The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai–Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.

Coptis is one of the most important medicinal plant genera in eastern Asia. To better understand the evolution of this genus, the complete chloroplast genome of C. chinensis var. brevisepala was obtained by next-generation sequencing. The plastome of C. chinensis var. brevisepala is 155,426 bp in length, and consists of large (LSC, 84,488 bp) and small (SSC, 17,402bp) single-copy regions, separated by pair of inverted repeat regions (IRs, 26,768 bp). It harbours 111 unique genes, including 78 protein-coding genes, 29 transfer RNA genes, and four ribosomal RNA genes. Rps19 and ycf1 were pseudogenized due to incomplete duplication in IR regions. The nucleotide composition is asymmetric (30.5% A, 19.4% C, 18.7% G, and 31.3% T) with an overall G + C content of 38.2%. The phylogeny of Ranunculaceae based on 75 CDSs of 27 taxa showed that Ranunculoideae is paraphyletic and thus needs redefinition.

Alismatales play an important role in the systematics of angiosperm, yet different phylogenetic topologies of Alismatales based on different species have been generated from several studies. Here we reported and characterized the first complete chloroplast (cp) genomes of two Alismataceae species, Alisma plantago-aquatica and Sagittaria trifolia, and analyzed the phylogenomic relationship of Alismatales based on the complete chloroplast sequences of 21 Alismatales species. The two chloroplast genomes have the typical quadripartite structure with 113 genes in total, including 79 protein-encoding genes, 30 transfer RNA genes and four ribosomal RNA genes. Both IR regeions of plastid genomes contain 8 protein-encoding genes, 7 tRNA genes and all the four rRNA genes. The genome of A. plantago-aquatica is 177,417 bp in length, with an overall G + C content of 35.7%, and the genome of Sagittaria trifolia is 167,642 bp in length, with an overall G + C content of 37.0%. Phylogenetic study showed that the three Alismataceae species comprise a monophyletic group with a high support rate, which was a sister to the Hydrocharitaceae clade. The core Alismatids, consisting of Potamogetonaceae, Zosteraceae, Hydrocharitaceae and Alismataceae, is sister to Tofieldiaceae. Alocasia macrorrhizos of Araceae is the basal taxon of Alismatales, and the other twelve Araceae species formed a sister group to the clade Tofieldaceae and core Alismatids.

Dysphania botrys belongs to Amaranthaceae and distributes in North Europe, Asia, and North America. It is a medicinal plant with diuretic, antispasmodic, carminative, antidiarrhoeic properties, and a candidate plant for cancer treatment. However, few studies focused on its phylogeny, and its taxonomic status is still controversial. To better understand the evolution of this species, the complete plastome of D. botrys was obtained by next-generation sequencing. It is the first plastome to be sequenced and reported in the genus Dysphania. The plastome is 152,055 bp in length, which consists of a large single-copy region (LSC, 83,769 bp; GC content: 34.7%), a small single-copy region (SSC, 17,916 bp; GC content: 30.1%), and a pair of inverted repeat regions (IRs, 25,185 bp; GC content: 42.7%). It harbors 112 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes with an overall G + C content of 36.8%. The phylogeny of Amaranthaceae based on the complete plastome sequences of 13 taxa showed that D. botrys belong to subfamily Chenopodioideae. Chenopodioideae, together with Betoideae formed a sister clade to the three subfamilies (Salicornioideae, Suaedoideae, and Salsoloideae), and this sister clade formed an evolutionary sister clade to Amaranthoideae. Our data will largely enrich the genetic information of Dysphania botrys and facilitate future studies on its evolutionary status.

Tamarix species play a significant ecological role in desert transformation and climate improvement, representing nearly 75% of Tamaricaceae. However, due to their high morphological variability and susceptibility to interspecific hybridization, Tamarix remains one of the most poorly classified genera among flowering plants, which has significantly impeded the utilization of Tamarix species in ecological restoration projects across desert regions. China is among the countries most severely affected by desertification. Therefore, this study aims to compare chloroplast genomes among Tamarix species distributed in China, clarify their phylogenetic relationships, and identify molecular markers for species identification. In this study, we obtained the complete chloroplast genomes (CPGs) of 16 Tamarix species (33 CPGs), 24 of which were newly generated. A total of 1,650 non-SSR-related indels and 1,428 non-indel-related SSRs were identified, with mononucleotide SSRs being the most abundant. Comparative analyses using mVISTA revealed high sequence similarity across Tamarix chloroplast genomes, indicating strong conservation, except for Tamarix androssowii (OR619632). Overall, inverted repeat (IR) and coding regions were more conserved than single-copy and noncoding regions. Several intergenic regions showed higher variability than commonly used universal DNA markers. Phylogenetic analyses strongly supported the monophyly of Tamarix with two Myricaria samples as outgroups. Using 35 CPGs, we reconstructed a well-resolved phylogeny of Tamarix. Variations in branch lengths and support values provide new insights into intrageneric relationships within the genus. The genomic resources generated in this study offer a valuable foundation for future research on population genetics, species identification, and conservation of Tamarix.

Introduction: Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families.MenispermumL. (Menispermaceae) consists of three species,M. dauricumDC.,M. canadenseL., andM. mexicanumRose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whetherM. mexicanumis a distinct species, a variety ofM. dauricum, or simply a synonym ofM. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses.Methods: In this study, we examined phylogenomics and phylogeography ofMenispermumacross its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships ofMenispermumand explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family.Results and discussion: Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show thatMenispermumclusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense+M. mexicanum). However,M. mexicanumis nested withinM. canadenseand, as a result, we support thatM. mexicanumis a synonym ofM. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK,ycf1), four introns (trnK intron,rpl16intron,rps16 intron,ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA,ndhF-rpl32,trnK-rps16, andtrnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.