Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae.

Mulberries (genus Morus; Moraceae) hold significant economic value in sericulture and have great potential in the horticultural industry, food industry, and human health arenas worldwide. Since the advent of the genomic era, biological macromolecules of Morus species such as whole genome and plastome sequences have been reported, but mitochondrial genome sequences are relatively scarce which greatly hinders the comprehensive understanding of the evolutionary history and processes at work with Morus. Here, four Morus mitogenomes were assembled using Illumina and PacBio HiFi data. The results elucidated that the structure of the four mitogenomes was greatly heterogeneous due to the presence of different numbers of repeat-mediated recombination events with multiple conformations existing simultaneously in the mitogenome for each species. The genome size ranged from 359,062 to 376,846 bp. The repeat sequences and gene transfers from plastome to mitogenome varied widely among the four mitogenomes, which was the main cause of variation in mitogenome size. Finally, the evolutionary history of Rosales was inferred based on the mitogenome sequences. The analyses revealed a strong difference in the phylogenetic placement of Rhamnaceae compared to earlier plastid or nuclear phylogenies, likely due to the effects of ancient hybridizations. Overall, the results presented here will provide important genetic resources for the utilization of this important economic plant.

Celtis is a Cannabaceae genus of 60–70 species of trees, or rarely shrubs, commonly known as hackberries. This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals. Although previous studies have identified its phylogenetic position, interspecific relationships within Celtis remain unclear. In this study, we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources. The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp, with a typical angiosperm quadripartite structure, and encoded a total of 132 genes with 20 duplicated in the IRs. Comparative analyses showed that plastome content and structure were relatively conserved. Whole plastomes showed no signs of gene loss, translocations, inversions, or genome rearrangement. Six plastid hotspot regions (trnH-psbA, psbA-trnK, trnG-trnR, psbC-trnS, cemA-petA and rps8-rpl14), 4097 polymorphic nuclear SSRs, as well as 62 low or single-copy gene fragments were identified within Celtis. Moreover, the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C. biondii as sister to the ((((C. koraiensis, C. sinensis), C. tetrandra), C. julianae), C. cerasifera) clade. These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny, population genetics, and conservation biology.

Plantago asiatica, an herbaceous perennial species of Plantaginaceae, has been used as a traditional herbal medicine plant in China. In this study, the complete chloroplast (cp) genome of P. asiatica was sequenced and assembled using genome skimming data. The cp genome was 165,045 bp in length including the large single-copy (LSC, 82,964 bp) and small single-copy (SSC, 4,633 bp) regions separated by two copies of inverted region (IR, 38,724 bp). The cp genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, additionally with 27 duplicated genes in the IR regions. Phylogenetic analysis indicated that the representative species from Plantago was monophyletic and they were divided into four subgenera. P. asiatica belongs to the subgenus Plantago and was sister to P. rigida with high bootstrap value support.

Leontice incerta, which belongs to Berberidaceae, is an endangered species in China. In this study, the chloroplast (cp) genome of L. incerta was assembled using genome skimming sequencing and the phylogeny of Berberidaceae was reconstructed based on whole cp genome. The cp genome of L. incerta is 156,923 bp in length, comprising two copies of IR (26,121 bp) regions separated by the LSC (85,622 bp) and SSC (19,059 bp) regions. The cp genome encodes 112 unique genes, consisting of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis indicates that L. incerta is sister to Gymnospermium microrrhynchum, subsequently is sister to Nandia domestica.

Tiarella polyphylla D. Don has been traditionally used to cure asthma and skin eruptions. However, the sequence and the structure of the mitogenome of T. polyphylla remained elusive, limiting the genomic and evolution analysis based on the mitogenome. Using a combination of Illumina and Nanopore sequencing reads, we de novo assembled the complete mitogenome of T. polyphylla. In addition to unveiling the major configuration of the T. polyphylla mitogenome was three circular chromosomes with lengths of 430,435 bp, 126,943 bp, and 55,269 bp, we revealed five (R01-R05) and one (R06) repetitive sequence could mediate the intra- and inter-chromosomal recombination, respectively. Furthermore, we identified 208 short and 25 long tandem segments, seven cp-derived mtDNAs, 106 segments of mtDNAs transferred to the nuclear genome, and 653 predicted RNA editing sites. Based on the sequence of the mitogenomes, we obtained the resolved phylogeny of the seven Saxifragales species. These results presented the mitogenome features and expanded its potential applications in phylogenetics, species identification, and cytoplasmic male sterility (CMS) in the future.