MISA-web: a web server for microsatellite prediction

Exploring the innate immune system of Urechis unicinctus: Insights from full-length transcriptome analysis

The Echiura worm Urechis unicinctus refers to a common benthic invertebrate found in the intertidal zone of Huanghai as well as Bohai Bay. U. unicinctus is known to contain various physiologically active substances, making it highly valuable in terms of its edibility, medicinal properties, and economic potential. Nonetheless, the limited study on the immune system of U. unicinctus poses difficulties for its aquaculture and artificial reproduction. Marine invertebrates, including shellfish and U. unicinctus, are thought to primarily depend on their innate immune system for disease protection, owing to the severalinnate immune molecules they possess. Herein, we employed PacBio single-molecule real-time (SMRT) sequencing technology to perform the full-length transcriptome analysis of U. unicinctus individuals under five different conditions (room temperature (RT), low temperature (LT), high temperature (HT), without water (DRY), ultraviolet irradiation (UV)). Concequently, we identified 59,371 unigenes that had a 2,779 bp average length, 2,613 long non-coding RNAs (lncRNAs), 59,190 coding sequences (CDSs), 35,166 simple sequence repeats (SSRs), and 1,733 transcription factors (TFs), successfully annotating 90.58 % (53,778) of the unigenes. Subsequently, key factors associated with immune-related processes, such as non-self-recognition, cellular immune defenses, and humoral immune defenses, were searched. Our study also identified pattern recognition receptors (PRRs) that included 17 peptidoglycan recognition proteins (PGRPs), 13 Gram-negative binding proteins (GNBPs), 18 scavenger receptors (SRs), 74 toll-like receptors (TLRs), and 89 C-type lectins (CLTs). Altogether, the high-quality transcriptome obtained data will offer valuable insights for further investigations into U. unicinctus innate immune response, laying the foundation for subsequent molecular biology studies and aquaculture.

Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion

BACKGROUND

Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal ("SP"), double-petal ("DP"), and multi-petal ("MP"). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions.

RESULTS

Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, "SP", "DP", and "MP-hutou" ("HT"), with PacBio reads and the "HT" chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in "HT". We identified a 14.3 kb "HT"-specific insertion on Chr7 of the "HT" nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that "DP" and "HT" evolved from "SP", with "HT" being the most recent derivative of "DP".

CONCLUSION

The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.

Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales

Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions.

Comparative phylogenomic study of East Asian endemic genus, Corchoropsis Siebold & Zucc. (Malvaceae s.l.), based on complete plastome sequences

BACKGROUND

Endemic plants are key to understanding the evolutionary history and enhancing biodiversity within their unique regions, while also offering significant economic potential. The East Asian endemic genus Corchoropsis Siebold & Zucc., classified within the subfamily Dombeyoideae of Malvaceae s.l., comprises three species.

RESULTS

This study characterizes the complete plastid genomes (plastomes) of C. crenata var. crenata Siebold & Zucc. and C. crenata var. hupehensis Pamp., which range from 160,093 to 160,724 bp. These genomes contain 78 plastid protein-coding genes, 30 tRNA, and four rRNA, except for one pseudogene, infA. A total of 316 molecular diagnostic characters (MDCs) specific to Corchoropsis were identified. In addition, 91 to 92 simple sequence repeats (SSRs) in C. crenata var. crenata and 75 in C. crenata var. hupehensis were found. Moreover, 49 long repeats were identified in both the Chinese C. crenata var. crenata and C. crenata var. hupehensis, while 52 were found in the South Korean C. crenata var. crenata. Our phylogenetic analyses, based on 78 plastid protein-coding genes, reveal nine subfamilies within the Malvaceae s.l. with high support values and confirm Corchoropsis as a member of Dombeyoideae. Molecular dating suggests that Corchoropsis originated in the Oligocene, and diverged during the Miocene, influenced by the climate shift at the Eocene-Oligocene boundary.

CONCLUSIONS

The research explores the evolutionary relationships between nine subfamilies within the Malvaceae s.l. family, specifically identifying the position of the Corchoropsis in the Dombeyoideae. Utilizing plastome sequences and fossil data, the study establishes that Corchoropsis first appeared during the Eocene and experienced further evolutionary divergence during the Miocene, paralleling the evolutionary patterns observed in other East Asian endemic species.

Comparative mitochondrial genomics of Terniopsis yongtaiensis in Malpighiales: structural, sequential, and phylogenetic perspectives

BACKGROUND

Terniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported.

RESULTS

In current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes.

CONCLUSIONS

This study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.

An expanded odorant-binding protein mediates host cue detection in the parasitic wasp Baryscapus dioryctriae basis of the chromosome-level genome assembly analysis

BACKGROUND

Baryscapus dioryctriae (Chalcidodea: Eulophidae) is a parasitic wasp that parasitizes the pupae of many Pyralidae members and has been used as a biological control agent against Dioryctria pests of pinecones.

RESULTS

This B. dioryctriae assembly has a genome size of 485.5 Mb with a contig N50 of 2.17 Mb, and scaffolds were assembled onto six chromosomes using Hi-C analysis, significantly increasing the scaffold N50 to 91.17 Mb, with more than 96.13% of the assembled bases located on chromosomes, and an analysis revealed that 94.73% of the BUSCO gene set. A total of 54.82% (279.27 Mb) of the assembly was composed of repetitive sequences and 24,778 protein-coding genes were identified. Comparative genomic analysis demonstrated that the chemosensory perception, genetic material synthesis, and immune response pathways were primarily enriched in the expanded genes. Moreover, the functional characteristics of an odorant-binding protein (BdioOBP45) with ovipositor-biased expression identified from the expanded olfactory gene families were investigated by the fluorescence competitive binding and RNAi assays, revealing that BdioOBP45 primarily binds to the D. abietella-induced volatile compounds, suggesting that this expanded OBP is likely involved in locating female wasp hosts and highlighting a direction for future research.

CONCLUSIONS

Taken together, this work not only provides new genomic sequences for the Hymenoptera systematics, but also the high-quality chromosome-level genome of B. dioryctriae offers a valuable foundation for studying the molecular, evolutionary, and parasitic processes of parasitic wasps.

Comparative analysis of the complete chloroplast genomes of thirteen Bougainvillea cultivars from South China with implications for their genome structures and phylogenetic relationships

Bougainvillea spp., belonging to the Nyctaginaceae family, have high economic and horticultural value in South China. Despite the high similarity in terms of leaf appearance and hybridization among Bougainvillea species, especially Bougainvillea × buttiana, their phylogenetic relationships are very complicated and controversial. In this study, we sequenced, assembled and analyzed thirteen complete chloroplast genomes of Bougainvillea cultivars from South China, including ten B. × buttiana cultivars and three other Bougainvillea cultivars, and identified their phylogenetic relationships within the Bougainvillea genus and other species of the Nyctaginaceae family for the first time. These 13 chloroplast genomes had typical quadripartite structures, comprising a large single-copy (LSC) region (85,169-85,695 bp), a small single-copy (SSC) region (18,050-21,789 bp), and a pair of inverted-repeat (IR) regions (25,377-25,426 bp). These genomes each contained 112 different genes, including 79 protein-coding genes, 29 tRNAs and 4 rRNAs. The gene content, codon usage, simple sequence repeats (SSRs), and long repeats were essentially conserved among these 13 genomes. Single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were detected among these 13 genomes. Four divergent regions, namely, trnH-GUG_psbA, trnS-GCU_trnG-UCC-exon1, trnS-GGA_rps4, and ccsA_ndhD, were identified from the comparative analysis of 16 Bougainvillea cultivar genomes. Among the 46 chloroplast genomes of the Nyctaginaceae family, nine genes, namely, rps12, rbcL, ndhF, rpoB, rpoC2, ndhI, psbT, ycf2, and ycf3, were found to be under positive selection at the amino acid site level. Phylogenetic relationships within the Bougainvillea genus and other species of the Nyctaginaceae family based on complete chloroplast genomes and protein-coding genes revealed that the Bougainvillea genus was a sister to the Belemia genus with strong support and that 35 Bougainvillea individuals were divided into 4 strongly supported clades, namely, Clades Ⅰ, Ⅱ, Ⅲ and Ⅳ. Clade Ⅰ included 6 individuals, which contained 2 cultivars, namely, B. × buttiana 'Gautama's Red' and B. spectabilis 'Flame'. Clades Ⅱ only contained Bougainvillea spinosa. Clade Ⅲ comprised 7 individuals of wild species. Clade Ⅳ included 21 individuals and contained 11 cultivars, namely, B. × buttiana 'Mahara', B. × buttiana 'California Gold', B. × buttiana 'Double Salmon', B. × buttiana 'Double Yellow', B. × buttiana 'Los Banos Beauty', B. × buttiana 'Big Chitra', B. × buttiana 'San Diego Red', B. × buttiana 'Barbara Karst', B. glabra 'White Stripe', B. spectabilis 'Splendens' and B. × buttiana 'Miss Manila' sp. 1. In conclusion, this study not only provided valuable genome resources but also helped to identify Bougainvillea cultivars and understand the chloroplast genome evolution of the Nyctaginaceae family.

Characterisation of the complete chloroplast genome of Solanum tuberosum cv. White Lady

Potato (Solanum tuberosum) is considered worldwide as one of the most important non-cereal food crops. As a result of its adaptability and worldwide production area, potato displays a vast phenotypical variability as well as genomic diversity. Chloroplast genomes have long been a core issue in plant molecular evolution and phylogenetic studies, and have an important role in revealing photosynthetic mechanisms, metabolic regulations and the adaptive evolution of plants. We sequenced the complete chloroplast genome of the Hungarian cultivar White Lady, which is 155 549 base pairs (bp) in length and is characterised by the typical quadripartite structure composed of a large- and small single-copy region (85 991 bp and 18 374 bp, respectively) interspersed by two identical inverted repeats (25 592 bp). The genome consists of 127 genes of which 82 are protein-coding, eight are ribosomal RNAs and 37 are transfer RNAs. The overall gene content and distribution of the genes on the White Lady chloroplast was the same as found in other potato chloroplasts. The alignment of S. tuberosum chloroplast genome sequences resulted in a highly resolved tree, with 10 out of the 13 nodes recovered having bootstrap values over 90%. By comparing the White Lady chloroplast genome with available S. tuberosum sequences we found that gene content and synteny are highly conserved. The new chloroplast sequence can support further studies of genetic diversity, resource conservation, evolution and applied agricultural research. The new sequence can support further potato genetic diversity and evolutionary studies, resource conservation, and also applied agricultural research.

Mining expressed sequence tag (EST) microsatellite markers to assess the genetic differentiation of five Hynobius species endemic to Taiwan

Taiwan harbors five endemic species of salamanders (Hynobius spp.) that inhabit distinct alpine regions, contributing to population fragmentation across isolated "sky islands". With an evolutionary history spanning multiple glacial-interglacial cycles, these species represent an exceptional paradigm for exploring biogeography and speciation. However, a lack of suitable genetic markers applicable across species has limited research efforts. Thus, developing cross-amplifying markers is imperative. Expressed sequence-tag simple-sequence repeats (EST-SSRs) that amplify across divergent lineages are ideal for species identification in instances where phenotypic differentiation is challenging. Here, we report a suite of cross-amplifying EST-SSRs from the transcriptomes of the five Hynobius species that exhibit an interspecies transferability rate of 67.67%. To identify individual markers exhibiting cross-species polymorphism and to assess interspecies genetic diversity, we assayed 140 individuals from the five species across 84 sampling sites. A set of EST-SSRs with a high interspecies polymorphic information content (PIC = 0.63) effectively classified these individuals into five distinct clusters, as supported by discriminant analysis of principal components (DAPC), STRUCTURE assignment tests, and Neighbor-joining trees. Moreover, pair-wise FST values > 0.15 indicate notable between-cluster genetic divergence. Our set of 20 polymorphic EST-SSRs is suitable for assessing population structure within and among Hynobius species, as well as for long-term monitoring of their genetic composition.

Genomic changes and stabilization following homoploid hybrid speciation of the Oxford ragwort Senecio squalidus

Oxford ragwort (Senecio squalidus) is one of only two homoploid hybrid species known to have originated very recently, so it is a unique model for determining genomic changes and stabilization following homoploid hybrid speciation. Here, we provide a chromosome-level genome assembly of S. squalidus with 95% of the assembly contained in the 10 longest scaffolds, corresponding to its haploid chromosome number. We annotated 30,249 protein-coding genes and estimated that ∼62% of the genome consists of repetitive elements. We then characterized genome-wide patterns of linkage disequilibrium, polymorphism, and divergence in S. squalidus and its two parental species, finding that (1) linkage disequilibrium is highly heterogeneous, with a region on chromosome 4 showing increased values across all three species but especially in S. squalidus; (2) regions harboring genetic incompatibilities between the two parental species tend to be large, show reduced recombination, and have lower polymorphism in S. squalidus; (3) the two parental species have an unequal contribution (70:30) to the genome of S. squalidus, with long blocks of parent-specific ancestry supporting a very rapid stabilization of the hybrid lineage after hybrid formation; and (4) genomic regions with major parent ancestry exhibit an overrepresentation of loci with evidence for divergent selection occurring between the two parental species on Mount Etna. Our results show that both genetic incompatibilities and natural selection play a role in determining genome-wide reorganization following hybrid speciation and that patterns associated with homoploid hybrid speciation-typically seen in much older systems-can evolve very quickly following hybridization.

Complete mitochondrial genome of Agropyron cristatum reveals gene transfer and RNA editing events

BACKGROUND

As an important forage in arid and semi-arid regions, Agropyron cristatum provides livestock with exceptionally high nutritional value. Additionally, A. cristatum exhibits outstanding genetic characteristics to endure drought and disease. Therefore, rich genetic diversity serves as a cornerstone for the improvement of major food crops. The purposes of this study were to systematically describe mitogenome of A.cristatum and preliminarily analyze its internal variations.

RESULT

The A. cristatum mitogenome was a single-ring molecular structure of 381,065 bp that comprised 52 genes, including 35 protein-coding, 3 rRNA and 14 tRNA genes. Among these, two pseudoprotein-coding genes and multiple copies of tRNA genes were observed. A total of 320 repetitive sequences was found to cover more than 10% of the mitogenome (105 simple sequences, 185 dispersed and 30 tandem repeats), which led to a large number of fragment rearrangements in the mitogenome of A. cristatum. Leucine was the most frequent amino acid (n = 1087,10.8%) in the protein-coding genes of A. cristatum mitogenome, and the highest usage codon was ATG (initiation codon). The number of A/T changes at the third base of the codon was much higher than that of G/C. Among 23 PCGs, the range of Pi values is from 0.0021 to 0.0539, with an average of 0.013. Additionally, 81 RNA editing sites were predicted, which were considerably fewer than those reported in other plant mitogenomes. Most of the RNA editing site base positions were concentrated at the first and second codon bases, which were C to T transitions. Moreover, we identified 95 sequence fragments (total length of 34, 343 bp) that were transferred from the chloroplast to mitochondria genes, introns, and intergenic regions. The stability of the tRNA genes was maintained during this process. Selection pressure analysis of 23 protein-coding genes shared by 15 Poaceae plants, showed that most genes were subjected to purifying selection during evolution, whereas rps4, cob, mttB, and ccmB underwent positive selection in different plants. Finally, a phylogenetic tree was constructed based on 22 plant mitogenomes, which showed that Agropyron plants have a high degree of independent heritability in Triticeae.

CONCLUSION

The findings of this study provide new data for a better understanding of A. cristatum genes, and demonstrate that mitogenomes are suitable for the study of plant classifications, such as those of Agropyron. Moreover, it provides a reference for further exploration of the phylogenetic relationships within Agropyron species, and establishes a theoretical basis for the subsequent development and utilization of A. cristatum plant germplasm resources.

The adaptive evolution of Quercus section Ilex using the chloroplast genomes of two threatened species

Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, introgression, and incomplete lineage sorting. Therefore, we wanted to gain a better understanding of this genus at the level of the maternally inherited chloroplast genome. Here, we sequenced, assembled, and annotated the cp genomes of the threatened Quercus marlipoensis (160,995 bp) and Q. kingiana (161,167 bp), and mined these genomes for repeat sequences and codon usage bias. Comparative genomic analyses, phylogenomics, and selection pressure analysis were also performed in these two threatened species along with other species of Quercus. We found that the guanine and cytosine content of the two cp genomes were similar. All 131 annotated genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes, had the same order in the two species. A strong A/T bias was detected in the base composition of simple sequence repeats. Among the 59 synonymous codons, the codon usage pattern of the cp genomes in these two species was more inclined toward the A/U ending. Comparative genomic analyses indicated that the cp genomes of Quercus section Ilex are highly conserved. We detected eight highly variable regions that could be used as molecular markers for species identification. The cp genome structure was consistent and different within and among the sections of Quercus. The phylogenetic analysis showed that section Ilex was not monophyletic and was divided into two groups, which were respectively nested with section Cerris and section Cyclobalanopsis. The two threatened species sequenced in this study were grouped into the section Cyclobalanopsis. In conclusion, the analyses of cp genomes of Q. marlipoensis and Q. kingiana promote further study of the taxonomy, phylogeny and evolution of these two threatened species and Quercus.

A near-complete chromosome-level genome assembly of looseleaf lettuce (Lactuca sativa var. crispa)

Lettuce (Lactuca sativa L., Asteraceae) is one of the most important vegetable crops, known for its various horticultural types and significant morphological variation. The first reference genome of lettuce, a crisphead type (L. sativa var. capitata cv. Salinas), was previously released. Here, we reported a near-complete chromosome-level reference genome for looseleaf lettuce (L. sativa var. crispa). PacBio high-fidelity sequencing, Oxford Nanopore, and Hi-C technologies were employed to produce genome assembly. The final assembly is 2.59 Gb in length with a contig N50 of 205.47 Mb, anchored onto nine chromosomes, containing 14 recognizable telomeres and only 11 gaps. Repetitive sequences account for 77.11% of the genome, and 41,375 protein-coding genes were predicted, with 99.10% of these assigned functional annotations. This chromosome-level genome enriched genomic resources for various horticultural types of lettuce and will facilitate the characterization of morphological variation and genetic improvement in lettuce.

Phylogenomics analysis of Scutellaria (Lamiaceae) of the world

BACKGROUND

Scutellaria, a sub-cosmopolitan genus, stands as one of the Lamiaceae family's largest genera, encompassing approximately 500 species found in both temperate and tropical montane regions. Recognized for its significant medicinal properties, this genus has garnered attention as a research focus, showcasing anti-cancer, anti-inflammatory, antioxidant, and hepatoprotective qualities. Additionally, it finds application in agriculture and horticulture. Comprehending Scutellaria's taxonomy is pivotal for its effective utilization and conservation. However, the current taxonomic frameworks, primarily based on morphological characteristics, are inadequate. Despite several phylogenetic studies, the species relationships and delimitations remain ambiguous, leaving the genus without a stable and reliable classification system.

RESULTS

This study analyzed 234 complete chloroplast genomes, comprising 220 new and 14 previously published sequences across 206 species, subspecies, and varieties worldwide. Phylogenetic analysis was conducted using six data matrices through Maximum Likelihood and Bayesian Inference, resulting in a robustly supported phylogenetic framework for Scutellaria. We propose three subgenera, recommending the elevation of Section Anaspis to subgeneric rank and the merging of Sections Lupulinaria and Apeltanthus. The circumscription of Subgenus Apeltanthus and Section Perilomia needs to be reconsidered. Comparative analysis of chloroplast genomes highlighted the IR/SC boundary feature as a significant taxonomic indicator. We identified a total of 758 SSRs, 558 longer repetitive sequences, and ten highly variable regions, including trnK-rps16, trnC-petN, petN-psbM, accD-psaI, petA-psbJ, rpl32-trnL, ccsA-ndhD, rps15-ycf1, ndhF, and ycf1. These findings serve as valuable references for future research on species identification, phylogeny, and population genetics.

CONCLUSIONS

The phylogeny of Scutellaria, based on the most comprehensive sample collection to date and complete chloroplast genome analysis, has significantly enhanced our understanding of its infrageneric relationships. The extensive examination of chloroplast genome characteristics establishes a solid foundation for the future development and utilization of Scutellaria, an important medicinal plant globally.

Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae)

Vanda R.Br. is an epiphytic orchid genus with significant horticultural and ornamental value. Previous molecular studies expanded Vanda including some members from five other genera. However, the interspecific relationships of this recently radiated genus have remained unclear based on several DNA markers until now. In this study, the complete plastome has been used to infer the phylogenetic relationships of Vanda s.l. The five newly obtained plastomes ranged from 146,340 bp to 149,273 bp in length, with a GC content ranging from 36.5% to 36.7%. The five plastomes contained 74 protein-coding genes (CDSs), 38 tRNAs, and 8 rRNAs, and their ndh genes underwent loss or pseudogenization. Comparative plastome analyses of 13 Vanda species revealed high conservation in terms of genome size, structure, and gene order, except for a large inversion from trnGGCC to ycf3 in V. coerulea. Moreover, six CDSs and five non-CDSs were selected as candidate DNA barcodes. Our phylogenetic analyses demonstrated that Vanda s.l. is a monophyletic group with high supporting values based on five different datasets (complete plastome with one IR, 68 CDSs, LSC, five hypervariable non-CDSs, and six hypervariable CDSs), while the phylogenetic relationships among species were fully resolved based on the complete plastome with one IR dataset. Our results confirmed that the complete plastome has a great power in resolving the phylogenetic relationships of recently radiated lineages.

The genomic landscape of 2,023 colorectal cancers

Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2-9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia colipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11-13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.

Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae

Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra-species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.

Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii

Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16 Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25 Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.

Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement

Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.

De novo transcriptome assembly, annotation and SSR mining data of Hellula undalis (Fabr.) (Lepidoptera: Pyralidae), the cabbage webworm

BACKGROUND

The cabbage webworm, Hellula undalis (Fabricius) (Lepidoptera: Pyralidae), is a significant pest of brassicas and other cruciferous plants in warm regions worldwide. Transcriptome analysis is valuable for investigation of molecular mechanisms underlying the insect development and reproduction. De novo assembly is particularly useful for acquiring complete transcriptome information of insect species when there is no reference genome available. In case of Hellula undalis, only 17 nucleotide records are currently available throughout NCBI nucleotide database. Genes associated with metabolic processes, general development, reproduction, defense and functional genomics were not previously predicted in the Hellula undalis at the genomic level.

METHODS & RESULTS

To address this issue, we constructed Hellula undalis transcriptome using Illumina NovaSeq6000 technology. Approximately 48 million 150 bp paired-end reads were obtained from sequencing. A total of 30,451 contigs were generated by de novo assembly of sample and were compared with the sequences in the NCBI non-redundant protein database (Nr). In total, 71 % of contigs were matched to known proteins in public databases including Nr, Gene Ontology (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 123 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we compared the ortholog gene family of the Hullula undalis, transcriptome to Spodoptera frugiperda, spodotera litura and spodoptera littoralis and found that 391 orthologous gene families are specific to Hullula undalis. A total of 1,913 potential SSRs was discovered in Hullula undalis contigs.

CONCLUSIONS

This study is the first transcriptome data for Hullula undalis. Additionally, it serves as a valuable resource for identifying target genes and developing effective and environmentally friendly strategies for pest control.

Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB

The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515-151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1-H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10-3, respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis.

Analysis of the Spatholobus suberectus full-length transcriptome identified an R2R3-MYB transcription factor-encoding gene SsMYB158 that regulates flavonoid biosynthesis

Spatholobus suberectus Dunn (Leguminosae) has been used for medicinal purposes for a long period. Flavonoids are the major bioactive components of S. suberectus. However, there is still limited knowledge of the exact method via which transcription factors (TFs) regulate flavonoid biosynthesis. The full-length transcriptome of S. suberectus was analyzed using SMRT sequencing; 61,548 transcripts were identified, including 12,311 new gene loci, 53,336 novel transcripts, 44,636 simple sequence repeats, 36,414 complete coding sequences, 871 long non-coding RNAs and 6781 TFs. The SsMYB158 TF, which is associated with flavonoid biosynthesis, belongs to the R2R3-MYB class and is localized subcellularly to the nucleus. The overexpression of SsMYB158 in Nicotiana benthamiana and the transient overexpression of SsMYB158 in S. suberectus resulted in a substantial enhancement in both flavonoids and catechin levels. In addition, there was a remarkable upregulation in the expression of essential enzyme-coding genes associated with the flavonoid biosynthesis pathways. Our study revealed SsMYB158 as a critical regulator of flavonoid biosynthesis in S. suberectus and laying the foundation for its molecular breeding.

Deciphering the complete chloroplast genome sequence of Meconopsis torquata Prain: Insights into genome structure, comparative analysis and phylogenetic relationship

In the present study, we have characterized the complete chloroplast (Cp) genome of Meconopsis torquata Prain (family Papaveraceae), revealing the plastome size of 153,290 bp, and a GC content of 38.72 %. The cp genome features the typical circular quadripartite structure found in flowering plants, including a pair of inverted repeat regions (25,816 bp), isolated by a small single-copy region (17,740 bp) and a large single-copy (83,918 bp). Genome annotation revealed 132 genes: 87 protein-coding genes, 37 tRNAs and eight rRNAs. This comparative study demonstrated that the genome structure, gene number and GC ratio are consistent with several other cp genomes of Meconopsis and Papaver genera. A total of 120 SSRs were detected in the plastome, the majority (111) of which were mononucleotide repeats. Among the longer repeats, palindromic sequences were most common, followed by forward, reverse, and complement repeats. The whole genome alignment revealed the conserved nature of the inverted repeat region over single-copy zones. Nucleotide diversity unveiled hypervariable sites (ycf1, rps16, accD, atpB and psbD) in both the small and large single-copy regions, which could be useful for designing molecular markers for taxonomic identification. Phylogenetic analysis revealed a close alliance of M. torquata with other Meconopsis species, such as M. pinnatifolia and M. paniculata, with strong bootstrap support. Molecular dating suggests that M. torquata originated during the Tortonian age of the Miocene epoch of the Cenozoic era. These findings provide valuable insights for biological research, especially in understanding the genetic and evolutionary divergence within the Papaveraceae family.

The complete chloroplast genome sequence of red raspberry (Rubus idaeus L.) and phylogenetic analysis

Red raspberries, Rubus idaeus L. 1753 are famous fruits which possess high value bioactive compounds. In this study, we report the complete chloroplast genome of R. idaeus, it displayed a typical quadripartite structure with 155687 bp in length. The genome encodes 127 genes including 79 protein coding genes, 8 rRNA genes and 40 tRNA genes, the overall GC content is 37.2%. Phylogenetic analysis revealed a close relationship between R. idaeus and R. sachalinensis in Section Malaehobatus.

Illumina-based transcriptomic analysis of the fast-growing leguminous tree Acacia crassicarpa: functional gene annotation and identification of novel SSR-markers

Acacia crassicarpa is a fast-growing leguminous tree that is widely cultivated in tropical areas such as Indonesia, Malaysia, Australia, and southern China. This tree has versatile utility in timber, furniture, and pulp production. Illumina sequencing of A. crassicarpa was conducted, and the raw data of 124,410,892 reads were filtered and assembled de novo into 93,317 unigenes, with a total of 84,411,793 bases. Blast2GO annotation, Benchmark Universal Single-Copy Ortholog evaluation, and GO-term classification produced a catalogue of unigenes for studying primary metabolism, phytohormone signaling, and transcription factors. Massive transcriptomic analysis has identified microsatellites composed of simple sequence repeat (SSR) loci representing di-, tri-, and tetranucleotide repeat units in the predicted open reading frames. Polymorphism was induced by PCR amplification of microsatellite loci located in several genes encoding auxin response factors and other transcription factors, which successfully distinguished 16 local trees of A. crassicarpa tested, representing potentially exploitable molecular markers for efficient tree breeding for plantation and biomass exploitation.

Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution

The para rubber tree (Hevea brasiliensis) is the world's sole commercial source of natural rubber, a vital industrial raw material. However, the narrow genetic diversity of this crop poses challenges for rubber breeding. Here, we generate high-quality de novo genome assemblies for three H. brasiliensis cultivars, two H. brasiliensis wild accessions, and three other Hevea species (H. nitida, H. pauciflora, and H. benthamiana). Through analyzing genomes of 94 Hevea accessions, we identify five distinct lineages that do not align with their previous species delineations. We discover multiple accessions with hybrid origins between these lineages, indicating incomplete reproductive isolation between them. Only two out of four wild lineages have been introduced to commercial rubber cultivars. Furthermore, we reveal that the rubber production traits emerged following the development of a large REF/SRPP gene cluster and its functional specialization in rubber-producing laticifers within this genus. These findings would enhance rubber breeding and benefit research communities.

Comparative analysis of the complete mitogenomes of Camellia sinensis var. sinensis and C. sinensis var. assamica provide insights into evolution and phylogeny relationship

Introduction

Among cultivated tea plants (Camellia sinensis), only four mitogenomes for C. sinensis var. assamica (CSA) have been reported so far but none for C. sinensis var. sinensis (CSS). Here, two mitogenomes of CSS (CSSDHP and CSSRG) have been sequenced and assembled.

Methods

Using a combination of Illumina and Nanopore data for the first time. Comparison between CSS and CSA mitogenomes revealed a huge heterogeneity.

Results

The number of the repetitive sequences was proportional to the mitogenome size and the repetitive sequences dominated the intracellular gene transfer segments (accounting for 88.7%- 92.8% of the total length). Predictive RNA editing analysis revealed that there might be significant editing in NADH dehydrogenase subunit transcripts. Codon preference analysis showed a tendency to favor A/T bases and T was used more frequently at the third base of the codon. ENc plots analysis showed that the natural selection play an important role in shaping the codon usage bias, and Ka/Ks ratios analysis indicated Nad1 and Sdh3 genes may have undergone positive selection. Further, phylogenetic analysis shows that six C. sinensis clustered together, with the CSA and CSS forming two distinct branches, suggesting two different evolutionary pathway.

Discussion

Altogether, this investigation provided an insight into evolution and phylogeny relationship of C. sinensis mitogenome, thereby enhancing comprehension of the evolutionary patterns within C. sinensis species.

Comparative and phylogenetic analyses of plastid genomes of the medicinally important genus Alisma (Alismataceae)

Alisma L. is a medicinally important genus of aquatic and wetland plants consisting of c. 10 recognized species. However, largely due to polyploidy and limited taxon and gene sampling, the phylogenomic relationships of Alisma remain challenging. In this study, we sequenced 34 accessions of Alismataceae, including eight of the ten species of Alisma, one species of Echinodorus and one species of Luronium, to perform comparative analyses of plastid genomes and phylogenetic analyses. Comparative analysis of plastid genomes revealed high sequence similarity among species within the genus. Our study analyzed structural changes and variations in the plastomes of Alisma, including IR expansion or contraction, and gene duplication or loss. Phylogenetic results suggest that Alisma is monophyletic, and constitutes four groups: (1) A. lanceolatum and A. canaliculatum; (2) the North American clade of A. subcordatum and A. triviale; (3) A. wahlenbergii and A. gramineum; and (4) A. plantago-aquatica from Eurasia and northern Africa with the eastern Asian A. orientale nested within it. Hence the results challenge the recognition of A. orientale as a distinct species and raise the possibility of treating it as a synonym of the widespread A. plantago-aquatica. The well-known Alismatis Rhizoma (Zexie) in Chinese medicine was likely derived from the morphologically variable Alisma plantago-aquatica throughout its long history of cultivation in Asia. The plastome phylogenetic results also support the tetraploid A. lanceolatum as the likely maternal parent of the hexaploid eastern Asian A. canaliculatum.

Comprehensive analysis of the Lycopodium japonicum mitogenome reveals abundant tRNA genes and cis-spliced introns in Lycopodiaceae species

Lycophytes and ferns represent one of the earliest-diverging lineages of vascular plants, with the Lycopodiaceae family constituting the basal clade among lycophytes. In this research, we successfully assembled and annotated the complete Lycopodium japonicum Thunb. (L. japonicum) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule with a size of 454,458 bp. 64 unique genes were annotated altogether, including 34 protein-coding genes, 27 tRNAs and 3 rRNAs. It also contains 32 group II introns, all of which undergo cis-splicing. We identified 195 simple sequence repeats, 1,948 dispersed repeats, and 92 tandem repeats in the L. japonicum mitogenome. Collinear analysis indicated that the mitogenomes of Lycopodiaceae are remarkably conserved compared to those of other vascular plants. We totally identified 326 RNA editing sites in 31 unique protein-coding genes with 299 sites converting cytosine to uracil and 27 sites the reverse. Notably, the L. japonicum mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% of the mitogenome. The maximum likelihood phylogenetic analysis based on 23 diverse land plant mitogenomes and plastid genomes supports the basal position of lycophytes within vascular plants and they form a sister clade to all other vascular lineages, which is consistent with the PPG I classification system. As the first reported mitogenome of Lycopodioideae subfamily, this study enriches our understanding of Lycopodium mitogenomes, and sets the stage for future research on mitochondrial diversity and evolution within the lycophytes and ferns.

Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia

Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia, used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.

Comparative and phylogenetic analysis of chloroplast genomes from ten species in Quercus section Cyclobalanopsis

The genus Quercus L. is widely acknowledged as a significant assemblage within East Asia tropical and subtropical broadleaf evergreen forests, possessing considerable economic importance. Nevertheless, the differentiation of Quercus species is deemed arduous, and the interrelations among these species remain enigmatic. Leveraging Illumina sequencing, we undertook the sequencing and assembly of the chloroplast (cp) genomes of seven species belonging to Quercus section Cyclobalanopsis (Quercus argyrotricha, Q. augustinii, Q. bambusifolia, Q. bella, Q. edithiae, Q. jenseniana, and Q. poilanei). Furthermore, we collated three previously published cp genome sequences of Cyclobalanopsis species (Q. litseoides, Q. obovatifolia, and Q. saravanensis). Our primary objective was to conduct comparative genomics and phylogenetic analyses of the complete cp genomes of ten species from Quercus section Cyclobalanopsis. This investigation unveiled that Quercus species feature a characteristic circular tetrad structure, with genome sizes ranging from 160,707 to 160,999 base pairs. The genomic configuration, GC content, and boundaries of inverted repeats/single copy regions exhibited marked conservation. Notably, four highly variable hotspots were identified in the comparative analysis, namely trnK-rps16, psbC-trnS, rbcL-accD, and ycf1. Furthermore, three genes (atpF, rpoC1, and ycf2) displayed signals of positive selection pressure. Phylogenetic scrutiny revealed that the four sections of Cyclobalanopsis clustered together as sister taxa. The branch support values ranged from moderate to high, with most nodes garnering 100% support, underscoring the utility of cp genomic data in elucidating the relationships within the genus. Divergence time analysis revealed that Section Cyclobalanopsis represents the earliest type of Quercus genus. The outcomes of this investigation establish a foundation for forthcoming research endeavors in taxonomy and phylogenetics.

Genome sequencing and assembly of Indian major carp, Cirrhinus mrigala (Hamilton, 1822)

The freshwater aquaculture species, Cirrhinus mrigala, commonly known as mrigal, holds significance in the carp-dominated aquaculture system, globally. Despite constituting 1.08% of the total freshwater aquaculture production, mrigal is the third most important Indian major carp. However, its genome and associated information is not available. This study aims to address this gap by generation high quality genome assembly using PacBio long reads, Illumina short reads and Hi-C scaffolding. The characterization of assembled highly contiguous genome, 1.057 Gb in size, revealed 39,091 genes with functional annotations. The orthology analysis based on direct orthologs and single copy ortholgs places C. mrigala in a distinct position within the Otophysi clade. Additionally, the study delves into Hox gene clusters, identifying 38 Hox genes distributed in seven clusters. The present genomic information offers potential applications for sustainable aquaculture management, including selection programs for economic traits.

Analysis of chloroplast genome structure and phylogeny of the traditional medicinal of Ardisia crispa (Myrsinaceae)

Ardisia crispa(Myrsinaceae) is an ethnomedicine with horticultural and important medicinal values. Its morphology is complex, and its identification is difficult. We analyse the chloroplast genome characteristics and phylogenetic position of A. crispa to provide basic research data for the identification of A. crispa species and resource conservation. This study assemble and annotate the chloroplast genome of A. crispa and to compare it with the chloroplast genome within Ardisia. The A. crispa chloroplast genome is 156,785 bp in length, with a typical quadripartite structure containing 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes; a total of 59 SSRs sites were identified, and the codon preference of this chloroplast genome is greater in A/U than in G/C, and leucine is the amino acid with the highest frequency of use. The chloroplast genomes of the nine Ardisia species are conserved in gene content and number, with more stable boundaries and less variation. In the phylogenetic tree, A. crispa is clustered on a branch with A. crispa var dielsii, and is closely related to A. mamillata and A. pedalis. In this study, we constructed and analyzed the chloroplast genome structure of A. crispa, and conducted phylogenetic analysis using the whole chloroplast genome sequence data of Ardisia plants, which is of great significance in understanding the genetic basis of A. crispa and adaptive evolution in Ardisia plants, and this will lay the foundation for the future research on A. crispa resource conservation and species identification.

Phylogeny, adaptive evolution, and taxonomy of Acronema (Apiaceae): evidence from plastid phylogenomics and morphological data

Introduction

The genus Acronema, belonging to Apiaceae, includes approximately 25 species distributed in the high-altitude Sino-Himalayan region from E Nepal to SW China. This genus is a taxonomically complex genus with often indistinct species boundaries and problematic generic delimitation with Sinocarum and other close genera, largely due to the varied morphological characteristics.

Methods

To explore the phylogenetic relationships and clarify the limits of the genus Acronema and its related genera, we reconstructed a reliable phylogenetic framework with high support and resolution based on two molecular datasets (plastome data and ITS sequences) and performed morphological analyses.

Results

Both phylogenetic analyses robustly supported that Acronema was a non-monophyletic group that fell into two clades: Acronema Clade and East-Asia Clade. We also newly sequenced and assembled sixteen Acronema complete plastomes and performed comprehensively comparative analyses for this genus. The comparative results showed that the plastome structure, gene number, GC content, codon bias patterns were high similarity, but varied in borders of SC/IR and we identified six different types of SC/IR border. The SC/IR boundaries of Acronema chienii were significantly different from the other Acronema members which was consistent with the type VI pattern in the genus Tongoloa. We also identified twelve potential DNA barcode regions (ccsA, matK, ndhF, ndhG, psaI, psbI, rpl32, rps15, ycf1, ycf3, psaI-ycf4 and psbM-trnD) for species identification in Acronema. The molecular evolution of Acronema was relatively conservative that only one gene (petG) was found to be under positive selection (ω = 1.02489).

Discussion

The gene petG is one of the genes involved in the transmission of photosynthetic electron chains during photosynthesis, which plays a crucial role in the process of photosynthesis in plants. This is also a manifestation of the adaptive evolution of plants in high-altitude areas to the environment. In conclusion, our study provides novel insights into the plastome adaptive evolution, phylogeny, and taxonomy of genus Acronema.

Chromosome-level genome provides new insight into the overwintering process of Korla pear (Pyrus sinkiangensis Yu)

Korla pear has a unique taste and aroma and is a breeding parent of numerous pear varieties. It is susceptible to Valsa mali var. pyri, which invades bark wounded by freezing injury. Its genetic relationships have not been fully defined and could offer insight into the mechanism for freezing tolerance and disease resistance. We generated a high-quality, chromosome-level genome assembly for Korla pear via the Illumina and PacBio circular consensus sequencing (CCS) platforms and high-throughput chromosome conformation capture (Hi-C). The Korla pear genome is ~ 496.63 Mb, and 99.18% of it is assembled to 17 chromosomes. Collinearity and phylogenetic analyses indicated that Korla might be derived from Pyrus pyrifolia and that it diverged ~ 3.9-4.6 Mya. During domestication, seven late embryogenesis abundant (LEA), two dehydrin (DHN), and 54 disease resistance genes were lost from Korla pear compared with P. betulifolia. Moreover, 21 LEA and 31 disease resistance genes were common to the Korla pear and P. betulifolia genomes but were upregulated under overwintering only in P. betulifolia because key cis elements were missing in Korla pear. Gene deletion and downregulation during domestication reduced freezing tolerance and disease resistance in Korla pear. These results could facilitate the breeding of novel pear varieties with high biotic and abiotic stress resistance.

Sequencing of the complete plastome of the thermal adder's-tongue fern, Ophioglossum thermale Kom. (Ophioglossaceae)

The Ophioglossaceae family, one of the oldest orders of extant ferns, exhibits diverse morphological and chromosomal characteristics. This study presents the first complete plastome sequence of thermal adder's-tongue fern (Ophioglossum thermale), a species renowned for its antioxidant properties in traditional Chinese medicine. Our analyses revealed 27 simple sequence repeats (SSRs) in the plastome, with variations in SSR frequencies compared to related genera. Our phylogenetic analyses placed O. thermale within the Ophioglossum s.s. clade, supporting previous studies and suggesting polyphyly within the genus Ophioglossum based on the sensu PPG I system. The enlarged noncoding regions in fern organelles (ENRFOs) resulting from foreign DNA insertions in O. thermale were identified in the ycf2-trnH and trnT-trnfM regions, similar to other Ophioglossum species. ENRFOs were found at the LSC and SSC, but not in IRs in Ophioglossaceae. Consequently, foreign DNA insertions and lineage-specific SSRs shed light on plastome evolution in the Ophioglossaceae family.

The complete chloroplast genome of rhododendron williamsianum (ericaceae)

Rhododendron williamsianum Rehder & E. H. Wilson 1913, is a plant with important horticultural value. Here we report its chloroplast genome. The total length of the chloroplast genome was 205,424 bp, with a GC content of 35.8%. It consisted of a 107,968 bp large single copy, a 2606 bp small single copy, and a pair of 47,425 bp inverted repeats separating them. Within the chloroplast genome, there were a total of 110 unique genes, which included 76 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Our phylogenetic analyses indicated that R. williamsianum was closely genetically related to R. sutchuenense and R. jingangshanicum. The findings from this study not only contribute to the genetic database of Rhododendron plants but also have implications for evolutionary research within the family Ericaceae.

Chloroplast genomes of Eriobotrya elliptica and an unknown wild loquat "YN-1"

The chloroplast genomes of wild loquat can help to determine their place in the history of evolution. Here, we sequenced and assembled two novel wild loquat's chloroplast genomes, one is Eriobotrya elliptica, and the other is an unidentified wild loquat, which we named "YN-1". Their sizes are 159,471 bp and 159,399 bp, respectively. We also assembled a cultivated loquat named 'JFZ', its chloroplast genome size is 159,156 bp. A comparative study was conducted with six distinct species of loquats, including five wild loquats and one cultivated loquat. The results showed that both E. elliptica and "YN-1" have 127 genes, one gene more than E. fragrans, which is psbK. Regions trnF-GAA-ndhJ, petG-trnP-UGG, and rpl32-trnL-UAG were found to exhibit high variability. It was discovered that there was a positive selection on rpl22 and rps12. RNA editing analysis found several chilling stress-specific RNA editing sites, especially in rpl2 gene. Phylogenetic analysis results showed that "YN-1" is closely related to E. elliptica, E. obovata and E. henryi.

Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome

Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly impact human health. Yet, no current method can accurately identify complete HGT events, including the transferred sequence and the associated deletion and insertion breakpoints from shotgun metagenomic data. Here, we develop LocalHGT, which facilitates the reliable and swift detection of complete HGT events from shotgun metagenomic data, delivering an accuracy of 99.4%-verified by Nanopore data-across 200 gut microbiome samples, and achieving an average F1 score of 0.99 on 100 simulated data. LocalHGT enables a systematic characterization of HGT events within the human gut microbiome across 2098 samples, revealing that multiple recipient genome sites can become targets of a transferred sequence, microhomology is enriched in HGT breakpoint junctions (P-value = 3.3e-58), and HGTs can function as host-specific fingerprints indicated by the significantly higher HGT similarity of intra-personal temporal samples than inter-personal samples (P-value = 4.3e-303). Crucially, HGTs showed potential contributions to colorectal cancer (CRC) and acute diarrhoea, as evidenced by the enrichment of the butyrate metabolism pathway (P-value = 3.8e-17) and the shigellosis pathway (P-value = 5.9e-13) in the respective associated HGTs. Furthermore, differential HGTs demonstrated promise as biomarkers for predicting various diseases. Integrating HGTs into a CRC prediction model achieved an AUC of 0.87.

The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd (Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination

Introduction

Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding.

Methods

A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes.

Results

The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing.

Conclusion

In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.

The first high-quality genome assembly and annotation of Anthocidaris crassispina

Anthocidaris crassispina is a very popular edible sea urchin distributed along the coast of the South China Sea. In this study, we performed whole-genome sequencing and generated a chromosome-level assembly of this species. The total length of the genomic contig sequence was 891.02 Mb, and contig N50 was 808.15 kb when Hifiasm was used for assembly. The Hi-C library was constructed and sequenced, yielding approximately 68.61 Gb of data. After Hi-C assembly, approximately 886.72 Mb of sequence was able to be mapped onto 21 chromosomes, accounting for 99.52% of the total genome length. Among the sequences located on the chromosomes, those for which the order and direction could be determined accounted for approximately 826.82 Mb, or 93.24% of the total length. These results provide valuable resources for further study of A. crassispina at the genetic level.

Complete mitochondrial genome assembly of Zizania latifolia and comparative genome analysis

Zizania latifolia (Griseb.) Turcz. ex Stapf has been cultivated as a popular aquatic vegetable in China due to its important nutritional, medicinal, ecological, and economic values. The complete mitochondrial genome (mitogenome) of Z. latifolia has not been previously studied and reported, which has hindered its molecular systematics and understanding of evolutionary processes. Here, we assembled the complete mitogenome of Z. latifolia and performed a comprehensive analysis including genome organization, repetitive sequences, RNA editing event, intercellular gene transfer, phylogenetic analysis, and comparative mitogenome analysis. The mitogenome of Z. latifolia was estimated to have a circular molecule of 392,219 bp and 58 genes consisting of three rRNA genes, 20 tRNA genes, and 35 protein-coding genes (PCGs). There were 46 and 20 simple sequence repeats (SSRs) with different motifs identified from the mitogenome and chloroplast genome of Z. latifolia, respectively. Furthermore, 49 homologous fragments were observed to transfer from the chloroplast genome to the mitogenome of Z. latifolia, accounting for 47,500 bp, presenting 12.1% of the whole mitogenome. In addition, there were 11 gene-containing homologous regions between the mitogenome and chloroplast genome of Z. latifolia. Also, approximately 85% of fragments from the mitogenome were duplicated in the Z. latifolia nuclear genome. Selection pressure analysis revealed that most of the mitochondrial genes were highly conserved except for ccmFc, ccmFn, matR, rps1, and rps3. A total of 93 RNA editing sites were found in the PCGs of the mitogenome. Z. latifolia and Oryza minuta are the most closely related, as shown by collinear analysis and the phylogenetic analysis. We found that repeat sequences and foreign sequences in the mitogenomes of Oryzoideae plants were associated with genome rearrangements. In general, the availability of the Z. latifolia mitogenome will contribute valuable information to our understanding of the molecular and genomic aspects of Zizania.

Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant

BACKGROUND

Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported.

RESULTS

The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense.

CONCLUSIONS

In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.

A single origin and high genetic diversity of cultivated medicinal herb Glehnia littoralis subsp. littoralis (Apiaceae) deciphered by SSR marker and phenotypic analysis

Ten SSR markers based on transcriptome sequencing were employed to genotype 231 samples of G. littoralis subsp. littoralis (Apiaceae) from nine cultivated populations and seven wild populations, aiming to assess the genetic diversity and genetic structure, and elucidate the origin of the cultivated populations. Cultivated populations exhibited relatively high genetic diversity (h = 0.441, I = 0.877), slightly lower than that of their wild counterparts (h = 0.491, I = 0.930), likely due to recent domestication and ongoing gene flow between wild and cultivated germplasm. The primary cultivated population in Shandong have the crucial genetic status. A single origin of domestication was inferred through multiple analysis, and wild populations from Liaoning and Shandong are inferred to be potentially the ancestor source for the present cultivated populations. Phenotypic analysis revealed a relatively high heritability of root length across three growth periods (0.683, 0.284, 0.402), with significant correlations observed between root length and petiole length (Pearson correlation coefficient = 0.30, P<0.05), as well as between root diameter and leaf area (Pearson correlation coefficient = 0.36, P<0.01). These parameters can serve as valuable indicators for monitoring the developmental progress of medicinal plants during field management. In summary, this study can shed light on the intricate genetic landscape of G. littoralis subsp. littoralis, providing foundational insights crucial for conservation strategies, targeted breeding initiatives, and sustainable management practices in both agricultural and natural habitats.

Complete mitochondrial genome of Hippophae tibetana: insights into adaptation to high-altitude environments

Hippophae tibetana, belonging to the Elaeagnaceae family, is an endemic plant species of the Qinghai-Tibet Plateau, valued for its remarkable ecological restoration capabilities, as well as medicinal and edible properties. Despite being acknowledged as a useful species, its mitochondrial genome data and those of other species of the Elaeagnaceae family are lacking to date. In this study, we, for the first time, successfully assembled the mitochondrial genome of H. tibetana, which is 464,208 bp long and comprises 31 tRNA genes, 3 rRNA genes, 37 protein-coding genes, and 3 pseudogenes. Analysis of the genome revealed a high copy number of the trnM-CAT gene and a high prevalence of repetitive sequences, both of which likely contribute to genome rearrangement and adaptive evolution. Through nucleotide diversity and codon usage bias analyses, we identified specific genes that are crucial for adaptation to high-altitude conditions. Notably, genes such as atp6, ccmB, nad4L, and nad7 exhibited signs of positive selection, indicating the presence of unique adaptive traits for survival in extreme environments. Phylogenetic analysis confirmed the close relationship between the Elaeagnaceae family and other related families, whereas intergenomic sequence transfer analysis revealed a substantial presence of homologous fragments among the mitochondrial, chloroplast, and whole genomes, which may be linked to the high-altitude adaptation mechanisms of H. tibetana. The findings of this study not only enrich our knowledge of H. tibetana molecular biology but also advance our understanding of the adaptive evolution of plants on the Qinghai-Tibet Plateau. This study provides a solid scientific foundation for the molecular breeding, conservation, and utilization of H. tibetana genetic resources.

Comparative analysis of complete chloroplast genomes of Synotis species (Asteraceae, Senecioneae) for identification and phylogenetic analysis

BACKGROUND

The Synotis (C. B. Clarke) C. Jeffrey & Y. L. Chen is an ecologically important genus of the tribe Senecioneae, family Asteraceae. Because most species of the genus bear similar morphology, traditional morphological identification methods are very difficult to discriminate them. Therefore, it is essential to develop a reliable and effective identification method for Synotis species. In this study, the complete chloroplast (cp.) genomes of four Synotis species, S. cavaleriei (H.Lév.) C. Jeffrey & Y.L. Chen, S. duclouxii (Dunn) C. Jeffrey & Y.L. Chen, S. nagensium (C.B. Clarke) C. Jeffrey & Y.L. Chen and S. erythropappa (Bureau & Franch.) C. Jeffrey & Y. L. Chen had been sequenced using next-generation sequencing technology and reported here.

RESULTS

These four cp. genomes exhibited a typical quadripartite structure and contained the large single-copy regions (LSC, 83,288 to 83,399 bp), the small single-copy regions (SSC, 18,262 to 18,287 bp), and the inverted repeat regions (IR, 24,837 to 24,842 bp). Each of the four cp. genomes encoded 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (ycf1 and rps19). The highly variable regions (trnC-GCA-petN, ccsA-psaC, trnE-UUC-rpoB, ycf1, ccsA and petN) may be used as potential molecular barcodes. The complete cp. genomes sequence of Synotis could be used as the potentially effective super-barcode to accurately identify Synotis species. Phylogenetic analysis demonstrated that the four Synotis species were clustered into a monophyletic group, and they were closed to the Senecio, Crassocephalum and Dendrosenecio in tribe Senecioneae.

CONCLUSIONS

This study will be useful for further species identification, evolution, genetic diversity and phylogenetic studies within this genus Synotis and the tribe Senecioneae.

The complete chloroplast genome of Rhododendronambiguum and comparative genomics of related species

Rhododendron Linnaeus, 1753, the largest genus of woody plants in the Northern Hemisphere, includes some of the most significant species in horticulture. Rhododendronambiguum Hemsl, 1911, a member of subsection Triflora Sleumer 1947, exemplifies typical alpine Rhododendron species. The analysis of the complete chloroplast genome of R.ambiguum offers new insights into the evolution of Rhododendron species and enhances the resolution of phylogenetic relationships. This genome is composed of 207,478 base pairs, including a pair of inverted repeats (IRs) of 47,249 bp each, separated by a large single-copy (LSC) region of 110,367 bp and a small single-copy (SSC) region of 2,613 bp. It contains 110 genes: 77 protein-coding genes, 29 tRNAs, four unique rRNAs (4.5S, 5S, 16S, and 23S), with 16 genes duplicated in the IRs. Comparative analyses reveal substantial diversity in the Rhododendron chloroplast genome structures, identifying a fourth variant pattern. Specifically, four highly divergent regions (trnI-rpoB, ndhE-psaC, rpl32-ndhF, rrn16S-trnI) were noted in the intergenic spacers. Additionally, 76 simple sequence repeats were identified. Positive selection signals were detected in four genes (cemA, rps4, rpl16, and rpl14), evidenced by high Ka/Ks ratios. Phylogenetic reconstruction based on two datasets (shared protein-coding genes and complete chloroplast genomes) suggests that R.ambiguum is closely related to R.concinnum Hemsley, 1889. However, the phylogenetic positions of subsection Triflora Pojarkova, 1952 species remain unresolved, indicating that the use of complete chloroplast genomes for phylogenetic research in Rhododendron requires careful consideration. Overall, our findings provide valuable genetic information that will enhance understanding of the evolution, molecular biology, and genetic improvement of Rhododendron spieces.

Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla

Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7-36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).

Chromosome-level genome assembly of marmalade hoverfly Episyrphus balteatus (Diptera: Syrphidae)

Episyrphus balteatus can provide dual ecosystem services including pest control and pollination, which the larvae are excellent predators of aphid pest whereas adults are efficient pollinator. In this study, we assembled a high-quality genome of E. balteatus from northern China geographical population at the chromosome level by using Illumina, PacBio long reads, and Hi-C technologies. The 467.42 Mb genome was obtained from 723 contigs, with a contig N50 of 9.16 Mb and Scaffold N50 of 118.85 Mb, and 90.25% (431.75 Mb) of the assembly was anchored to 4 pseudo-autosomes and one pseudo-heterosome. In total, 14,848 protein-coding genes were annotated, and 95.14% of genes were fully represented in NR, GO, KEGG databases. Besides, we also obtained the mitochondrial genome of E. balteatus of 16, 837 bp in length with 37 typical mitochondrial genes. Overall, this high-quality genome is valuable for evolutionary and genetic studies of E. balteatus and other Syrphidae hoverfly species.

Characterization of SSR markers from draft genome assembly and genotypic data in Hedychium spicatum (Zingiberaceae)

The plant family Zingiberaceae consists of many medicinally important tropical herbs. Here, we provide a contig level genome assembly for Hedychium spicatum, one of the medicinally utilized species in this family. We used genome assembly to identify candidate Simple Sequence Repeat (SSR) markers in the nuclear, chloroplast and mitochondrial compartments. We identified a total of 60,695 SSRs, which consisted of di-, tri-, tetra-, penta- and complex repeat types, and primers were designed for 14,851 SSR loci from both coding and non-coding parts of the genome. A total of 62 sets of candidate SSR primers were tested, out of which a final set of 20 SSR markers were characterized and they met the criteria of amplification success and retention of the repeat motif and homology. Out of these 20 markers, we genotyped 11 markers by amplifying and sizing 99 accessions of H. spicatum from 13 different geographic locations. The 11 markers were also characterised for four congeneric species, H. ellipticum, H. gomezianum, H. venustum, and H. yunnanense. All 11 SSR markers were found to be polymorphic and showed cross-species amplification. The total number of alleles per locus varied from 5 to 25. SSR markers continue to be a valuable tool for researchers because of their cost-effectiveness and simplicity. The cross-species amplification and variability of the SSR markers generated here further extend the utility of the markers to other Hedychium spp. The markers presented in this dataset can be used for a variety of studies, such as population genetics of invasive Hedychium species, QTL mapping, DNA fingerprinting, parentage analysis and genetic diversity assessments.