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Introduction: Citrus canker, caused by Xanthomonas citri subsp. citri (Xcc), is a devastating disease worldwide. Previously, we successfully generated cankerresistant Citrus sinensis cv. Hamlin lines in the T0 generation. This was achieved through the transformation of embryogenic protoplasts using the ribonucleoprotein (RNP) containing Cas12a and one crRNA to edit the canker susceptibility gene, CsLOB1, which led to small indels. Methods: Here, we transformed embryogenic protoplasts of Hamlin with RNP containing Cas12a and three crRNAs. Results: Among the 10 transgene-free genome-edited lines, long deletions were obtained in five lines. Additionally, inversionswere observed in three of the five edited lines with long deletions, but not in any edited lines with short indel mutations, suggesting long deletions maybe required for inversions. Biallelic mutations were observed for each of the three target sites in four of the 10 edited lines when three crRNAs were used, demonstrating that transformation of embryogenic citrus protoplasts with Cas12a and three crRNAs RNP can be very efficient for multiplex editing. Our analysis revealed the absence of off-target mutations in the edited lines. These cslob1 mutant lines were canker-resistant and no canker symptoms were observed after inoculation with Xcc and Xcc growth was significantly reduced in the cslob1 mutant lines compared to the wild type plants. Discussion: Taken together, RNP (Cas12a and three crRNAs) transformation of embryogenic protoplasts of citrus provides a promising solution for transgene-free multiplex genome editing with high efficiency and for deletion of long fragments. [ABSTRACT FROM AUTHOR]

Introduction: During plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed. Methods: In this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome). Results and Discussion: We identified the putative functional transfers of the mitochondrial genes 5' rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineagespecific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome. This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae. [ABSTRACT FROM AUTHOR]

Elymus nutans is an allopolyploid with a genome constitution of StStYYHH (2 n = 6 x = 42). Highly frequent intergenomic translocations and chromosomal variations with repeat amplification and deletions in E. nutans have been identified in the previous studies. However, more complicated structural variations such as chromosomal inversions or intra-genomic translocations are still unknown in this species, so does the reason for the origin of the chromosomal variations. Heterozygotes with rearranged chromosomes always present irregular meiosis behaviors, which subsequently cause the secondary chromosome rearrangements. Investigation on the meiosis of heterozygotes, especially on the individual chromosome level, may provide the important clues to identify the more complicated chromosome structural variations in the populations, and clarify the origin of the chromosome variations. In this study, meiotic analysis was conducted on a heterozygote plant of Elymus nutans , which showed high intra- and inter-genome chromosomal variations, by sequential fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH), with each chromosome clearly recognized. The results showed chromosomal abnormalities at every meiotic stage and abnormalities in frequency variations between different sub-genomes and different individual chromosomes. The abnormalities were revealed as univalent, fragment, rod, or Y shape bivalent in diakinesis; univalent and rod bivalent in metaphase I; lagged and segregated chromatid, bridge, fragment of the sister chromatid, fragment, bridge accompanied with fragment, and unequal segregated chromosome in anaphase I; bridge and lagged chromatid in ana-telophase II; and micronucleus at uninucleate stage. Generally, the St and H genomes harbor more abnormalities than the Y genome. Moreover, a paracentric inversion in 2St was exclusively determined, and another paracentric inversion in 6Y was tentatively identified. In addition, novel deletions were clearly detected in 3H, 4H, 1Y, and 3Y homologous chromosomes; in particular, de novo pericentric inversion in 3H was repeatedly identified in metaphase I. The study revealed the chromosomal inversions pre-existed in parents or populations, as well as de novo inversions and deletions originated in the meiosis of the heterozygote in E. nutans. Moreover, it indicated wide range of meiosis abnormalities on different stages and different chromosomes, and suggests that secondary rearrangements contribute much to the chromosome variations in E. nutans. [ABSTRACT FROM AUTHOR]

Elymus nutans is an allopolyploid with a genome constitution of StStYYHH (2n = 6x = 42). Highly frequent intergenomic translocations and chromosomal variations with repeat amplification and deletions in E. nutans have been identified in the previous studies. However, more complicated structural variations such as chromosomal inversions or intra-genomic translocations are still unknown in this species, so does the reason for the origin of the chromosomal variations. Heterozygotes with rearranged chromosomes always present irregular meiosis behaviors, which subsequently cause the secondary chromosome rearrangements. Investigation on the meiosis of heterozygotes, especially on the individual chromosome level, may provide the important clues to identify the more complicated chromosome structural variations in the populations, and clarify the origin of the chromosome variations. In this study, meiotic analysis was conducted on a heterozygote plant of Elymus nutans, which showed high intra- and inter-genome chromosomal variations, by sequential fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH), with each chromosome clearly recognized. The results showed chromosomal abnormalities at every meiotic stage and abnormalities in frequency variations between different sub-genomes and different individual chromosomes. The abnormalities were revealed as univalent, fragment, rod, or Y shape bivalent in diakinesis; univalent and rod bivalent in metaphase I; lagged and segregated chromatid, bridge, fragment of the sister chromatid, fragment, bridge accompanied with fragment, and unequal segregated chromosome in anaphase I; bridge and lagged chromatid in ana-telophase II; and micronucleus at uninucleate stage. Generally, the St and H genomes harbor more abnormalities than the Y genome. Moreover, a paracentric inversion in 2St was exclusively determined, and another paracentric inversion in 6Y was tentatively identified. In addition, novel deletions were clearly detected in 3H, 4H, 1Y, and 3Y homologous chromosomes; in particular, de novo pericentric inversion in 3H was repeatedly identified in metaphase I. The study revealed the chromosomal inversions pre-existed in parents or populations, as well as de novo inversions and deletions originated in the meiosis of the heterozygote in E. nutans. Moreover, it indicated wide range of meiosis abnormalities on different stages and different chromosomes, and suggests that secondary rearrangements contribute much to the chromosome variations in E. nutans.

Introduction: Citrus canker, caused by Xanthomonas citri subsp. citri ( Xcc ), is a devastating disease worldwide. Previously, we successfully generated canker-resistant Citrus sinensis cv. Hamlin lines in the T0 generation. This was achieved through the transformation of embryogenic protoplasts using the ribonucleoprotein (RNP) containing Cas12a and one crRNA to edit the canker susceptibility gene, CsLOB1 , which led to small indels., Methods: Here, we transformed embryogenic protoplasts of Hamlin with RNP containing Cas12a and three crRNAs., Results: Among the 10 transgene-free genome-edited lines, long deletions were obtained in five lines. Additionally, inversions were observed in three of the five edited lines with long deletions, but not in any edited lines with short indel mutations, suggesting long deletions maybe required for inversions. Biallelic mutations were observed for each of the three target sites in four of the 10 edited lines when three crRNAs were used, demonstrating that transformation of embryogenic citrus protoplasts with Cas12a and three crRNAs RNP can be very efficient for multiplex editing. Our analysis revealed the absence of off-target mutations in the edited lines. These cslob1 mutant lines were canker- resistant and no canker symptoms were observed after inoculation with Xcc and Xcc growth was significantly reduced in the cslob1 mutant lines compared to the wild type plants., Discussion: Taken together, RNP (Cas12a and three crRNAs) transformation of embryogenic protoplasts of citrus provides a promising solution for transgene-free multiplex genome editing with high efficiency and for deletion of long fragments., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Su, Wang, Xu, Omar, Grosser and Wang.)

Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M2 lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects. [ABSTRACT FROM AUTHOR]

Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M2 lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects.

Hepatica is a small genus of Ranunculaceae with medicinal and horticultural value. We characterized nine complete chloroplast (cp) genomes of Hepatica, which ranged from 159,549 to 161,081 bp in length and had a typical quadripartite structure with a large single-copy region (LSC; 80,270–81,249 bp), a small single-copy region (SSC; 17,029–17,838 bp), and two copies of inverted repeat (IR; 31,008–31,100 bp). The cp genomes of Hepatica possess 76 protein-coding genes (PCGs), 29 tRNAs, and four rRNA genes. Comparative analyses revealed a conserved ca. 5-kb IR expansion in Hepatica and other Anemoneae; moreover, multiple inversion events occurred in Hepatica and its relatives. Analyses of selection pressure (dN/dS) showed that most of the PCGs are highly conserved except for rpl20 and rpl22 in Hepatica falconeri, Hepatica americana, and Hepatica acutiloba. Two genes (rps16 and infA) were identified as pseudogenes in Hepatica. In contrast, rpl32 gene was completely lost. The phylogenetic analyses based on 76 PCGs resolved the phylogeny of Hepatica and its related genera. Non-monophyly of Anemone s.l. indicates that Hepatica should be reclassified as an independent genus. In addition, Hepatica nobilis var. japonica is not closely related to H. nobilis.

Hepatica is a small genus of Ranunculaceae with medicinal and horticultural value. We characterized nine complete chloroplast (cp) genomes of Hepatica , which ranged from 159,549 to 161,081 bp in length and had a typical quadripartite structure with a large single-copy region (LSC; 80,270–81,249 bp), a small single-copy region (SSC; 17,029–17,838 bp), and two copies of inverted repeat (IR; 31,008–31,100 bp). The cp genomes of Hepatica possess 76 protein-coding genes (PCGs), 29 tRNAs, and four rRNA genes. Comparative analyses revealed a conserved ca. 5-kb IR expansion in Hepatica and other Anemoneae; moreover, multiple inversion events occurred in Hepatica and its relatives. Analyses of selection pressure (dN / dS) showed that most of the PCGs are highly conserved except for rpl20 and rpl22 in Hepatica falconeri , Hepatica americana , and Hepatica acutiloba. Two genes (rps16 and infA) were identified as pseudogenes in Hepatica. In contrast, rpl32 gene was completely lost. The phylogenetic analyses based on 76 PCGs resolved the phylogeny of Hepatica and its related genera. Non-monophyly of Anemone s.l. indicates that Hepatica should be reclassified as an independent genus. In addition, Hepatica nobilis var. japonica is not closely related to H. nobilis. [ABSTRACT FROM AUTHOR]

This finding agrees with the previous studies on the independent loss of I rpsl2, rps16 i , and I clpP i introns in the MP clade (Guo et al.,[6]; Schwarz et al., [10]; Kaila et al., [7]). Inversion, Leguminosae, Plastome, the Millettioid/Phaseoloid clade, evolutionary relationships, IR expansion/contraction This finding agrees with the previous studies on the independent loss of I rpsl2, rps16 i , and I clpP i introns in the MP clade (Guo et al., [6]; Schwarz et al., [10]; Kaila et al., [7]). Keywords: evolutionary relationships; inversion; IR expansion/contraction; Leguminosae; Plastome; the Millettioid/Phaseoloid clade EN evolutionary relationships inversion IR expansion/contraction Leguminosae Plastome the Millettioid/Phaseoloid clade N.PAG N.PAG 4 03/03/21 20210301 NES 210301 In the original article, there was a mistake in the legend for Table 1 as published. [Extracted from the article]

The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced Corydalis plastomes that represent all the three subgenera of Corydalis, we detected (1) two independent relocations of the same five genes (trnV-UAC-rbcL) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the atpH gene in Corydalis saxicola or the trnK-UUU gene in both Corydalis davidii and Corydalis hsiaowutaishanensis; (2) relocation of the rps16 gene from the LSC region to the inverted repeat (IR) region in Corydalis adunca; (3) uniform inversion of an 11–14 kb segment (ndhB-trnR-ACG) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes (accD, clpP, and 11 ndh genes). In addition, we also found that the four Corydalis plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three Corydalis subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of Corydalis.

The size of the chloroplast genome (plastome) of autotrophic angiosperms is generally conserved. However, the chloroplast genomes of some lineages are greatly expanded, which may render assembling these genomes from short read sequencing data more challenging. Here, we present the sequencing, assembly, and annotation of the chloroplast genomes of Cypripedium tibeticum and Cypripedium subtropicum. We de novo assembled the chloroplast genomes of the two species with a combination of short-read Illumina data and long-read PacBio data. The plastomes of the two species are characterized by expanded genome size, proliferated AT-rich repeat sequences, low GC content and gene density, as well as low substitution rates of the coding genes. The plastomes of C. tibeticum (197,815 bp) and C. subtropicum (212,668 bp) are substantially larger than those of the three species sequenced in previous studies. The plastome of C. subtropicum is the longest one of Orchidaceae to date. Despite the increase in genome size, the gene order and gene number of the plastomes are conserved, with the exception of an ∼75 kb large inversion in the large single copy (LSC) region shared by the two species. The most striking is the record-setting low GC content in C. subtropicum (28.2%). Moreover, the plastome expansion of the two species is strongly correlated with the proliferation of AT-biased non-coding regions: the non-coding content of C. subtropicum is in excess of 57%. The genus provides a typical example of plastome expansion induced by the expansion of non-coding regions. Considering the pros and cons of different sequencing technologies, we recommend hybrid assembly based on long and short reads applied to the sequencing of plastomes with AT-biased base composition. [ABSTRACT FROM AUTHOR]

The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced Corydalis plastomes that represent all the three subgenera of Corydalis , we detected (1) two independent relocations of the same five genes (trnV-UAC - rbcL) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the atpH gene in Corydalis saxicola or the trnK-UUU gene in both Corydalis davidii and Corydalis hsiaowutaishanensis ; (2) relocation of the rps16 gene from the LSC region to the inverted repeat (IR) region in Corydalis adunca ; (3) uniform inversion of an 11–14 kb segment (ndhB - trnR-ACG) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes (accD , clpP , and 11 ndh genes). In addition, we also found that the four Corydalis plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three Corydalis subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of Corydalis. [ABSTRACT FROM AUTHOR]

The Millettioid/Phaseoloid (MP) clade from the subfamily Papilionoideae (Leguminosae) consists of six tribes and ca. 3,000 species. Previous studies have revealed some plastome structural variations (PSVs) within this clade. However, many deep evolutionary relationships within the clade remain unresolved. Due to limited taxon sampling and few genetic markers in previous studies, our understanding of the evolutionary history of this clade is limited. To address this issue, we sampled 43 plastomes (35 newly sequenced) representing all the six tribes of the MP clade to examine genomic structural variations and phylogenetic relationships. Plastomes of the species from the MP clade were typically quadripartite (size ranged from 140,029 to 160,040 bp) and contained 109–111 unique genes. We revealed four independent gene losses (ndhF, psbI, rps16, and trnS-GCU), multiple IR-SC boundary shifts, and six inversions in the tribes Desmodieae, Millettieae, and Phaseoleae. Plastomes of the species from the MP clade have experienced significant variations which provide valuable information on the evolution of the clade. Plastid phylogenomic analyses using Maximum Likelihood and Bayesian methods yielded a well-resolved phylogeny at the tribal and generic levels within the MP clade. This result indicates that plastome data is useful and reliable data for resolving the evolutionary relationships of the MP clade. This study provides new insights into the phylogenetic relationships and PSVs within this clade.

The Millettioid/Phaseoloid (MP) clade from the subfamily Papilionoideae (Leguminosae) consists of six tribes and ca. 3,000 species. Previous studies have revealed some plastome structural variations (PSVs) within this clade. However, many deep evolutionary relationships within the clade remain unresolved. Due to limited taxon sampling and few genetic markers in previous studies, our understanding of the evolutionary history of this clade is limited. To address this issue, we sampled 43 plastomes (35 newly sequenced) representing all the six tribes of the MP clade to examine genomic structural variations and phylogenetic relationships. Plastomes of the species from the MP clade were typically quadripartite (size ranged from 140,029 to 160,040 bp) and contained 109–111 unique genes. We revealed four independent gene losses (ndhF , psbI , rps16 , and trnS-GCU), multiple IR-SC boundary shifts, and six inversions in the tribes Desmodieae, Millettieae, and Phaseoleae. Plastomes of the species from the MP clade have experienced significant variations which provide valuable information on the evolution of the clade. Plastid phylogenomic analyses using Maximum Likelihood and Bayesian methods yielded a well-resolved phylogeny at the tribal and generic levels within the MP clade. This result indicates that plastome data is useful and reliable data for resolving the evolutionary relationships of the MP clade. This study provides new insights into the phylogenetic relationships and PSVs within this clade. [ABSTRACT FROM AUTHOR]

Bimodal karyotypes are characterized by the presence of two sets of chromosomes of contrasting size. Eleutherine bulbosa (2n = 12) presents a bimodal karyotype with a large chromosome pair, which has a pericentric inversion in permanent heterozygosity with suppressed recombination, and five pairs of three to four times smaller chromosomes. Aiming to understand whether high copy number sequence composition differs between both chromosome sets, we investigated the repetitive DNA fraction of E. bulbosa and compared it to the chromosomal organization of the related Eleutherine latifolia species, not containing the pericentric inversion. We also compared the repetitive sequence proportions between the heteromorphic large chromosomes of E. bulbosa and between E. bulbosa and E. latifolia to understand the influence of the chromosome inversion on the dynamics of repetitive sequences. The most abundant repetitive families of the genome showed a similar chromosomal distribution in both homologs of the large pair and in both species, apparently not influenced by the species-specific inversions. The repeat families Ebusat1 and Ebusat4 are localized interstitially only on the large chromosome pair, while Ebusat2 is located in the centromeric region of all chromosomes. The four most abundant retrotransposon lineages are accumulated in the large chromosome pair. Replication timing and distribution of epigenetic and transcriptional marks differ between large and small chromosomes. The differential distribution of retroelements appears to be related to the bimodal condition and is not influenced by the nonrecombining chromosome inversions in these species. Thus, the large and small chromosome subgenomes of the bimodal Eleutherine karyotype are differentially organized and probably evolved by repetitive sequences accumulation on the large chromosome set.

Introduction: During plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed., Methods: In this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome)., Results and Discussion: We identified the putative functional transfers of the mitochondrial genes 5' rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineage-specific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome . This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Park and Park.)

Bimodal karyotypes are characterized by the presence of two sets of chromosomes of contrasting size. Eleutherine bulbosa (2 n = 12) presents a bimodal karyotype with a large chromosome pair, which has a pericentric inversion in permanent heterozygosity with suppressed recombination, and five pairs of three to four times smaller chromosomes. Aiming to understand whether high copy number sequence composition differs between both chromosome sets, we investigated the repetitive DNA fraction of E. bulbosa and compared it to the chromosomal organization of the related Eleutherine latifolia species, not containing the pericentric inversion. We also compared the repetitive sequence proportions between the heteromorphic large chromosomes of E. bulbosa and between E. bulbosa and E. latifolia to understand the influence of the chromosome inversion on the dynamics of repetitive sequences. The most abundant repetitive families of the genome showed a similar chromosomal distribution in both homologs of the large pair and in both species, apparently not influenced by the species-specific inversions. The repeat families Ebusat1 and Ebusat4 are localized interstitially only on the large chromosome pair, while Ebusat2 is located in the centromeric region of all chromosomes. The four most abundant retrotransposon lineages are accumulated in the large chromosome pair. Replication timing and distribution of epigenetic and transcriptional marks differ between large and small chromosomes. The differential distribution of retroelements appears to be related to the bimodal condition and is not influenced by the nonrecombining chromosome inversions in these species. Thus, the large and small chromosome subgenomes of the bimodal Eleutherine karyotype are differentially organized and probably evolved by repetitive sequences accumulation on the large chromosome set. [ABSTRACT FROM AUTHOR]

Structural rearrangements of Anemone species' chloroplast genome has been reported based on genetic mapping of restriction sites but has never been confirmed by genomic studies. We used a next-generation sequencing method to characterize the complete chloroplast genomes of five species in the tribe Anemoneae. Plastid genomes were assembled using de novo assembling methods combined with conventional Sanger sequencing to fill the gaps. The gene order of the chloroplast genomes of tribe Anemoneae was compared with that of other Ranunculaceae species. Multiple inversions and transpositions were detected in tribe Anemoneae. Anemoclema, Anemone, Hepatica, and Pulsatilla shared the same gene order, which contained three inversions in the large single copy region (LSC) compared to other Ranunculaceae genera. Archiclematis, Clematis, and Naravelia shared the same gene order containing two inversions and one transposition in LSC. A roughly 4.4 kb expansion region in inverted repeat (IR) regions was detected in tribe Anemoneae, suggesting that this expansion event may be a synapomorphy for this group. Plastome phylogenomic analyses using parsimony and a Bayesian method with implementation of partitioned models generated a well resolved phylogeny of Ranunculaceae. These results suggest that evaluation of chloroplast genomes may result in improved resolution of family phylogenies. Samples of Anemone, Hepatica, and Pulsatilla were tested to form paraphyletic grades within tribe Anemoneae. Anemoclema was a sister clade to Clematis. Structual variation of the plastid genome within tribe Anemoneae provided strong phylogenetic information for Ranunculaceae.

The subfamily Cercidoideae is an early-branching legume lineage, which consists of 13 genera distributed in the tropical and warm temperate Northern Hemisphere. A previous study detected two plastid genomic variations in this subfamily, but the limited taxon sampling left the overall plastid genome (plastome) diversification across the subfamily unaddressed, and phylogenetic relationships within this clade remained unresolved. Here, we assembled eight plastomes from seven Cercidoideae genera and conducted phylogenomic-comparative analyses in a broad evolutionary framework across legumes. The plastomes of Cercidoideae all exhibited a typical quadripartite structure with a conserved gene content typical of most angiosperm plastomes. Plastome size ranged from 151,705 to 165,416 bp, mainly due to the expansion and contraction of inverted repeat (IR) regions. The order of genes varied due to the occurrence of several inversions. In Tylosema species, a plastome with a 29-bp IR-mediated inversion was found to coexist with a canonical-type plastome, and the abundance of the two arrangements of isomeric molecules differed between individuals. Complete plastome data were much more efficient at resolving intergeneric relationships of Cercidoideae than the previously used selection of only a few plastid or nuclear loci. In sum, our study revealed novel insights into the structural diversification of plastomes in an early-branching legume lineage, and, thus, into the evolutionary trajectories of legume plastomes in general.

The subfamily Cercidoideae is an early-branching legume lineage, which consists of 13 genera distributed in the tropical and warm temperate Northern Hemisphere. A previous study detected two plastid genomic variations in this subfamily, but the limited taxon sampling left the overall plastid genome (plastome) diversification across the subfamily unaddressed, and phylogenetic relationships within this clade remained unresolved. Here, we assembled eight plastomes from seven Cercidoideae genera and conducted phylogenomic-comparative analyses in a broad evolutionary framework across legumes. The plastomes of Cercidoideae all exhibited a typical quadripartite structure with a conserved gene content typical of most angiosperm plastomes. Plastome size ranged from 151,705 to 165,416 bp, mainly due to the expansion and contraction of inverted repeat (IR) regions. The order of genes varied due to the occurrence of several inversions. In Tylosema species, a plastome with a 29-bp IR-mediated inversion was found to coexist with a canonical-type plastome, and the abundance of the two arrangements of isomeric molecules differed between individuals. Complete plastome data were much more efficient at resolving intergeneric relationships of Cercidoideae than the previously used selection of only a few plastid or nuclear loci. In sum, our study revealed novel insights into the structural diversification of plastomes in an early-branching legume lineage, and, thus, into the evolutionary trajectories of legume plastomes in general. [ABSTRACT FROM AUTHOR]

Wild emmer (Triticum turgidum ssp. dicoccoides) is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. ‘Langdon’ x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum–Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.

Wild emmer (Triticum turgidum ssp. dicoccoides) is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. 'Langdon' x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 cosegregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum-Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling. [ABSTRACT FROM AUTHOR]

Structural rearrangements of Anemone species' chloroplast genome has been reported based on genetic mapping of restriction sites but has never been confirmed by genomic studies. We used a next-generation sequencing method to characterize the complete chloroplast genomes of five species in the tribe Anemoneae. Plastid genomes were assembled using de novo assembling methods combined with conventional Sanger sequencing to fill the gaps. The gene order of the chloroplast genomes of tribe Anemoneae was compared with that of other Ranunculaceae species. Multiple inversions and transpositions were detected in tribe Anemoneae. Anemoclema, Anemone, Hepatica , and Pulsatilla shared the same gene order, which contained three inversions in the large single copy region (LSC) compared to other Ranunculaceae genera. Archiclematis, Clematis , and Naravelia shared the same gene order containing two inversions and one transposition in LSC. A roughly 4.4 kb expansion region in inverted repeat (IR) regions was detected in tribe Anemoneae, suggesting that this expansion event may be a synapomorphy for this group. Plastome phylogenomic analyses using parsimony and a Bayesian method with implementation of partitioned models generated a well resolved phylogeny of Ranunculaceae. These results suggest that evaluation of chloroplast genomes may result in improved resolution of family phylogenies. Samples of Anemone, Hepatica , and Pulsatilla were tested to form paraphyletic grades within tribe Anemoneae. Anemoclema was a sister clade to Clematis . Structual variation of the plastid genome within tribe Anemoneae provided strong phylogenetic information for Ranunculaceae.