Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

Chloroplast-nuclear genome interaction drives asymmetric inverted repeats in chloroplast genome of Huperzia

Huperzia plants are important natural medicine species that have attracted increased amounts of attention due to the presence of huperzine A (Hup A), which efficiently, selectively, and reversibly inhibits acetylcholinesterase activity. However, due to the complexity of the genome structure and lack of genetic information, the phylogenetic and evolutionary relationships of Huperzia species are still unclear. In this study, seven chloroplast genome structures of Huperzia were verified and comparatively analyzed, and the phylogenetic relationships between Huperzia and other related ferns were evaluated. The results showed that a 58 kb insertion in the middle of the IRb region in the seven chloroplast genomes led to large differences in sequence size, GC content and tRNA number between IRa and IRb. All seven chloroplast genomes exhibited asymmetric structural conformations in the IR regions. We used sequence alignment and screening of the organelle and nuclear genomes to identify the source of the gene. The inserted sequence had no homologous region with the mitochondrial genome, and the same sequence as another segment was found in the nuclear genome. Then, the chloroplast genomes of Huperzia were comparatively analyzed. Phylogenetic tree showed that Phlegmariurus and Huperzia were closely related and belonged to the same branch. H. javanica and Huperzia serrata are closely related. From the perspective of phylogenetic tree, their phylogenetic relationship is closely related to geographical distribution. In conclusion, this study provides insights into the interaction mechanism between chloroplast genome and nuclear genome and the phylogeny of Huperzia. In addition, by comparing the chloroplast genomes of Huperzia, we analyzed its genetic diversity and provided important molecular information for the protection of these endangered species.

Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra

Licorice (Glycyrrhiza L.), a medicinally and economically significant genus in the Fabaceae, is known for synthesizing glycyrrhizin. Here, we present a newly assembled genome of Glycyrrhiza uralensis, a key species distributed across Central and East Asia. Using Oxford Nanopore, Hi-C, and Illumina sequencing, we assembled a 415 Mbp genome with an N50 of 47 Mbp. While the genome structure was similar to previously reported assemblies, structural variations were observed across all eight chromosomes. Re-sequencing data from 29 individuals, including G. uralensis, G. glabra, and their hybrids, revealed significant genetic diversity, population structure, and hybridization events. Phylogenomic analyses using nuclear and plastid genomes demonstrated phylogenetic incongruence, supporting hybridization between G. uralensis and G. glabra. Our species network and gene flow test identified hybrid groups (Ggu1, Ggu2, and Gug) acting as genetic bridges between the species. Demographic history inferred via PSMC showed Glycyrrhiza species thrived during the Middle Pleistocene, with population size fluctuations in G. uralensis and hybrids. Current low heterozygosity and high genetic differentiation suggest long-term geographic and ecological isolation, reducing gene flow. Our findings advance the understanding of evolutionary history in Glycyrrhiza species and help conservation and molecular breeding of these species.

A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum

Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible and functional foods. In this study, we compared the plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that the PJ accessions were monophyletic within the genus Peucedanum. However, ten plastomes were classified into two different groups according to their length of inverted repeat (IR) block, the short-type (S-type) plastome group containing the 18.6 kbp of the original IR and the long-type (L-type) plastome group containing the 35.7 kbp of expanded IR by duplication of the 17.1 kbp of the large single copy region. A total of nine single nucleotide polymorphisms and eight insertions or deletions were identified among the five L-type plastomes, whereas large variations were identified among the five S-type plastomes. Calculation of synonymous substitution rates and divergence time estimation suggested that the 17 kbp IR expansion occurred recently. Molecular markers were developed and validated to classify the 55 PJ germplasm according to their plastome types. Our study would be useful for unraveling the dynamic evolution of plastomes in the Apiaceae family and for the molecular breeding of PJ.

Complete chloroplast genome sequence of Solanum mochiquense, one of the tuber-bearing potato relatives

Solanum mochiquense is one of the wild tuber-bearing Solanum species belonging to the Solanaceae family. In this study, the chloroplast genome sequence of the species was completed with Illumina sequencing technology. The total length of the chloroplast genome is 155,547 bp with a GC content of 37.87%. It comprises a large single copy (LSC) region of 85,941 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,612 bp. Additionally, 158 functional genes in the genome were identified, including 105 protein-coding genes, eight ribosomal RNA genes, and 45 transfer RNA genes. Phylogenetic analysis revealed that S. mochiquense is grouped into a large clade with other Solanum species including cultivated potatoes (S. tuberosum). This study provides useful genomic information for future breeding and evolutionary studies of S. mochiquense and other Solanum species.

Characterization and Phylogenetic Analysis of the First Complete Chloroplast Genome of Shizhenia pinguicula (Orchidaceae: Orchideae)

BACKGROUND

Genomic analysis is crucial for better understanding the evolutionary history of species and for their conservation. Shizhenia pinguicula is a rare medicinal plant endemic to China. However, the complete chloroplast genome of this species has not been reported to date. Insufficient genomic research on S. pinguicula has hindered effective conservation efforts for this valuable plant.

METHODS

In this study, we sequenced and assembled the first complete chloroplast genome of S. pinguicula using Illumina sequencing technology. We conducted a comparative analysis of its chloroplast genome with related species and reconstructed phylogenetic relationships.

RESULTS

The chloroplast genome of S. pinguicula exhibited a typical quadripartite structure with a length of 158,658 bp. A total of 123 genes, 118 simple sequence repeats, and 51 dispersed repetitive sequences were identified. The inverted repeat boundaries were significantly expanded, along with the pseudogenization and loss of multiple NDH genes. Codon usage bias is primarily influenced by natural selection and other factors, with the ycf3 gene under positive selection. Additionally, 10 hypervariable regions were detected for species identification and evolutionary studies. Phylogenetic analysis indicated that Ponerorchis gracilis and Hemipilia yajiangensis form a clade, with S. pinguicula as their sister species, located at the basal position of the Ponerorchis-Hemipilia alliance.

CONCLUSIONS

The chloroplast genome structure and gene content of S. pinguicula exhibit certain degrees of variation compared to other species within the Orchidinae subtribe. This genome should be useful for further investigations into the biology of Shizhenia and the development of biodiversity conservation strategies.

Chloroplast genome sequencing and divergence analysis of 18 Pyrus species: insights into intron length polymorphisms and evolutionary processes

Pears constitute an essential temperate crop and are primarily produced through interspecific hybridization owing to self-incompatibility that complicates their breeding history. To address this, we sequenced the complete chloroplast (cp) genomes of 18 Pyrus and one Malus species using the Illumina HiSeq4000 platform. The cp genomes ranged from 159,885 bp to 160,153 bp and exhibited a conserved circular DNA structure with an average GC content of 36.5%. Each cp genome contained 127 genes, including 83 protein-coding, 36 tRNA, and 8 rRNA genes. Divergence analysis with mVISTA showed high conservation in the coding regions and notable variations in the non-coding regions. All species shared 17 intron-containing genes, with ycf3 and clpP each having two introns. Five intron-containing genes (ndhB, rpl2, rps12, trnA-UGC, and trnE-UUC) were located in the inverted repeat regions, while trnL-UAA was located in the large single-copy region, with conserved intron lengths across Pomoideae. We identified polymorphic intron sequences in the rpl22, petB, clpP, ndhA, and rps16 genes and designed primers for these regions. Notably, the two Pyrus ussuriensis accessions Doonggeullebae and Cheongdangrori showed intron-length polymorphisms despite being classified as the same species. Phylogenetic analysis of the cp genome sequences revealed two major clusters, indicating distinct maternal lineages and evolutionary origins. This study underscores the importance of cp gene polymorphisms in P. fauriei, P. calleryana, P. ussuriensis, and P. pyrifolia, providing valuable insights into Pyrus evolution as well as aiding in the conservation and breeding of pear germplasm.

Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance

The indica rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including Pi2, Pib and Ptr, and bacterial blight resistance gene Xa27, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges.

The complete chloroplast genome sequence and phylogenetic analysis of Asplenium antiquum Makino 1929, an Endangered species in Korea

Asplenium antiquum Makino 1929 is one of the Endangered endemic species on the Korean Peninsula. The complete chloroplast of A. antiquum is 150,690 bp in length with typical quadripartite structure comprised of large single-copy region of (83,166 bp), a small single copy region (21,932 bp), and two inverted repeat regions, each 22,796 bp in length. 114 genes were detected in the chloroplast genome of A. antiquum, comprising 84 protein-encoding genes, 26 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed a monophyletic relationship, placing A. antiquum as a sister to voth A. Prolongatum and A. nidus, forming a subclade of Asplenium species within the Aspleniaceae family. The genomic data obtained from this study will serve as valuable information for the species' genetic classification of Asplenium.

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

Introduction

Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety.

Methods

The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum.

Results and discussion

The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium.

Conclusion

Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.

Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome

Aster L. is an economically and phylogenetically important genus in the tribe Astereae. Here, the complete plastomes of the eight Aster species were assembled and characterized using next-generation sequencing datasets. The results indicated the complete plastomes of Aster had a quadripartite structure. These genomes were 152,045-152,729 bp in length and contained 132-133 genes, including 87 protein-coding genes, 37-38 tRNA genes, and eight rRNA genes. Expansion or contraction of inverted repeat regions and forward, palindromic, complement, and reverse repeats were detected in the eight Aster species. Additionally, our analyses showed the richest type of simple sequence repeats was A/T mononucleotides, and 14 highly variable regions were discovered by analyzing the border regions, sequence divergence, and hotspots. Phylogenetic analyses indicated that 27 species in Astereae were clustered into six clades, i.e., A to D, North American, and outgroup clades, and supported that the genera Heteropappus, Kalimeris, and Heteroplexis are nested within Aster. The results indicated the clades B to D might be considered as genera. Divergence time estimate showed the clades A, B, C, and D diverged at 23.15 Mya, 15.13 Mya, 24.29 Mya, and 21.66 Mya, respectively. These results shed light on the phylogenetic relationships of Aster and provided new information on species identification of Aster and its related genera.

Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species

BACKGROUND

Jasmine (Jasminum), renowned for its ornamental value and captivating fragrance, has given rise to numerous species and accessions. However, limited knowledge exists regarding the evolutionary relationships among various Jasminum species.

RESULTS

In the present study, we sequenced seven distinct Jasminum species, resulting in the assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that the size of the 12 cp genomes ranged from 159 to 165 kb and encoded 134-135 genes, including 86-88 protein-coding genes, 38-40 tRNA genes, and 8 rRNA genes. J. nudiflorum exhibited a larger genome size compared to other species, mainly attributed to the elevated number of forward repeats (FRs). Despite the typically conservative nature of chloroplasts, variations in the presence or absence of accD have been observed within J. sambac. The calculation of nucleotide diversity (Pi) values for 19 cp genomes indicated that potential mutation hotspots were more likely to be located in LSC regions than in other regions, particularly in genes ycf2, rbcL, atpE, ndhK, and ndhC (Pi > 0.2). Ka/Ks values revealed strong selection pressure on the genes rps2, atpA, rpoA, rpoC1, and rpl33 when comparing J. sambac with the three most closely related species (J. auriculatum, J. multiflorum, and J. dichotomum). Additionally, SNP identification, along with the results of Structure, PCA, and phylogenetic tree analyses, divided the Jasminum cp genomes into six groups. Notably, J. polyanthum showed gene flow signals from both the G5 group (J. nudiflorum) and the G3 group (J. tortuosum and J. fluminense). Phylogenetic tree analysis reflected that most species from the same genus clustered together with robust support in Oleaceae, strongly supporting the monophyletic nature of cp genomes within the genus Jasminum.

CONCLUSION

Overall, this study provides comprehensive insights into the genomic composition, variation, and phylogenetic relationships among various Jasminum species. These findings enhance our understanding of the genetic diversity and evolutionary history of Jasminum.

Complete Chloroplast Genomes of Four Oaks from the Section Cyclobalanopsis Improve the Phylogenetic Analysis and Understanding of Evolutionary Processes in the Genus Quercus

Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ-trnG-GCC, rbcL-accD, and rpl32-trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus.

The complete chloroplast genome sequences of four Liparis species (Orchidaceae) and phylogenetic implications

Liparis Richard (Malaxideae, Epidendroideae) is a large and diverse genus of the family Orchidaceae, the taxonomy of which is complicated and controversial. In this study, we sequenced, assembled and analyzed four complete chloroplast genomes of Liparis species including L. kumokiri, L. makinoana, L. pauliana, and L. viridiflora, and evaluated their phylogenetic relationships with related species for the first time. These four chloroplast genomes (size range 153,095 to 158,239 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 83,533-86,752 bp), a small single copy (SSC, 17,938-18,156 bp) and a pair of inverted repeats (IRs, 26,421-26,933 bp). The genomes contain 133 genes, including 87 protein coding genes, 38 tRNAs and 8 rRNA genes. The genome arrangements, gene contents, gene order, long repeats and simple sequence repeats were similar with small differences observed among these four chloroplast genomes. Five highly variable regions including ycf1, ndhA, ndhF, trnQ and trnK were identified from the comparative analysis with other nine related Liparis species, which had the potential to be used as DNA markers for species identification and phylogenetic studies of Liparis species. Phylogenetic analysis based on the complete chloroplast genome sequences strongly supported the polyphyly of Liparis and its further division into three branches. These results provided valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the Liparis genus.

The complete mitogenome of the entomopathogenic fungus Metarhizium pinghaense 15R

In this study, the complete mitogenome of the entomopathogenic fungus Metarhizium pinghaense 15 R, which is highly virulent to aphids and was isolated from Korean soil, was assembled and annotated for three ATP synthase subunits (atp6, atp8, and atp9), three cytochrome oxidase subunits (cox1, cox2, and cox3), apocytochrome b (cob), seven subunits of NADH dehydrogenase (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), two ribosomal RNAs (rnl and rns), and 19 tRNA genes. Five genes were carrying a total of eight introns, and they may encode ribosomal protein S3, LAGLIDADG and GIY-YIG endonucleases. Phylogenetic analysis based on the mitochondrial nucleotide sequence confirmed that the M. pinghaense 15 R is a member of the Clavicipitaceae, and is closely related to the species M. anisopliae, M. robertsii, and M. brunneum. The mtDNA base sequence of the M. pinghaense 15 R strain reported in this study is thought to be useful for biological resource genetic data.

Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure

The Araliaceae contain many valuable species in medicinal and industrial aspects. We performed intensive phylogenomics using the plastid genome (plastome) and 45S nuclear ribosomal DNA sequences. A total of 66 plastome sequences were used, 13 of which were newly assembled in this study, 12 from new sequences, and one from existing data. While Araliaceae plastomes showed conserved genome structure, phylogenetic reconstructions based on four different plastome datasets revealed phylogenetic discordance within the Asian Palmate group. The divergence time estimation revealed that splits in two Araliaceae subfamilies and the clades exhibiting phylogenetic discordances in the Asian Palmate group occurred at two climatic optima, suggesting that global warming events triggered species divergence, particularly the rapid diversification of the Asian Palmate group during the Middle Miocene. Nucleotide substitution analyses indicated that the Hydrocotyloideae plastomes have undergone accelerated AT-biased mutations (C-to-T transitions) compared with the Aralioideae plastomes, and the acceleration may occur in their mitochondrial and nuclear genomes as well. This implies that members of the genus Hydrocotyle, the only aquatic plants in the Araliaceae, have experienced a distinct evolutionary history from the other species. We also discussed the intercontinental disjunction in the genus Panax and proposed a hypothesis to complement the previously proposed hypothesis. Our results provide the evolutionary trajectory of Araliaceae and advance our current understanding of the evolution of Araliaceae species.

Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA

Allium ulleungense (AU) and A. microdictyon (AM) are valuable medicinal and edible vegetables, referred to as mountain garlic in Korea. The identification of AU, AM and a neighboring species A. ochotense (AO) is difficult because of their morphological similarities. We collected samples from three species and 46 cultivated collections to understand the genetic diversity of these valuable Allium species. Among them, we sequenced six collections, including three species and three cultivating collections to obtain data from the plastid genome (plastome) and nuclear 45S ribosomal DNA (nrDNA) for super-barcoding. The AM and AO showed around 60 single nucleotide polymorphisms (SNPs) and 39 Insertion/Deletion (InDels) in the plastome but no variations in the nrDNA sequences. Conversely, the AU and AM showed more than 170 SNPs and 80 InDels in the plastomes, and 20 SNPs and 1 InDel were found in the 45S nrDNA sequences. Among the three cultivating collections, one TB collection was determined to be the AU type in both plastome and nrDNA sequences. However, the other two collections, JB and SA, showed the AM type plastome but were heterozygous in the 45S nrDNA sequences, indicating both AU and AM types (putative AM x AU hybrid). Ten molecular markers were developed based on sequence variations to identify these three species and assess their genetic diversity. A total of 49 collections were genotyped using the ten developed markers and classified into five groups: 14 AU, 22 AM, 1 AO, 3 putative AM x AU hybrids, and 9 putative AU x AM hybrid collections. Super-barcoding with plastomes and nrDNAs revealed the genetic diversity of the three Allium species and putative hybrids between species. The newly developed markers will facilitate species and hybrid identification, thereby benefiting marker-assisted molecular breeding of Allium species.

Comparative analysis of mitochondrial genomes of Schisandra repanda and Kadsura japonica

The family Schisandraceae is a basal angiosperm plant group distributed in East and Southeast Asia and includes many medicinal plant species such as Schisandra chinensis. In this study, mitochondrial genomes (mitogenomes) of two species, Schisandra repanda and Kadsura japonica, in the family were characterized through de novo assembly using sequencing data obtained with Oxford Nanopore and Illumina sequencing technologies. The mitogenomes of S. repanda were assembled into one circular contig (571,107 bp) and four linear contigs (10,898-607,430 bp), with a total of 60 genes: 38 protein-coding genes (PCGs), 19 tRNA genes, and 3 rRNA genes. The mitogenomes of K. japonica were assembled into five circular contigs (211,474-973,503 bp) and three linear contigs (8,010-72,712 bp), with a total of 66 genes: 44 PCGs, 19 tRNA genes, and 3 rRNA genes. The mitogenomes of the two species had complex structural features with high repeat numbers and chloroplast-derived sequences, as observed in other plant mitogenomes. Phylogenetic analysis based on PCGs revealed the taxonomical relationships of S. repanda and K. japonica with other species from Schisandraceae. Finally, molecular markers were developed to distinguish between S. repanda, K. japonica, and S. chinensis on the basis of InDel polymorphisms present in the mitogenomes. The mitogenomes of S. repanda and K. japonica will be valuable resources for molecular and taxonomic studies of plant species that belong to the family Schisandraceae.

Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers

Rice (Oryza sativa L.) is a staple food for more than 50% of the world's population. Rice cultivar improvement is critical in order to feed the world's growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security.

The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

BACKGROUND

Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated.

RESULTS

In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya.

CONCLUSIONS

The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.

Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin

The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA-psbE, ndhF-rpl32, and psbM-trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.

Complete chloroplast genome sequence of Solanum iopetalum, one of the tuber-bearing wild potato relatives

Solanum iopetalum belongs to the Solanaceae family and is one of the tuber-bearing wild Solanum species. In this study, chloroplast genome sequencing of the species, completed with Illumina sequencing technology, is presented. The length of the chloroplast genome is 155,625 bp with a GC content of 37.86%. It comprises a large single copy (LSC) region of 86,057 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,593 bp. Additionally, 158 functional genes in the genome are identified, including 105 protein-coding genes, 8 ribosomal RNAs, and 45 transfer RNAs. Phylogenetic analysis revealed that S. iopetalum is grouped into a large clade with other Solanum species, including cultivated potatoes (S. tuberosum) and is closely related to Mexican Solanum species (S. stoloniferum, S. verrucosum, S. hougasii, S. hjertingii, and S. demissum). This study provides useful genomic information for future breeding and evolutionary studies of S. iopetalum and other Solanum species.

The complete plastome of Cynanchum rostellatum (Apocynaceae), an indigenous plant in Korea

The climbing plant Cynanchum rostellatum (Turcz.) Liede & Khanum is widely distributed throughout Korea and Northeast Asia as a member of the Apocynaceae family. Although this plant has a high value in medicinal and industrial purposes, genetic research on this plant is insufficient. This study announces the complete plastid genome (plastome) sequence of C. rostellatum with 663× mean coverage, which was assembled using 763 Mbp short-read data generated by the Illumina HiSeq X platform. The C. rostellatum plastome was 158,018 bp in length and displayed the typical quadripartite structure composed of the large single-copy (LSC) region (89,058 bp), the small single-copy (SSC) region (18,718 bp), and a pair of inverted repeat (IR) regions (25,116 bp). A total of 129 genes have been annotated, including 84 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis indicated the genus Cynanchum including 12 Cynanchum plastome sequences, was monophyletic and was located within the sub-family Asclepiadoideae. Two C. rostellatum plastomes, including the plastome assembled in this study, formed a subclade and were sister to the C. thesioides plastome, whereas the other C. rostellatum, which was previously reported one, was located within the clade of C. wilfordii and C. bungei.

High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants

Chimeric plants composed of green and albino tissues have great ornamental value. To unveil the functional genes responsible for albino phenotypes in chimeric plants, we inspected the complete plastid genomes (plastomes) in green and albino leaf tissues from 23 ornamental chimeric plants belonging to 20 species, including monocots, dicots, and gymnosperms. In nine chimeric plants, plastomes were identical between green and albino tissues. Meanwhile, another 14 chimeric plants were heteroplasmic, showing a mutation between green and albino tissues. We identified 14 different point mutations in eight functional plastid genes related to plastid-encoded RNA polymerase (rpo) or photosystems which caused albinism in the chimeric plants. Among them, 12 were deleterious mutations in the target genes, in which early termination appeared due to small deletion-mediated frameshift or single nucleotide substitution. Another was single nucleotide substitution in an intron of the ycf3 and the other was a missense mutation in coding region of the rpoC2 gene. We inspected chlorophyll structure, protein functional model of the rpoC2, and expression levels of the related genes in green and albino tissues of Reynoutria japonica. A single amino acid change, histidine-to-proline substitution, in the rpoC2 protein may destabilize the peripheral helix of plastid-encoded RNA polymerase, impairing the biosynthesis of the photosynthesis system in the albino tissue of R. japonica chimera plant.

Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution

Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.

The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

Salix floderusii is a rare alpine tree species in the Salix genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of S. floderusii for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The S. floderusii cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of S. floderusii and Salix caprea were shorter than those of Salix cinerea, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the rpl22 coding region, psbM/trnD-GUC non-coding region, petA/psbJ non-coding region, and ycf1 coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future Salix species. In addition, phylogenetic analysis indicated that the cp genome of S. floderusii is sister to Salix cupularis and belongs to the Subgenus Vetrix. Genes (Sf-trnI, Sf-PpsbA, aadA, Sf-TpsbA, Sf-trnA) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene aadA. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the aadA gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent S. floderusii cp transformation systems and developing strategies for the genetic improvement of S. floderusii.

Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis

Background

Calanthe(Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of theCalanthealliance (Calanthe,Cephalantheropsis, andPhaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed ade novoassembly, and did a comparative analysis of 8Calanthegroup species' plastomes: 6Calantheand 2Phaiusspecies. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.

Results

The complete plastomes of theCalanthegroup species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost inC.delavayi(P. delavayi), includingndhC,ndhF, andndhKgenes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in theCalanthegroup, and confirmed the position ofPhaius delavayiin the genusCalantheas opposed to its previous placement inPhaius.

Conclusion

This study provides a report on the complete plastomes of 6Calantheand 2Phaiusspecies and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.

Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis

BACKGROUND

Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.

RESULTS

The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius.

CONCLUSION

This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.

Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow Endemic Calligonum bakuense

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice.

A large deletion within intron 20 sequence of single-copy PolA1 gene as a useful marker for the speciation in Oryza AA-genome species

Oryza AA-genome complex comprises five wild species, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1, a single-copy nuclear gene, was short (S-type: 141-142 bp) in O. rufipogon, O. barthii, and O. glumaepatula, while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis. Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata. As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AA-genome species.

Organization, Phylogenetic Marker Exploitation, and Gene Evolution in the Plastome of Thalictrum (Ranunculaceae)

Thalictrum is a phylogenetically and economically important genus in the family Ranunculaceae, but is also regarded as one of the most challengingly difficult in plants for resolving the taxonomical and phylogenetical relationships of constituent taxa within this genus. Here, we sequenced the complete plastid genomes of two Thalictrum species using Illumina sequencing technology via de novo assembly. The two Thalictrum plastomes exhibited circular and typical quadripartite structure that was rather conserved in overall structure and the synteny of gene order. By updating the previously reported plastome annotation of other nine Thalictrum species, we found that the expansion or contraction of the inverted repeat region affect the boundary of the single-copy regions in Thalictrum plastome. We identified eight highly variable noncoding regions-infA-rps8, ccsA-ndhD, trnSUGA-psbZ, trnHGUG-psbA, rpl16-rps3, ndhG-ndhI, ndhD-psaC, and ndhJ-ndhK-that can be further used for molecular identification, phylogenetic, and phylogeographic in different species. Selective pressure and codon usage bias of all the plastid coding genes were also analyzed for the 11 species. Phylogenetic relationships showed Thalictrum is monophyly and divided into two major clades based on 11 Thalictrum plastomes. The availability of these plastomes offers valuable genetic information for accurate identification of species and taxonomy, phylogenetic resolution, and evolutionary studies of Thalictrum, and should assist with exploration and utilization of Thalictrum plants.

The complete plastid genome sequence of Peucedanum hakuunense Nakai (Apiaceae), an endemic and rare species in Korea

Peucedanum hakuunense Nakai is one of the rare species in the Korean Peninsula. This study characterized the complete plastid genome (plastome) sequence of P. hakuunense by de novo assembly with next-generation sequencing data. The complete plastome of P. hakuunense is 147,426 bp in length with a typical quadripartite structure comprising a large single-copy region of 91,915 bp, a small single-copy region of 17,425 bp, and two inverted repeat regions of 19,043 bp in length. The plastome of P. hakuunense is composed of 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis revealed that two Peucedanum species formed an independent subclade, sister to the subclade of Angelica species within the tribe Selineae.

The complete chloroplast genome of Echeveria lilacina Kimnach & Moran 1980 (Saxifragales: Crassulaceae)

Echeveria lilacina Kimnach & Moran 1980 is a succulent plant having ornamental and ecological importance. In this study, the first complete chloroplast genome of Echeveria lilacina, a species belonging to the Crassulaceae family, was characterized from the de novo assembly of Illumina NovaSeq 6000 paired-end sequencing data. The chloroplast genome of E. lilacina is 150,080 bp in length, which includes a large single-copy (LSC) region of 81,741 bp, a small single-copy (SSC) region of 16,747 bp, and a pair of identical inverted repeat regions (IRs) of 25,796 bp each. The genome annotation revealed a total of 138 genes, including 87 protein-coding genes, 41 transfer RNA (tRNA) genes, and 10 ribosomal RNA (rRNA) genes. The phylogenetic analysis with 15 complete chloroplast genome sequences including outgroup showed that E. lilacina formed the closest taxonomical relationship with Graptopetalum amethystinum in the Crassulaceae family.

Complete Mitochondrial Genome Sequence of Colletotrichum siamense Isolated in South Korea

The complete mitochondrial genome of Colletotrichum siamense is characterized. The circular genome has a size of 52,710 bp, with a GC content of 34.45%, and contains 15 protein-coding genes, 23 tRNA genes, and 2 rRNA genes.

Comparative analysis of the complete plastid genomes in Prunus subgenus Cerasus (Rosaceae): Molecular structures and phylogenetic relationships

Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.

Complete chloroplast genome sequence of Solanum hjertingii, one of the wild potato relatives

Solanum hjertingii is a wild tuber-bearing species classified in the Solanaceae family. The chloroplast genome of S. hjertingii was completed via de novo assembly using Illumina paired-end sequencing data. Total length of the chloroplast genome of S. hjertingii is 155,545 bp consisting of 85,976 bp in a large single copy, 18,383 bp in a small single copy, and 25,593 bp in a pair of inverted repeat regions. Its structure is circular and typically quadripartite. It contains 158 predicted genes in total, including 105 protein-coding, 45 tRNA, and eight rRNA genes. Maximum likelihood phylogenetic analysis of the sequence along with 33 species in the Solanaceae family revealed that S. hjertingii belongs to a large clade with other Solanum species including S. tuberosum and is most closely grouped in the clade with S. hougasii and S. stoloniferum in the clade.

The complete mitochondrial genome of Turbo cornutus (Trochida: Turbinidae) and its phylogeny analysis

The complete mitochondrial genome sequence of Turbo cornutus, a species of the Turbinidae family, was characterized from the de novo assembly of Illumina paired-end sequencing data. The complete mitochondrial genome of T. cornutus was 17,297 bp in length and comprised of 13 protein-coding genes, 25 tRNAs, and two rRNAs. The base composition of T. cornutus exhibited a high A + T content of 71.17%. The phylogenetic analysis of T. cornutus with 14 species from GenBank revealed that the ancestor of Astralium haematragum and Bolma rugosa was diverged from T. cornutus.

High-throughput SNP markers for authentication of Korean wheat cultivars based on seven complete plastomes and the nuclear genome

Wheat (Triticum aestivum) has diverse uses in the food industry, and different cultivars have unique properties; therefore, it is important to select the optimal cultivar for the intended end use. Here, to establish an identification system for Korean wheat cultivars, we obtained the complete plastome sequences of seven major Korean cultivars. Additionally, the open access database CerealsDB was queried to discover single-copy genomic single-nucleotide polymorphisms (SNPs) in the hexaploid wheat genome. Ten SNPs were developed into allele-specific PCR (ASP) markers, and eight of the SNPs used for ASP markers were converted into TaqMan high-throughput genotyping markers. Phylogenetic analysis using SNP genotypes revealed the genetic diversity and relationships among 137 wheat lines from around the world, including 35 Korean cultivars. This research thus presents a high-throughput authentication system for Korean wheat cultivars that may promote food industry uses of Korean wheat.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01043-w.

Genetic and chemical markers for authentication of three Artemisia species: A. capillaris, A. gmelinii, and A. fukudo

The genus Artemisia is an important source of medicines in both traditional and modern pharmaceutics, particularly in East Asia. Despite the great benefits of herbal medicine, quality assessment methods for these medicinal herbs are lacking. The young leaves from Artemisia species are generally used, and most of the species have similar morphology, which often leads to adulteration and misuse. This study assembled five complete chloroplast genomes of three Artemisia species, two accessions of A. gmelinii and A. capillaris, and one A. fukudo. Through comparative analysis, we revealed genomic variations and phylogenetic relationships between these species and developed seven InDel-based barcode markers which discriminated the tested species from each other. Additionally, we analyzed specialized metabolites from the species using LC-MS and suggested chemical markers for the identification and authentication of these herbs. We expect that this integrated and complementary authentication method would aid in reducing the misuse of Artemisia species.

A Temporary Immersion System Improves Regeneration of In Vitro Irradiated Recalcitrant Indica Rice (Oryza sativa L.) Embryogenic Calli

The development of gamma ray-mutated rice lines is a solution for introducing genetic variability in indica rice varieties already being used by farmers. In vitro gamma ray (⁶⁰Co) mutagenesis reduces chimeras and allows for a faster selection of desirable traits but requires the optimization of the laboratory procedure. The objectives of the present work were sequencing of matK and rbcL, the in vitro establishment of recalcitrant rice embryogenic calli, the determination of their sensitivity to gamma radiation, and optimization of the generation procedure. All sequenced genes matched perfectly with previously reported matK and rbcL O. sativa genes. Embryogenic calli induction improved using MS medium containing 2 mg L^-1 2,4-D, and regeneration was achieved with MS medium with 3 mg L^-1 BA and 0.5 mg L^-1 NAA. The optimized radiation condition was 60 Gy, (LD20 = 64 Gy) with 83% regeneration. An immersion system (RITA^®, Saint-Mathieu-de-Tréviers, France) of either 60 or 120 s every 8 h allowed systematic and homogeneous total regeneration of the recalcitrant line. Other well-known recalcitrant cultivars, CR1821 and CR1113, also had improved regeneration in the immersion system. To our knowledge, this is the first study reporting the use of an immersion system to allow for the regeneration of gamma-ray mutants from recalcitrant indica rice materials.

Genome structure and diversity among Cynanchum wilfordii accessions

BACKGROUND

Cynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information.

RESULTS

We collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events.

CONCLUSIONS

Cw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.

PanaxGDB: A Comprehensive Platform for Panax

The genus Panax is a valuable natural medicinal source used worldwide that contains high levels of triterpenoid saponins with extensive pharmacological activities. In past decades, molecular biotechnology and breeding techniques have been respectively used to generate omics data and information on cultivars primarily from Panax ginseng (ginseng), Panax quinquefolium (American ginseng), and Panax notoginseng (Sanqi) to biosynthesize valuable saponins, improve product quality, and conduct cost-controlled cultivation. Although much data have been produced, there are concerns that redundant data might be generated and that relatively scattered data might be overlooked. Therefore, many scientists desire a reliable, comprehensive omics database of the Panax genus that could save time and promote integrated analysis. Therefore, to provide all-inclusive, reliable, and valuable information on the Panax genus, PanaxGDB, an open comprehensive database that integrates data on omics and information on varieties, was established. The database contains information on nearly 600 compounds from 12 Panax species, draft genomic sequences with annotations and gene expression levels, single nucleotide polymorphisms, genome-wide association analysis based on agronomic traits, globally collected germplasm information, summaries, omics data of the Panax genus, and online versatile analytic tools. The Panax genus database will be updated when new data are released to continue serving as a central portal to boost research on the biology and functions of Panax. PanaxGDB is available at: http://panaxGDB.ynau.edu.cn.

Complete Chloroplast Genome of the Inverted Repeat-Lacking Species Vicia bungei and Development of Polymorphic Simple Sequence Repeat Markers

BACKGROUND

Vicia bungei is an economically important forage crop in South Korea and China. Although detailed genetic and genomic data can improve population genetic studies, conservation efforts, and improved breeding of crops, few such data are available for Vicia species in general and none at all for V. bungei. Therefore, the main objectives of this study were to sequence, assemble, and annotate V. bungei chloroplast genome and to identify simple sequence repeats (SSRs) as polymorphic genetic markers.

RESULTS

The whole-genome sequence of V. bungei was generated using an Illumina MiSeq platform. De novo assembly of complete chloroplast genome sequences was performed for the low-coverage sequence using CLC Genome Assembler with a 200-600-bp overlap size. Vicia bungei chloroplast genome was 130,796-bp long. The genome lacked an inverted repeat unit and thus resembled those of species in the inverted repeat-lacking clade within Fabaceae. Genome annotation using Dual OrganellarGenoMe Annotator (DOGMA) identified 107 genes, comprising 75 protein-coding, 28 transfer RNA, and 4 ribosomal RNA genes. In total, 432 SSRs were detected in V. bungei chloroplast genome, including 64 mononucleotides, 14 dinucleotides, 5 trinucleotides, 4 tetranucleotides, 233 pentanucleotides, 90 hexanucleotides, and 14 complex repeated motifs. These were used to develop 232 novel chloroplast SSR markers, 39 of which were chosen at random to test amplification and genetic diversity in Vicia species (20 accessions from seven species). The unweighted pair group method with arithmetic mean cluster analysis identified seven clusters at the interspecies level and intraspecific differences within clusters.

CONCLUSION

The complete chloroplast genome sequence of V. bungei was determined. This reference genome should facilitate chloroplast resequencing and future searches for additional genetic markers using population samples. The novel chloroplast genome resources and SSR markers will greatly contribute to the conservation of the genus Vicia and facilitate genetic and evolutionary studies of this genus and of other higher plants.

Complete chloroplast genome of Gypsophila oldhamiana Miq. (Caryophyllales: Caryophyllaceae)

The complete chloroplast genome sequence of Gypsophila oldhamiana Miq., a species of the Caryophyllaceae family, was assembled and analyzed from the de novo assembly of Illumina paired-end sequencing data. The total length of the chloroplast genome of G. oldhamiana was 152,675 bp including a large single-copy (LSC) region of 83,552 bp, a small single-copy (SSC) region of 17,349 bp, and a pair of identical inverted repeat regions (IRs) of 25,887 bp. The genome possessed a total of 130 genes, including 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis of G. oldhamiana with 14 related species discovered the closest taxonomical relationship with Gypsophila vaccaria voucher in the Caryophyllaceae family.

Complete Plastome of Three Korean Asarum (Aristolochiaceae): Confirmation Tripartite Structure within Korean Asarum and Comparative Analyses

The genus Asarum (Aristolochiaceae) is a well-known resource of medicinal and ornamental plants. However, the taxonomy of Korean Asarum is ambiguous due to their considerable morphological variations. Previously, a unique plastome structure has been reported from this genus. Therefore, we investigated the structural change in the plastomes within three Korean Asarum species and inferred their phylogenetic relationships. The plastome sizes of Asarum species assembled here range from 190,168 to 193,356 bp, which are longer than a typical plastome size (160 kb). This is due to the incorporation and duplication of the small single copy into the inverted repeat, which resulted in a unique tripartite structure. We first verified this unique structure using the Illumina Miseq and Oxford Nanopore MinION platforms. We also investigated the phylogeny of 26 Aristolochiaceae species based on 79 plastid protein-coding genes, which supports the monophyly of Korean Asarum species. Although the 79 plastid protein-coding gene data set showed some limitations in supporting the previous classification, it exhibits its effectiveness in delineating some sections and species. Thus, it can serve as an effective tool for resolving species-level phylogeny in Aristolochiaceae. Last, we evaluated variable sites and simple sequence repeats in the plastome as potential molecular markers for species delimitation.

Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis, identification of mutational hotspots and evolutionary dynamics with species of Solanales

Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa 'Evolvulus' could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01051-w.

Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships

The genus Pennisetum (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of Pennisetum (P. alopecuroides, P. clandestinum, P. glaucum, and P. polystachion) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions (psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL, and rpl32-trnL), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of Pennisetum. The phylogenetic analysis revealed a close relationship between P. polystachion and P. glaucum, followed by P. clandestinum and P. alopecuroides. The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of Pennisetum species.

Complete mitogenome and phylogenetic analysis of two species (Mareca penelope and Mareca falcate)

We determined the complete mitogenomes of two wigeons, Mareca penelope (16,603 bp) and Mareca falcata (16,597 bp) of the family Anatidae using Illumina next-generation sequencing to better understand phylogenetic relationships. Both species consisted of 37 genes (13 protein-coding genes), two ribosomal RNAs, 22 transfer RNAs, and one control region. A + T content (M. penelope 51.25%, M. falcata 51.2%) was slightly higher than G + C content (M. penelope 48.75%, M. falcata 48.8%). Phylogenetic analysis based on 13 concatenated PCG sequences indicated that M. penelope and M. falcata belong to the Mareca genus, with high bootstrap values.

Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia (Piperaceae)

Biological radiations provide unique opportunities to understand the evolution of biodiversity. One such radiation is the pepper plant family Piperaceae, an early-diverging and mega-diverse lineage that could serve as a model to study the diversification of angiosperms. However, traditional genetic markers lack sufficient variation for such studies, and testing hypotheses on poorly resolved phylogenetic frameworks becomes challenging. Limited genomic data is available for Piperaceae, which contains two of the largest genera of angiosperms, Piper (>2100 species) and Peperomia (>1300 species). To address this gap, we used genome skimming to assemble and annotate whole plastomes (152-161kbp) and >5kbp nuclear ribosomal DNA region from representatives of Piper and Peperomia. We conducted phylogenetic and comparative genomic analyses to study plastome evolution and investigate the role of hybridization in this group. Plastome phylogenetic trees were well resolved and highly supported, with a hard incongruence observed between plastome and nuclear phylogenetic trees suggesting hybridization in Piper. While all plastomes of Piper and Peperomia had the same gene content and order, there were informative structural differences between them. First, ycf1 was more variable and longer in Piper than Peperomia, extending well into the small single copy region by thousands of base pairs. We also discovered previously unknown structural variation in 14 out of 25 Piper taxa, tandem duplication of the trnH-GUG gene resulting in an expanded large single copy region. Other early-diverging angiosperms have a duplicated trnH-GUG, but the specific rearrangement we found is unique to Piper and serves to refine knowledge of relationships among early-diverging angiosperms. Our study demonstrates that genome skimming is an efficient approach to produce plastome assemblies for comparative genomics and robust phylogenies of species-rich plant genera.

Diversity and authentication of Rubus accessions revealed by complete plastid genome and rDNA sequences

Complete plastid genome (plastome) and ribosomal DNA (rDNA) sequences of three Rubus accessions (two Rubus longisepalus and one R. hirsutus) were newly assembled using Illumina whole-genome sequences. Rubus longisepalus Nakai and R. longisepalus var. tozawai, described as different varieties, have identical plastomes and rDNA sequences. The plastomes are 155,957 bp and 156,005 bp and the 45S rDNA transcription unit sizes are 5809 bp and 5811 bp in R. longisepalus and R. hirsutus, respectively. The 5S rDNA transcription unit is an identical 121 bp in three Rubus accessions. We developed three DNA markers to authenticate R. longisepalus and R. hirsutus based on plastome diversity. Phylogenomic analysis revealed that the Rubus species classified as two clades and R. longisepalus, R. hirsutus, and R. chingii are the most closely related species in clade 1.