genomes of four best known Ziziphus species, i.e., Ziziphus jujuba, Ziziphus acidojujuba, Ziziphus mauritiana, and Ziziphus spina-christi, based on the Illumina Paired-end sequencing method. The chloroplast genomes of the four Ziziphus species are all very similar to one another, and exhibit structural, gene content, and order characteristics that are similar to other flowering plants. The entire chloroplast genome encodes 113 predicted unique genes (85 protein-coding genes, 8 rRNA, and 37 tRNA), 17 of which are duplicated in the inverted repeat regions. Rich single sequence repeats loci (217) were detected in Z. jujuba and 106 SSR loci, composed of A/T, displayed polymorphism across the four species by comparative genomic analysis. We found only four genes under positive selection between Z. jujuba and Z. acidojujuba, and two genes for Z. mauritiana vs. Z. spina-christi, respectively, while half of the 78 protein-coding genes experienced positive selection between the two groups. Phylogenetic analyses revealed that Ziziphus (Rhamnaceae) was sister to Elaeagnaceae, and the four species of Ziziphus were clustered into two groups (Z. jujuba and Z. acidojujuba, Z. mauritiana and Z. spina-christi). Our results provide genomic resources for intrageneric classifications of Ziziphus, and valuable genetic markers for investigating the population genetics and biogeography of closely related Ziziphus species.

Molecular phylogeny and taxonomic implications of Asarum (Aristolochiaceae) based on ITS and matK sequences

AbstractThe genus Asarum (Aristolochiaceae) encompasses approximately 120 species from five sections. Taxonomic controversies concerning the genus Asarum and/or its intrageneric classification remain unresolved. In particular, sect. Heterotropa accounts for a large percentage of the genus (80 of 120 species) and is well diverged in the Sino–Japanese Forest subkingdom. Reconstruction of Heterotropa phylogeny and estimation of its divergence times would provide significant insight into the process of species diversity in the Sino–Japanese floristic region. This study encompassed 106 operational taxonomic units (OTUs), and phylogenetic analyses were conducted based on internal transcribed spacer (ITS) and matK sequences. Although the matK sequences provided informative results solely for section Geotaenium, phylogenetic trees based on ITS regions yielded a clear result for several sections. Three sections, Asarum, Geotaenium and Asiasarum, were supported as robust monophyletic groups, whereas Heterotropa had low support. Sect. Hexastylis was revealed to be polyphyletic, suggesting taxonomic reconstruction would be needed. Sect. Heterotropa comprises two clades, which correspond to species distribution ranges: mainland China and the island arc from Taiwan to mainland Japan via the Ryukyu Islands. It is notable that the common ancestry of the latter clade in the eastern Asian islands was highly supported, suggesting that the present species diversity of Heterotropa was initially caused by allopatric range fragmentation in East Asia.

Evolutionary Origin of Euglena.

Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and cell movement. Euglenids exhibit diverse modes of nutrition, including phagotrophy and photosynthesis. Photosynthetic species (Euglenophyceae) constitute a single subclade within euglenids. Their plastids embedded by three membranes arose as the result of a secondary endosymbiosis between phagotrophic eukaryovorous euglenid and the Pyramimonas-related green alga. Within photosynthetic euglenids three evolutionary lineages can be distinguished. The most basal lineage is formed by one mixotrophic species, Rapaza viridis. Other photosynthetic euglenids are split into two groups: predominantly marine Eutreptiales and freshwater Euglenales. Euglenales are divided into two families: Phacaceae, comprising three monophyletic genera (Discoplastis, Lepocinclis, Phacus) and Euglenaceae with seven monophyletic genera (Euglenaformis, Euglenaria, Colacium, Cryptoglena, Strombomonas, Trachelomonas, Monomorphina) and polyphyletic genus Euglena. For 150 years researchers have been studying Euglena based solely on morphological features what resulted in hundreds of descriptions of new taxa and many artificial intra-generic classification systems. In spite of the progress towards defining Euglena, it still remains polyphyletic and morphologically almost undistinguishable from members of the recently described genus Euglenaria; members of both genera have cells undergoing metaboly (dynamic changes in cell shape), large chloroplasts with pyrenoids and monomorphic paramylon grains. Model organisms Euglena gracilis Klebs, the species of choice for addressing fundamental questions in eukaryotic biochemistry, cell and molecular biology, is a representative of the genus Euglena.