Relaciones filogenéticas de especies de plantas que crecen en el desierto florido de la Región de Atacama

Objectives : Pinelliae Tuber has been used as a typical unauthentic herbal medicines. Due to the morphological similarity between Pinelliae Tuber and adulterants, the correct authentication is very difficult. Therefore, we introduced DNA barcode to establish a powerful tool for the authentication of Pinelliae Tuner from adulterants. Methods : To obtain DNA barcode regions, genomic DNA was extracted from nineteen specimens of Pinellia ternata, Pinellia pedatisecta, Pinellia tripartita, and Typhonium flagelliforme, and matK and rbcL genes were amplified. For identification of species specific sequences and analysis phylogenetic relationship, a comparative analysis were performed by the ClastalW and UPGMA based on entire sequences of matK and rbcL genes, respectively. Results : In comparison of two DNA barcode sequences, we elucidated the phylogenetic relationship showing distinct four groups depending on species and identified 40 and 20 species specific nucleotides enough to distinguish each species from matK and rbcL gene, respectively. The sequence differences at the corresponding positions were avaliable genetic marker nulceotides to discriminate the correct species among analyzed four species. These results indicated that phylogentic and comparative analysis of matK and rbcL genes are useful genetic markers to authenticate Pinelliae Tubers. Conclusions : The marker nucleotides enough to distinguish P. ternata, P. tripatrita, P. peditisecta, and T. flagelliform, were observed at 40 positions in matK gene and 20 positions in rbcL gene sequence, respectively. These differences can be used to authenticate Pinelliae Tuber from adulterants as well as discriminate each four species.

Simple SummaryBees exhibit exceptional efficiency in pollination processes. The family Andrenidae, comprising over 3000 described species, represents an important lineage of bees, yet limited molecular information has constrained insights into its evolutionary history. This study sequenced and assembled five mitochondrial genomes of Andrenidae collected from Xizang, Tibet. Comparative genomic approaches were used to analyze nucleotide composition, codon preferences, and Ka/Ks ratios of the newly obtained mitogenomes. Furthermore, previously published datasets have been integrated to reconstruct phylogenetic relationships among bees employing both Bayesian Inference and Maximum Likelihood methods. These findings significantly expand the available molecular resources for Andrenidae and offer valuable references for future investigations into the evolutionary biology of this family and bees more broadly.Andrenidae is a major pollinator lineage with considerable ecological importance, yet limited molecular resources have impeded comprehensive understanding of its evolutionary history. This study sequenced and assembled five mitogenomes of Andrenidae, which were collected from Xizang, Tibet. Analyses included sequence size, nucleotide composition, Ka/Ks ratios, and gene rearrangements. The assembled mitogenomes ranged from 15,631 to 18,506 bp in length. AT content (%) varied between 74.46 and 79.85. Relative synonymous codon usage analysis revealed that AUU, UUA, UUU, and UUA were the most frequently preferred codons. All 13 protein-coding genes displayed Ka/Ks values below one, with ATP8 showing the highest ratio and COX1 the lowest. Gene rearrangements occurred in all mitogenomes, and three distinct tRNA rearrangement patterns were detected. This study provided more available molecular data for future evolutionary biology studies of Andrenidae. Additionally, 24 previously published Apoidea mitogenomes (three outgroups and 26 ingroups) were incorporated to infer phylogenetic relationships using Maximum Likelihood and Bayesian Inference methods. The results supported Melittidae as the basal lineage of bees, while Andrenidae was recovered as the sister clade to Halictidae + Colletidae.

DNA barcoding and phylogeny in neotropical species of the genus Spondias

Durian is a tropic fruit having numerous variations on its fruits. Its variations are not only in its shape but also in its aril fruit, aril color, flavor, and aril thickness. In addition to its fruit variations, the genus Durio also has many species which quite hard to distinguish morphologically, except during flowering and fruiting times. This study aimed to determine the genetic relationship among Durian, Pelangi Atuturi Variety Durian, Durio graveolent, and Durio zibetinus based on chloroplast genes (RbcL and matK genes). The primers were previously designed for amplifying matK and rbcL genes based on the Durio zibethinus sequence. Both genes were used because of having great competence to describe genetic relationships between plant species. The rbcL primer could amplify all evaluated samples. Meanwhile, matK primer generated a smeared band in Durian Pelangi; thus, we did not obtain any sequence of this plant. Sequence analysis showed no variation of rbcL sequence in these evaluated species. A similar result was also observed on D. zibethinus and D. graveolent. Overall, both genes could not describe the genetic relationship among the evaluated durians, and they were grouped in the same cluster in phylogenetic.

Simple SummaryThe subfamily Coeliadinae (Lepidoptera: Hesperiidae) is a unique group of over 70 species in the butterfly family, and its mitochondrial genome data still needs to be supplemented. This study sequenced and analyzed five additional complete mitochondrial genomes of the Coeliadinae species (Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis) and compared them in detail with those of the other known skipper mitogenomes. All five of these mitogenomes have the typical lepidopteran mitogenome characteristics of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding region. Our results indicate that their structure, nucleotide composition, codon usage, secondary structure of tRNAs, and so on, are highly conserved. Expanded sampling and gene data from the GenBank, phylogenetic analyses using maximum likelihood, and Bayesian inference methods indicate that Coeliadinae is monophyletic. These results contribute toward refining the phylogeny.To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).

A molecular phylogenetic investigation was undertaken for 30 species belonging to 15 genera of the palm family Arecaceae in Bangladesh to infer evolutionary relationships and molecular dating utilizing plastid-based matK and rbcL genes through multifaceted-algorithm driven approaches with Neighbor-Joining, Maximum-Likelihood, and Bayesian Inference methods. The study revealed that matK has better species discrimination efficiency than rbcL gene due to its highly variable nature. Transition/transversion bias test corroborated this finding as matK showed higher bias (2.632) than rbcL (2.235). Nucleotide substitution patterns were visualized via HYPERMUT program, which unveiled higher variability in matK and lower variability in rbcL alignment. Phylogenetic trees constructed with matK revealed monophyletic nature of origin for all the three subfamilies, viz. Arecoideae, Coryphoideae and Calamoideae, while rbcL trees exhibited polyphyly for Coryphoideae and monophyly for Arecoideae and Calamoideae. All the nine tribes belonging to three subfamilies demonstrated monophyletic nature in matK trees. Bootstrap support and Bayesian posterior probability were found to be higher in matK topologies than that of rbcL. The molecular clock test unraveled an equal evolutionary rate for matK and unequal rate for rbcL sequences. Molecular dating approach unveiled Calamoideae to be the most ancient subfamily (65.75 MYA) among the three subfamilies that originated during the Late Cretaceous period in the Mesozoic era, whereas Coryphoideae and Arecoideae were found to have originated in the Cenozoic era. Bangladesh J. Plant Taxon. 30(2): 213-232, 2023 (December)

Golden camellia species are endangered species with great ecological significance and economic value in the section Chrysantha of the genus Camellia of the family Theaceae. Literature shows that more than 50 species of golden camellia have been found all over the world, but the exact number remains undetermined due to the complex phylogenetic background, the non-uniform classification criteria, and the presence of various synonyms and homonyms; and phylogenetic relationships among golden camellia species at the gene level are yet to be disclosed. Therefore, it is necessary to investigate the divergence time and phylogenetic relationships between all golden camellia species at the gene level to improve their classification system and achieve accurate identification of them. Phenotypic data and transcriptomic sequences of 20 golden camellia species commonly found in Guangxi, China were obtained. PCA and OPLS-DA analyses were conducted based on phenotypic data, and agglomerative clustering was performed to generate the clustering tree of the 20 golden camellia species. Single-copy homologous genes were used to generate phylogenetic trees using Neighbor-Joining, Maximum Likelihood, and Bayesian Inference methods, and the results obtained with these three methods were compared. Then the molecular dating analysis was performed to reveal the divergence time and evolutionary relationships. Rhododendron griersonianum, Diospyros lotus, and Impatiens glandulifera were used as outgroups. The phylogenetic tree based on single-copy homologous genes showed that golden camellia species with shorter geographical distances were closer phylogenetically. Phylogenetic relationships based on phenotypic traits and those based on single-copy homologous genes were inconsistent, suggesting that species with a close genetic evolutionary relationship may show high variation in phenotypic traits and thus the analysis of evolutionary relationships based on phenotypic traits may result in inaccurate outcomes. Among three phylogenetic trees constructed by the three methods, the evolutionary sequences were different, but evolutionary relationships between most species were consistent. For 6 species, the divergence time estimated by Maximum Likelihood and Bayesian Inference varied much, that estimated by Bayesian Inference later than that estimated by Maximum Likelihood. Using these two methods, the resulting divergence time of 14 species was 3.452 Mya. The divergence time predicted in our study is later than that in the literature. In the present study phylogenetic relationships among 20 golden camellia species were analyzed at the transcriptome level to provide a supplement to the phylogenetic classification and evolutionary relationships explored using morphological traits and some molecular markers. Our findings show that the 20 golden camellia species diverged at a later time than other known species in the genus Camellia. Since our analyses were based on the failed molecular clock hypothesis, our conclusions are tentative. Further research using more systematic analyses and more methods should be conducted to confirm the phylogenetic relationships among golden camellia species.

The Order Enoplida (Phylum Nematoda) has been proposed as a divergent nematode lineage—Enoplid nematodes are thought to exhibit morphological and developmental characteristics present in the ‘ancestral nematode’. However, previous molecular phylogenies have failed to unequivocally confirm the position of this group. The Enoplida is primarily comprised of free-living marine species; if these taxa represent close relatives of the nematode ancestor, this relationship would presumably imply a marine origin for the phylum. Prior to this investigation, few publically available gene sequences existed for Enoplid nematodes, and published sequences represented only shallow water fauna from Northwest Europe. This study has aimed to improve resolution at the base of the nematode tree, using drastically increased taxon-sampling within the previously neglected Enoplid clade. Morphological identifications, nuclear gene sequences (18S and 28S rRNA), and mitochondrial gene sequences (Cox1) were obtained from marine specimens representing a variety of deep-sea and intertidal habitats. Molecular data were used to assess the phylogenetic placement of the Enoplid clade, resolve internal taxonomic relationships within this group, and investigate relationships between shallow water and deep-sea fauna. Despite rigorous empirical testing and comprehensive taxon sampling, large-scale phylogenetic analyses based on 18S rRNA sequences (using both Maximum Likelihood and Bayesian Inference methods) failed to provide added resolution at the base of the nematode tree. Molecular data from the 18S rRNA gene was unable to confirm the placement of Enoplida as a divergent lineage representing the sister taxon to all other nematodes. These findings highlight the limitations of the 18S gene for resolving the deepest evolutionary splits amongst nematode clades. Analysis of internal relationships reveals that the Enoplida is split into two main clades, with groups consisting of terrestrial and primarily marine fauna, respectively. For marine taxa, deep-sea and shallow-water specimens from the same genus consistently appear as sister taxa. Deep-sea nematode species may have arisen via several evolutionary routes; some deep-sea clades appear to represent recently derived forms, while other groups seem to have radiated much earlier. Nematodes from deep-sea sites exhibit no obvious clustering according to depth or geographic location, and specimens represent a wide taxonomic range within the Enoplida. In addition, there seems to be some molecular evidence for purportedly cosmopolitan nematode species; identical gene sequences were recorded between distant shallow water locations, as well as between deep-sea and shallow water habitats. Data from Enoplid nematodes suggests an intriguing pattern for nematode species distributions—validating these preliminary insights will require a large amount of molecular data from many additional geographic locations. Future studies will also need to incorporate data from additional genetic loci (or use phylogenomic methods) in order to build robust deep phylogenies.

Seventeen species, one subspecies and one variety of Dioscorea sect. Stenophora Uline were investi- gated for their phylogenetic relationships based on a sequence analysis of chloroplast matK and rbcL genes and trnL-F intergenic spacer by maximum parsimony and maximum likelihood methods. The results showed that: (a) sect. Stenophora was a strongly supported monophyletic group; (b) D. rockii, D. membranacea, D. banzhuana, and D. simulans formed a moderately supported monophyletic group, and D. prazeri was weakly supported to be sister to this group; (c) D. althaeoides and D. nipponica ssp. nipponica formed a moderately supported clade, and D. nipponica ssp. rosthornii was not a member of this clade; (d) D. zingiberensis and D. sinoparviflora showed a moderate to strong sister relationship; and (e) D. collettii var. hypoglauca and D. collettii var. collettii were sister to each other, but with only weak support.

Sexual reproduction by conjugation characterizes the genus Spirofaenia, and based on this character alone it has long been considered a member of the class Zygnematophyceae (Streptophyta). The similarity in chloroplast morphology between the unicellular Spirotaenia (Mesotaeniaceae) and the filamentous Spirogyra (Zygnemataceae) has led to the assumption that the two genera are evolutionarily related, a view apparently supported by rbcL sequence comparisons (McCourt et a1. 2000). We sequenced the nuclear-encoded SSU rDNA and the rbcL genes from three Spirotaenia species and analysed their molecular phylogeny together with other streptophyte green algae (including representatives of the class Zygnematophyceae) and embryophytes using maximum likelihood, distance, maximum parsimony and Bayesian inference methods. The significance of the results was tested by bootstrap analyses,deletion of long-branch taxa and user-defined tree topologies. The two genes congruently revealed an unexpected position of the genus Spirofaenia within the streptophyte algae outside the class Zygnematophyceae, but associated with Chiorokybus. In contrast to a previously published rbcL phylogeny of conjugating green algae, our results suggest that Spirotaenia is not specifically related to Spirogyra and may not belong to the class Zygnematophyceae. The absence of the well-known zygnematophycean 1506 group I intron in all SSU rONA sequences of Spirotaenia supports this conclusion.

The completerbcL gene was sequenced for 21 species and 32 strains ofVaucheriaand for five other Xanthophyceae (Asterosiphon dichotomus(Kützing) Rieth,Botrydium becharianumVischer,B. cystosumVischer,B. stoloniferumMitra,Tribonema intermixtumPascher). ThepsbA‐rbcL spacer, upstream of therbcL gene, and the RUBISCO spacer between therbcL andrbcS genes were also completely sequenced for theVaucheriastrains andAsterosiphon.ThepsbA‐rbcL spacer was the most variable region that was sequenced, and only the 3′ end of the spacer could be aligned. Phylogenetic analyses (maximum parsimony, neighbor joining, and maximum likelihood) were conducted using the DNA sequence and the amino acid sequence for therbcL gene, and a second analysis was conducted using a portion of thepsbA‐rbcL spacer +rbcL gene + RUBISCO spacer. All analyses showed thatVaucheriaspecies formed monophyletic clades that corresponded with morphologically based subgeneric sections, including the section Racemosae. Species producing a gametophore (= fruiting branch, bearing both an antheridium and oogonium) formed a monophyletic clade in all analyses. The nongametophore species sometimes formed a monophyletic clade but other times formed a basal grade. Pair‐wise comparisons of nucleotides and amino acids showed that for some species, numerous nucleotide changes resulted in relatively few amino acid changes. Consequently, phylogenetic analysis of the amino acids produced numerous trees, which in a strict consensus tree resulted in numerous polychotomies. An original strain ofV. terrestristhat was deposited in two culture collections over 25 years ago had identical sequences, suggesting no rapid change was occurring in the sequenced regions. Two strains ofV. prona, isolated from Europe and North America, had identical sequences. Other species, for which two or more strains were examined, had different sequences. These results suggest that cryptic species complexes exist withinVaucheriabecause therbcL gene is a conservative gene that is identical in other protists.

Harankaha is important medicinal plant, which is used in Sri Lankan traditional medicine. However, three plants are reported under the same vernacular name (e.g. Curcuma albiflora, Curcuma zedoaria, and Zingiber zerumbet) and therefore the raw material may be adulterated or substituted with each other. Phylogenetic analysis of gene sequences and combining with complete genomic sequences helps to identify genetic basis of plants. Standard CTAB method with little modifications was used for the extraction and purification. Extracted DNA was amplified using universal primers for matK genes in chloroplast genome rbcL gene in chloroplast genome by PCR (polymerase chain reaction). The rbcL primers amplified about 600 bp, while matK was about 850 bp. Amplified fragments were sequenced and obtained the DNA sequences for the matK and rbcL genes. Sequenced fragments were analyzed and used for DNA barcoding. DNA barcode was submitted to BOLD (Barcoding of Life Database) online database and then uploaded to the GenBank through the BOLD system (Accession No KF 521885). The distance of interspecific were 0.0010 in rbcL and 0.05 in matK, which is less than or equal to 0.05 matK sequences were selected for identification of C. albiflora, C. zedoaria and Z. zerumbet. C. albiflora appeared as a different group as per the Neighbor-Joining method and therefore, it can be identified as a new group. The matK gene of C. albiflora and other species showed, totally 212 variable sites. However, rbcL gene of C. albiflora and other species showed only 2 variable sites. Therefore, matK gene is suggested to identify C. albiflora from other two species claimed as Harankaha plants.

Abstract. Arif MF, Aristya GR, Subositi D, Sai AN, Kasiamdari RS. 2019. Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia. Biodiversitas 20: 3575-3583. Green chireta (Andrographis paniculata (Burm.f.) Wall. ex Nees.) is often used by the traditional community as a medicinal herb in Indonesia. However, nucleotide study of green chireta from Indonesia has never been done. The objectives of this study were to analyze the rbcL and matK chloroplast gene composition of green chireta from Indonesia and to analyze the relationship with other Andrographis species. The result proved that all the DNA composition of green chireta used in this study was similar to the A. paniculata from GenBank. The rbcL composition was similar to A. paniculata KF521878, A. paniculata JQ922118, and A. paniculata JQ230990 from GenBank while the matK composition was similar to A. paniculata LC461762. Total 501 bp of rbcL and 639 bp of matK can be aligned produced 167 and 213 amino acid from translation. The amino acid translation result showed no different expression from rbcL genes but there was one sample expressed different translations from the matK gene. The phylogenetic tree was reconstructed using the Neighbor-Joining method with 1000 bootstrap values and the Kimura 2-Parameter (K2P) model in the MEGA7 software. Both rbcL and matK genes grouped the samples into the same clade as A. paniculata from GenBank. No variation was detected from the rbcL gene but two haplotypes were detected from the matK gene. This composition and sequence data serve as a database for Andrographis species from Indonesia which can be used for various studies.

The phylogenetic relationships among subspecies of Pomatorhinus ruficollis are not clear. In this paper we sequenced two mitochondrial genes (Cyt b and ND2, in total 2 184 bp) and examined twenty individuals representing ten of the eleven subspecies of P. ruficollis in China. Molecular phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference methods, with P. ruficollis and P. schisticeps as in-groups, P. montanus, P. ochraceiceps, P. ferruginosus and Xiphirhynchus superciliaris as out-groups. Results indicated that P. ruficollis was paraphyletic, in which P. schisticeps was embedded, and was divided into three phylogeographic groups: southwestern China group, southeastern China group and central China group. Our results also suggested discordances between phylogenetic relationships and morphological characteristics, and clarified some intraspecific taxonomic debates.

The Mediterranean Basin is one of the most significantly altered World Biodiversity Hotspots with extensive habitat loss and fast genetic population erosion, for which urgent biodiversity reconnaissance and preservation actions are required. In particular, Sicily has about 600 taxa classified as threatened or near-threatened. The correct recognition and identification of such biodiversity is required for supporting further activities. The objective of this work is to assess the ability of the DNA barcoding approach to identify different taxonomic groups from a collection of the most threatened plant taxa, throughout natural Sicilian populations. The evaluation of the DNA barcoding core markers, rbcL and matK, was carried out on 30 taxa belonging to 13 families. DNA barcode fragments were recovered from all taxa (100%). The rbcL gene was recovered from 97% of the taxa and matK gene from 73%. In this test, 19 taxa overall (63%) were totally resolved at the specific or subspecific level, by at least one of the core markers. Fourteen of the 17 most threatened taxa (EN, CR) included in this work were totally discriminated. The matK and rbcL locus, respectively, resolved 64% and 48% of the taxa successfully sequenced. The matK gene expressed the highest genetic distance (K2P value), from 0.4% to 8.6%, against a range of 0.1–2% of rbcL gene. However, the rbcL gene appeared a good compromise between PCR, sequencing success and species-level resolution. Cryptic groups suggest the implementation of additional barcoding markers or different primer combinations, particularly for matK, in order to increase the performances. However, this preliminary result confirms the potential of the barcoding approach for quick identification of unknown and heterogeneous plant groups to generate a dedicated reference data-set of the threatened Sicilian flora for a wide range of applications.