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

Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group

Melanoseris, a diverse genus in the Lactucinae subtribe, has 21 species in China, with 13 being endemic. The high diversity of this genus presents taxonomic challenges, particularly in the M. cyanea group, where overlapping distributions and transitional morphological traits complicate classification. This study aims to analyze the chloroplast genomes of Melanoseris, with a focus on the M. cyanea group, to explore structural differences and phylogenetic relationships among these closely related species. We analyzed the chloroplast genomes of 16 Melanoseris samples, including 12 new genomes from the M. cyanea group. The genome sizes ranged from 152,255 to 152,558 bp and exhibited a typical quadripartite structure, with an average GC content of 37.7%. Each genome encodes 132 genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat analysis identified 89 to 105 dispersed repeats, 24 to 28 tandem repeats, and 35 to 39 SSRs, with mononucleotide A/T repeats being the most common. Sequence alignment revealed that variable regions were mainly concentrated in the single-copy regions. Nucleotide diversity ranged from 0 to 0.00485, highlighting 10 mutation hotspot regions. Phylogenetic analysis showed a limited differentiation among species within the M. cyanea group. This research enhances our understanding of the genetic diversity of Melanoseris, laying the foundation for future taxonomic and phylogenetic studies.

Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet

MAIN CONCLUSION

Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.

Chromosome-level reference genome assembly provides insights into the evolution of Pennisetum alopecuroides

Pennisetum alopecuroides is an important forage grass resource, which plays a vital role in ecological environment improvement. Therefore, the acquisition of P. alopecuroides genome resources is conducive to the study of the adaptability of Pennisetum species in ecological remediation and forage breeding development. Here we assembled a P. alopecuroides cv. 'Liqiu' genome at the chromosome level with a size of approximately 845.71 Mb, contig N50 of 84.83Mb, and genome integrity of 99.13% as assessed by CEGMA. A total of 833.41-Mb sequences were mounted on nine chromosomes by Hi-C technology. In total, 60.66% of the repetitive sequences and 34,312 genes were predicted. The genomic evolution analysis showed that P. alopecuroides cv. 'Liqiu' was isolated from Setaria 7.53-13.80 million years ago and from Cenchrus 5.33-8.99 million years ago, respectively. The whole-genome event analysis showed that P. alopecuroides cv. 'Liqiu' underwent two whole-genome duplication (WGD) events in the evolution process, and the duplication events occurred at a similar time to that of Oryza sativa and Setaria viridis. The completion of the genome sequencing of P. alopecuroides cv. 'Liqiu' provides data support for mining high-quality genetic resources of P. alopecuroides and provides a theoretical basis for the origin and evolutionary characteristics of Pennisetum.

Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes

Aerides Lour. (Orchidaceae, Aeridinae) is a group of epiphytic orchids with high ornamental value, mainly distributed in tropical and subtropical forests, that comprises approximately 20 species. The species are of great value in floriculture and garden designing because of their beautiful flower shapes and colors. Although the morphological boundaries of Aerides are clearly defined, the relationship between Aerides and other closely related genera is still ambiguous in terms of phylogeny. To better understand their phylogenetic relationships, this study used next-generation sequencing technology to investigate the phylogeny and DNA barcoding of this taxonomic unit using genetic information from six Aerides plastid genomes. The quadripartite-structure plastomes ranged from 147,244 bp to 148,391 bp and included 120 genes. Among them, 74 were protein coding genes, 38 were tRNA genes and 8 were rRNA genes, while the ndh genes were pseudogenized or lost. Four non-coding mutational hotspots (rpl20-rpl33, psbM, petB, rpoB-trnCGCA, Pi > 0.06) were identified. A total of 71-77 SSRs and 19-46 long repeats (>30 bp) were recognized in Aerides plastomes, which were mostly located in the large single-copy region. Phylogenetic analysis indicated that Aerides was monophylic and sister to Renanthera. Moreover, our results confirmed that six Aerides species can be divided into three major clades. These findings provide assistance for species identification and DNA barcoding investigation in Aerides, as well as contributes to future research on the phylogenomics of Orchidaceae.

The complete chloroplast genome sequence of a warm season ornamental grass, Cenchrus alopecuroides Thunb. 1794 (Poaceae)

Cenchrus alopecuroides Thunb. 1794 is a warm-season ornamental grass with glossy foliage and showy inflorescence, which is widely distributed from eastern Asia to Australia. Although this species is of great economic importance, little genomic sequence data are available. Here, we report the complete chloroplast genome sequence of C. alopecuroides, which provides valuable plastid genomic resources for further studies on this ornamental grass. The chloroplast genome of C. alopecuroides was 138,053 bp in length and exhibited a typical quadripartite structure, which comprised a pair of inverted repeat regions (22,331 bp) separated by a large (81,177 bp) and a small single copy (12,214 bp) region. In total, 110 unique genes were annotated in the chloroplast genome, containing 76 protein-coding genes, 30 transfer RNAs and four ribosomal RNAs. The overall GC content of the chloroplast genome was 38.6%. Phylogenetic analysis based on 11 whole-chloroplast genome sequences of Cenchrus species suggested that C. alopecuroides and C. compressus were sisters to each other and joint sisters to C. clandestinus.

Comparative and phylogenetic analysis of the complete chloroplast genomes of six Polygonatum species (Asparagaceae)

Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported the size and gene contents of the plastomes, with little information on the comparative analysis of the plastid genomes of this genus. Additionally, there are still some species whose chloroplast genome information has not been reported. In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among them, the chloroplast genome of P. campanulatum was reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154,564 bp (P. multiflorum) to 156,028 bp (P. stenophyllum) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum1, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were five remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome strongly supported the placement of P. campanulatum with alternate leaves in sect. Verticillata, a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. This study revealed that the characters of plastomes in Polygonatum and Heteropolygonatum maintained a high degree of similarity. Five highly variable regions were found to be potential specific DNA barcodes in Polygonatum. Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.

Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?-A Case Study of Pulsatilla patens (L.) Mill

Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD-ccsA, rps4-rps16, and trnL(UAG)-ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes-11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset.

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

Owing to its attractive flower shape and color, Renanthera (Orchidaceae), comprising about 19 species, has significant ornamental value as a houseplant, in floral design and in landscape gardens. Two species of Renanthera are categorized as endangered and critically endangered in China’s Red List and international trade in these orchids is currently strictly monitored by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). This paper reports on the de novo assembled and annotated plastome of four species of Renanthera; R. citrina, R. coccinea, R. imschootiana, and R. philippinensis. The length of the plastome sequences ranged from 144,673 bp (R. imschootiana) to 149,007 bp (R. coccinea) with GC content of 36.6–36.7%. The plastomes showed a typical quadripartite structure, including a large single-copy (84,241–86,404 bp), a small single-copy (11,468–12,167 bp), and a pair of inverted repeats (24,482–25,715 bp) regions. Of the 120 genes detected, 74 were protein coding, 38 were tRNA, and eight were rRNA genes. The plastome of Renanthera is rather conserved, but nucleotide variations that could distinguish them apart are noticeable—the total number of tandem repeats ranged from 62 (in R. imschootiana) to 74 (in R. citrina); while the number of long repeats ranged from 21 (in R. imschootiana and R. philippinensis) to 43 (in R. citrina). Three hypervariable regions (psbI-trnS-GCU, trnG-GCC, rpl32) were identified. Phylogenetic analyses based on the CDS using maximum likelihood (ML) and Bayesian inference (BI) revealed that Renanthera is closely related to Holcoglossum, Neofinetia, Pendulorchis, and Vanda. The relationship between the four species of Renanthera was fully resolved; a monophyletic clade was formed and R. coccinea was recorded as the first to diverge from the rest. The genetic data obtained from this study could serve as a useful resource for species identification in Renanthera as well as contribute to future research on the phylogenomics of Orchidaceae.

Fusarium oxysporum Associated with Fusarium Wilt on Pennisetum sinese in China

Pennisetum sinese, a versatile and adaptable plant, plays an essential role in phytoremediation, soil reclamation, and fodder production. From 2018 to 2021, the occurrence of Fusarium wilt, with symptoms of foliar blight and internal discoloration of the stem, was observed in Chongqing, China. Pathogens were isolated from the symptomatic leaves. Based on morphological characteristics as well as DNA sequences of the 18S ribosomal RNA (SSU), translation elongation factor 1-α (EF1-α), RNA polymerase II subunit 1 (rpb1), and RNA polymerase II second largest subunit (rpb2) genes, the causal agents were identified as Fusarium oxysporum. Phylogenetic analysis of the combined dataset of EF1-α, rpb1 and rpb2 showed that pathogenic isolates clustered with F. oxysporum strains. The pathogen was reisolated from inoculated and diseased tissues; thus, Koch’s postulates were fulfilled. This is the first report of F. oxysporum causing Fusarium wilt on P. sinese in China and worldwide.

Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae)

Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite or whorled leaves. C. bungei, C. fargesii f. duclouxii and C. fargesii are sources of traditional precious wood in China, known as the “kings of wood”. Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within Catalpa. Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus Catalpa and analyzed their basic structure and evolutionary relationships. The chloroplast genome of Catalpa shows a typical tetrad structure with a total length ranging from 157,765 bp (C. fargesii) to 158,355 bp (C. ovata). The length of the large single-copy (LSC) region ranges from 84,599 bp (C. fargesii) to 85,004 bp (C. ovata), that of the small single-copy (SSC) region ranges from 12,662 bp (C. fargesii) to 12,675 bp (C. ovata), and that of the inverted repeat (IR) regions ranges from 30,252 bp (C. fargesii) to 30,338 bp (C. ovata). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus Catalpa formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of Catalpa, which will facilitate future research efforts.

Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution

Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26-36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD -GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.