Abstract A DNA barcode is a fragment used to identify species. For land plants, fragments of plastid genome could be the primary consideration. Unfortunately, most candidate barcodes lack species-level resolution. The identification high resolution at species level critical success barcoding in plants. We searched available genomes for variable regions and tested best candidates using both large number tree seven well-sampled plant groups. Two gene ycf1 , b, were loci that better than...

The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one the most commonly used markers in plant phylogenetic and barcoding analyses, it has been recommended as a core barcode. Despite this popularity, universality specificity PCR primers for ITS region are not satisfactory, resulting amplification sequencing difficulties. By thoroughly surveying analysing 18S, 5.8S 26S sequences Plantae Fungi from GenBank, we designed new universal plant-specific amplifying whole part (ITS1 or...

Plastid genomes are an invaluable resource for plant biological studies. However, the number of completely sequenced plastid is still small compared with vast species. To provide alternative generalized approach, we designed a set 138 pairs universal primers amplifying (termed “short-range PCR”) and sequencing entire angiosperm genomes. The universality was tested by using species from basal to asterid angiosperms. polymerase chain reaction (PCR) success rate higher than 96%. We complete...

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes 75 complete plastomes were used to infer the phylogenetic relationships estimate historical biogeography apple genus Malus sensu lato, economically important lineage disjunctly distributed in Northern Hemisphere involved known suspected hybridization...

Angiosperms are the largest plant group and play an essential role in biosphere. Phylogenetic relationships of many families orders remain contentious, and, attempt to address these, we performed most extensive sampling mitochondrial genes date. We reconstructed a seed phylogenetic framework based on 41 protein-coding sequences (mtCDSs), representing 335 63 with 481 angiosperm species. The results for major clades angiosperms produced moderate strong support (> 70% bootstrap) more than 80%...

Crape myrtles are economically important ornamental trees of the genus Lagerstroemia L. (Lythraceae), with a distribution from tropical to northern temperate zones. They positioned phylogenetically large subclade rosids (in eudicots) which contain more than 25% all angiosperms. commonly bloom summer till fall and significant value in city landscape environmental protection. Morphological traits shared inter-specifically among plants certain extent also influenced by conditions different...

Universal conventional DNA barcodes will become more and popular in biological material identifications. However, many cases such as processed medicines or canned food, the universal are unnecessary and/or inapplicable due to degradation. mini-barcode is a solution for specific purposes. Here we exemplify how develop best mini-barcodes taxa using ginseng genus (Panax) an example. The chloroplast genome of P. notoginseng was sequenced. compared with that ginseng. Regions highest variability...

Machilus is a large (c. 100 sp.) genus of trees in the family Lauraceae, distributed tropical and subtropical East Asia. Both molecular species identification phylogenetic studies this morphologically uniform have been constrained by insufficient variable sites among frequently used biomarkers. To better understand mutation patterns chloroplast genome Machilus, complete plastomes two were sequenced. The yunnanensis M. balansae 152, 622 721 bp, respectively. Seven highly regions between...

Walnuts (Juglans of the Juglandaceae) are well-known economically important resource plants for edible nuts, high-quality wood, and medicinal use, with a distribution from tropical to temperate zones Asia Europe Americas. There about 21 species in Juglans. Classification Juglans at section level is problematic, because phylogenetic position cinerea disputable. Lacking morphological DNA markers severely inhibited development related researches. In this study, complete chloroplast genomes two...

Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher genomes generally used to reconstruct phylogenies. However, little attention has been paid evolution within orders. Here, we present of Sedum sarmentosum take advantage several available (or elucidated) examine in Saxifragales. The S. is 150,448 bp long includes 82,212 a large single-copy (LSC) region, 16.670 small (SSC) pair 25,783 sequences inverted...

Abstract Background Deep-branching phylogenetic relationships are often difficult to resolve because signals obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- shallow-scale across all branches tree life. The olive family (Oleaceae) is composed 25 genera classified into five tribes with tribe...

Abstract The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification the pear genus, Pyrus , widely distributed Eurasian lineage Rosaceae. This issue been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive sampling, encompassing 78 ingroup individuals representing 32 species, along with 4 outgroup species. comprehensive sampling strategy covers wide...

The origin of cultivated tree peonies, known as the ‘king flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses explicitly sampled traditional cultivars peonies and all wild species from shrubby section Moutan genus Paeonia based on sequences 14 fast-evolved chloroplast regions 25 presumably single-copy nuclear markers identified RNA-seq data. phylogeny inferred was fully resolved largely congruent...

Abstract The ideal DNA barcode for plants remains to be discovered, and the candidate rbc L has been met with considerable skepticism since its proposal. In fact, variability within this gene never fully explored across all plant groups from algae flowering plants, performance as a not adequately tested. By analysing of sequences currently available in G en B ank, we attempted determine how well region performs species discrimination. We found that b was more variable than frequently used...

The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. small trees or shrubs in this are referred as King of psammophytic plants, and perform important functions environmental protection, including wind control sand fixation deserts. To better understand these beneficial we sequenced chloroplast (cp) genomes ammodendron (HA) persicum (HP) conducted comparative genomic analyses on two other representative species. Similar higher found that cp genome is a...

Abstract Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea , Stranvaesia 68 species, distributed Asia North Central America. Despite previous efforts to clarify relationships this group, the generic delimitations have remained uncertain. Our goals were reconstruct a robust phylogeny close test monophyly genera, especially hybrid origin hypothesis bodinieri . This study employs complete...

Abstract Chaenomeles (family Rosaceae) is a genus of five diploid species deciduous spiny shrubs that are native to Central Asia and Japan. It an important horticultural crop (commonly known as flowering quinces) in Europe for its high yield fruits rich juice, aroma, dietary fiber. Therefore, the development effective genetic markers advantageous improvement through breeding selection. In this study, we successfully assembled analyzed chloroplast genome species. The genomes were very similar...

Abstract Background Crape myrtles, belonging to the genus Lagerstroemia L., have beautiful paniculate inflorescences and are cultivated as important ornamental tree species for landscaping gardening. However, phylogenetic relationships within remained unresolved likely caused by limited sampling insufficient number of informative sites used in previous studies. Results In this study, we sequenced 20 chloroplast genomes combined with 15 existing from investigate divergence times . The results...

Abstract The olive genus Olea includes c . 30–40 taxa in three subgenera ( , Tetrapilus and Paniculatae ) within the family Oleaceae. Historically, was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus poor resolution clades. These analyses also showed not monophyletic. Reliable identification species is important for both their conservation utilization this economically genus. In study, we used phylogenomic...

The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental distribution, Fraxinus was used as model organism integrate abundant fossil evidence with high-resolution phylogenies phytogeographic analysis. We constructed robust phylogenetic tree using genomic data, reconstructed geographic ancestral areas, evaluated effect incorporating information on biogeographic history....

We applied the phylogenomics to clarify concept of rice species, aid in identification and use germplasms, support biodiversity. Rice (genus Oryza) is one most important crops world, supporting half world's population. Breeding high-yielding quality cultivars relies on genetic resources from both cultivated wild which are collected maintained seed banks. Unfortunately, numerous seeds mislabeled due taxonomic issues or misidentifications. Here, we 58 complete chloroplast genomes two...

Abstract Plastid genomes play an important role in genomics and evolutionary biology. Next‐generation sequencing has revolutionized plastid genomic data acquisition to the point that genome assembly become a bottleneck for widespread utilization of data. To solve this problem, we developed open‐source, cross‐platform tool known as, NOVOWrap , which includes both command‐line graphical interfaces automatically assembling on personal computers. With minimal inputs, settings, user intervention,...