Plant Gene最新文献

{"title":"Decoding the evolution of dumbbell stomata: Insights from the developmental genes of sedges and grasses","authors":"Alison P.A. Menezes ,&nbsp;Emilio Petrone-Mendoza ,&nbsp;James W. Clark ,&nbsp;Salvatore Cozzolino","doi":"10.1016/j.plgene.2025.100494","DOIUrl":"10.1016/j.plgene.2025.100494","url":null,"abstract":"<div><div>Stomatal morphology is a defining trait among plant lineages. Grasses (Poaceae) have distinctive dumbbell-shaped stomata that enhance water-use efficiency compared to the more common kidney-shaped stomata. In the closely related sedges (Cyperaceae) dumbbell-like stomata can be found. Dumbbell-like stomata in sedges share morphological features with grasses, suggesting potential conservation or convergence of developmental pathways. To investigate the evolution of dumbbell and dumbbell-like stomata, we analyzed genomic and transcriptomic data from 29 sedge species and five grass species. Using their predicted proteomes, we identified orthologues involved in stomatal development and reconstructed their phylogenetic histories. Among the 16 gene families analyzed, <em>EPFL9, YODA, SCR</em>, and <em>SHR</em> were expanded in grasses but not in sedges. <em>POLAR, SPCH</em>, and <em>ABI</em> were expanded in both lineages, seven families were conserved in both, <em>BASL</em> is not present in both, and, in the <em>ICE1/SCRM2</em> family, <em>SCRM2</em> was lost while <em>ICE1</em> was duplicated in sedges. Gene family expansion in grasses occurred primarily in genes involved in early stages of stomatal development, while the non-duplicated or independently expanded genes shared by sedges and grasses contribute to the development of the two lateral subsidiary cells as well as the guard cells. The gene conservation and independent expansion suggest shared regulatory networks underlying the stomata morphology typical of the order Poales. This study serves as an evolutionary guide for testing functional proteins underlying paracytic dumbbell and dumbbell-like stomata development.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100494"},"PeriodicalIF":2.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143550263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome-guided selection of reference genes from field-grown adult trees and seedlings exposed to defense phytohormones in Erythrina velutina","authors":"Daisy Sotero Chacon ,&nbsp;Cibele Tesser da Costa ,&nbsp;Fábio Antônio Antonelo ,&nbsp;Bernardo Bonilauri ,&nbsp;Taffarel Melo Torres ,&nbsp;Raquel Brandt Giordani ,&nbsp;Arthur Germano Fett-Neto","doi":"10.1016/j.plgene.2025.100496","DOIUrl":"10.1016/j.plgene.2025.100496","url":null,"abstract":"<div><div><em>Erythrina velutina</em> Willd (Fabaceae) is an important non-model tree with pharmaceutical potential, traditionally used in folk medicine at the northeastern Brazilian semiarid region. The species shows anti-inflammatory properties and central nervous system modulation. Our previous work highlighted its capacity of biosynthesizing several bioactive compounds. It was also possible to identify enzyme and transcription factor genes involved in the response to both biotic and abiotic stresses. However, the identification of reference genes (RGs) for real-time quantitative polymerase chain reaction (RT-qPCR) assays and validation of molecular mechanisms is still lacking. Leaves and seeds of field-grown plants and shoots of seedlings exposed to defense phytohormones (sodium nitroprusside and methyl jasmonate, the former as source of nitric oxide) were examined. As a result, 60 transcripts had RPKM (log2) &gt; 2 and CV &lt; 10 %, from which the 11 most conserved were selected: <em>NADH</em>, <em>26S</em>, <em>UPF, PBL27</em>, <em>CYB5</em>, <em>ARP4</em>, <em>ARD2</em>, <em>OAT</em>, <em>CSTF64</em>, <em>NLE</em>, and <em>RAB7</em>. <em>CSTF64</em>, <em>RAB7</em>, <em>NLE</em>, <em>UPF</em> and <em>ARP4</em> exhibited the highest stability and showed positive, and significant correlations, while <em>NADH</em> and <em>PBL27</em> were the least stable genes. The use of two genes was sufficient for normalizing qPCR assays, and the best gene pairs were recommended. All reference genes were validated with target genes, sequenced, and showed adequate melting curves and amplification efficiency. This pioneering identification of reference genes in <em>Erythrina velutina</em> provides a platform for future molecular studies in this unique dryland species. The herein described approach can also be useful in identifying adequate housekeeping genes in other non-model plant species<em>.</em></div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100496"},"PeriodicalIF":2.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel genetic control of alpha-amylase activity during pre-harvest sprouting indicated by RNA sequencing of soft winter wheat varieties Cardinal and Logan","authors":"Bryan W. Penning","doi":"10.1016/j.plgene.2025.100495","DOIUrl":"10.1016/j.plgene.2025.100495","url":null,"abstract":"<div><div>Pre-harvest sprouting, the germination of wheat seeds still in the field, leads to decreased crop value and increased crop losses around the world. Pre-harvest sprouting causes low Falling Number that results in price reductions or rejection of soft winter wheat grain at the flour mill or grain elevator. Several pre-harvest sprouting resistance genes have been found. However, they act through seed dormancy-related signaling pathways which can affect winter wheat root establishment for overwintering and double-cropping wheat with soybean. Here, RNA sequencing has been performed on soft red winter wheat varieties Cardinal and Logan with 91 % of 1978 markers common between them but differing in pre-harvest sprouting resistance. Between 64 and 660 genes were differentially expressed in comparisons between Cardinal and Logan at different time points of seed development. A <em>glucan water diskinase</em> was a top five differentially expressed gene located near a recently reported quantitative trait locus for pre-harvest sprouting. It has potential to reduce alpha amylase activity and starch degradation during pre-harvest sprouting. Slowing starch degradation reduces starch damage, keeping flour pasting viscosity and Falling Number higher under pre-harvest sprouting conditions. Slowing starch damage rather than altering seed dormancy would reduce impact on some agronomic traits.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100495"},"PeriodicalIF":2.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143550262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a meiotic atlas and chromosomal mapping of abundant genome elements in the orphan crop golden thistle (Scolymus hispanicus L.)","authors":"Ahmet L. Tek,&nbsp;Sevim D. Kara Öztürk,&nbsp;Hümeyra Yıldız Akkamış,&nbsp;Elif Sena Köksal,&nbsp;Emir Can Kaya","doi":"10.1016/j.plgene.2025.100493","DOIUrl":"10.1016/j.plgene.2025.100493","url":null,"abstract":"<div><div>Orphan crops have great potential for sustainable agricultural production. Meiosis in sexually reproducing organisms is a crucial process for maintaining the chromosome complement and ensuring genetic diversity by meiotic crossover and segregation of homologous chromosomes. Repetitive DNA elements differ in quantity, sequence, and distribution pattern among species. These elements are useful for taxonomic, phylogenetic, and evolutionary studies, as well as for establishing species-specific karyotypes. The golden thistle (<em>Scolymus hispanicus</em> L.), an orphan crop, is a diploid plant species (2<em>n</em> = 2<em>×</em> = 20) of the Asteraceae family and is common in the Mediterranean region. Despite some research on its phytochemical properties, there are few studies on its molecular biology, genetics, and cytogenetics. Therefore, we aimed to construct an atlas of the meiosis of golden thistle and to discover repetitive genome elements. A novel 180-bp repetitive DNA element, Sh180, of the golden thistle was identified by bioinformatic, molecular and cytogenetic methods. Chromosomal domains containing Sh180, the telomeric repeat TTTAGGGn, 5S and 35S rDNA were mapped on mitotic metaphase chromosomes by fluorescence in situ hybridization (FISH). The Sh180 signals were mapped in the subtelomeric regions of all mitotic metaphase chromosomes. Our findings provide the first information for future genetics and breeding studies such as meiotic, karyotype and phylogenetic analyses of this underutilized crop.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100493"},"PeriodicalIF":2.2,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143388467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple origin of organellar genomes of cultivated pea (Pisum sativum L. subsp. sativum)","authors":"Vera S. Bulgakova,&nbsp;Natalia V. Shatskaya,&nbsp;Oleg E. Kosterin,&nbsp;Gennadiy V. Vasiliev","doi":"10.1016/j.plgene.2025.100492","DOIUrl":"10.1016/j.plgene.2025.100492","url":null,"abstract":"<div><div>The initial area and gene pool involved in plant domestication are a matter of ongoing debates. Earlier we found that pea cultivar Cameor had plastid and mitochondrial genomes related to wild peas of different provenance. We sequenced complete plastid and mitochondrial genomes from 27 accessions to compile a sample of 91 peas including 26 landraces of traditional cultivation. The vast majority of plastid genomes of cultivated peas tightly clustered and was closely related to wild peas primarily from Ponto-Caspian area and Zagros. However, two accessions from Central Asia showed affinity to a different wild pea lineage. Mitochondrial genomes of most cultivated peas were found in three clusters. Accessions most related to wild peas from the domestication ‘Core Area’ originated from periphery of traditional pea cultivation: Africa, Central Asia and Himalaya. Another cluster, related to wild peas from the Balkan Peninsula and Sicily, was present in Central Asia and Greece. Accessions most related to the cultivar Cameor were found throughout the pea cultivation range. We hypothesise that the pea cultivation area, initially occupied by peas domesticated in the ‘Core Area’, underwent two subsequent waves of invasion of cultivated peas with mitochondria introgressed from wild peas from elsewhere. One of the waves spread from South-East Europe and/or West Asia, and the second was associated with relatively recent expansion of crops of European origin. Mitochondrial genomes were supposed to introgress readily from wild to cultivated peas. Knowledge on diversity of organellar genomes of wild and cultivated peas may facilitate appropriate choice of co-adapted nuclear-organellar combinations for breeding programs.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100492"},"PeriodicalIF":2.2,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143372663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution of flavonoids in Paeonia suffruticosa and analyses of the genes involved in flavonoid biosynthesis in plants","authors":"Seungki Lee ,&nbsp;Nam-Il Park ,&nbsp;Yeri Park ,&nbsp;Kweon Heo ,&nbsp;Yongsoo Kwon ,&nbsp;Eun Sil Kim ,&nbsp;Youn Kyoung Son ,&nbsp;Kyung Jin Lee ,&nbsp;Seung Young Choi ,&nbsp;Beom-Soon Choi ,&nbsp;Nam-Soo Kim ,&nbsp;Ik-Young Choi","doi":"10.1016/j.plgene.2025.100490","DOIUrl":"10.1016/j.plgene.2025.100490","url":null,"abstract":"<div><div><em>Paeonia suffriticosa</em> is a woody peony that is an important medicinal plant in Korea, China, and Japan. Flavonoids are a class of polyphenolic secondary metabolites. We analyzed seven flavonoid compounds in various tissues of Korean landrace <em>P. suffriticosa</em>. Of these, flavonols were more abundant compared with other flavonoids in the roots, leaves, and petals, whereas flavones (apigenin and luteolin) were present in low abundance in all tissues. The root tissues generally contained higher flavonoid content compared with the other tissues. Because molecular analyses of the genes involved in flavonoid biosynthesis genes have not been systematically conducted in <em>P. suffriticosa</em>, we performed a transcriptome analysis, which identified 34,629 unigenes in the transcriptome. Our functional matching results using the NCBI Nr and in EMBL-EBI EMBL Interpro databases were similar to those of previous reports in <em>P. suffriticosa</em>. The highest matching species for the annotated genes was <em>V. vinifera,</em> which was corroborated in reports from other <em>Paeonia</em> species. The genes encoding enzymes in the shikimate pathway and aromatic amino acids biosynthesis genes were identified from the transcriptome data. We also identified homologous genes in other <em>Paeonia</em> species as well as Arabidopsis and rice. The number of gene copies varied from one in DHQS and CS to seven to ten in 4CL. Sequence and phylogenetic analyses revealed that several conserved blocks were observed in 4CLs from nonvascular to vascular plants. A <em>CHS</em> analysis revealed that there were at least three homologs of CHSs in the genus <em>Paeonia</em>. The sequences of the catalytic residues, CoA binding sites, and structural activity of the CHSs were conserved from the basal plant of liverwort to vascular flowering plants. In a phylogenetic analysis of CHS and CHI, the CHSs from the major plant lineages formed their own cluster, whereas CHIs from diverse plant lineages were clustered together. Protein sequences were highly conserved among the CHIs within clades, but diverged between clades. Thus, CHSs of each major plant lineage may have evolved independently following divergence, whereas CHIs in each clade in the phylogenetic analysis may have evolved separately from basal plants to angiosperms.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100490"},"PeriodicalIF":2.2,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the complete CDS sequence of Bibenzyl synthase (BBS) gene in Pholidota articulata and its transcriptional regulation under different stress conditions","authors":"Swagata Debnath,&nbsp;Suman Kumaria","doi":"10.1016/j.plgene.2025.100491","DOIUrl":"10.1016/j.plgene.2025.100491","url":null,"abstract":"<div><div>Bibenzyl synthase (BBS) is one of the key enzymes for the formation of bibenzyls, a class of specialized therapeutic metabolites that are predominantly found in the family Orchidaceae. The present study reports the complete transcript of the <em>BBS</em> gene isolated and sequenced from an ethnomedicinally important orchid, <em>Pholidota articulata</em> Lindl. The <em>BBS</em> transcript of <em>P. articulata</em> (<em>PaBBS</em>) was found to comprise a total of 1494 bp with an open reading frame coding for 390 amino acids. Multiple sequence analysis and phylogenetic analysis highlighted its close association with <em>BBS</em> sequences and type III polyketide synthase (PKS III) genes of other plant species. Three-dimensional structure analysis has revealed that the PaBBS protein is a homodimer with each subunit having a molecular weight of 42.83 KDa. <em>In silico</em> studies of the putative PaBBS protein revealed the presence of the characteristic conserved regions of the BBS enzyme as well as the PKS III superfamily. The present study also revealed that expression <em>PaBBS</em> is influenced by the age of the plant, tissue type, abiotic stress, and exposure to elicitors. The expression of <em>PaBBS</em> transcript was recorded to be higher in young plantlets as compared to mature plants, and among the plant parts the root tissue exhibited the highest expression. Further, it was found that the expression of <em>PaBBS</em> was upregulated by abiotic stresses such as wounding and heat treatment, downregulated by high-intensity UV exposure and cold treatment, and increased many-fold when exposed to elicitors like chitosan and yeast extract. The results obtained in the present study provide an understanding of the transcriptional regulation of <em>PaBBS</em> gene which plays a crucial role in the ecological adaptation of <em>P. articulata</em>, an orchid of medicinal importance<em>.</em></div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100491"},"PeriodicalIF":2.2,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic patterns of understudied species within the plant genus Brassica: Future prospects in the post genomics-era","authors":"Parthiban Subramanian ,&nbsp;Hemavathi Brijesh ,&nbsp;Bum-Soo Hahn","doi":"10.1016/j.plgene.2024.100489","DOIUrl":"10.1016/j.plgene.2024.100489","url":null,"abstract":"<div><div><em>Brassica</em> remains to be one of the agriculturally important genera of plants worldwide due to its diverse nature of crops cultivated all across the globe. Despite the rich species diversity within the genus <em>Brassica</em>, detailed studies on phylogeny and evolutionary origins have primarily focused on just six species, which have given rise to nearly all of the currently cultivated Brassica crops. Continuous breeding practices for specific traits in these six species have led to significant challenges, including nutrient depletion, increased susceptibility to plant pathogens, and vulnerability to changing climate conditions in the present generation of crops. Lack of established phylogenetic relationships among the species of <em>Brassica</em> remains to be a significant barrier hindering error-free conservation and use of <em>Brassica</em> resources. We have identified putative phylogenetic relationships between <em>Brassica</em> crop wild relatives (CWRs) by reinforcing data from several genetic markers and metabolite based studies. Supplementation of genomic data for a robust phylogeny and current status of availability of genomic data of <em>Brassica</em> crop wild relatives (CWRs) from public database has been highlighted. This report identifies critical gaps in <em>Brassica</em> research addressing of which would facilitate effective conservation and use of <em>Brassica</em> genetic resources.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100489"},"PeriodicalIF":2.2,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Saffron corms transcriptome analysis reveals genes associated with corm rot disease","authors":"Ali Darvishian ,&nbsp;Farhad Nazarian-Firouzabadi ,&nbsp;Ahmad Ismaili ,&nbsp;Mostafa Darvishnia","doi":"10.1016/j.plgene.2024.100488","DOIUrl":"10.1016/j.plgene.2024.100488","url":null,"abstract":"<div><div>Saffron (<em>Crocus sativus</em> L.) is by far the most expensive spice in the world. Low water requirements, straightforward agricultural practices, diverse applications in the food, pharmaceutical and textile industries, are major advantages for its widely cultivation worldwide. Saffron is genetically sterile and hence it is propagated through corms. As a perennial plant, its corms remain in the field for at least three consecutive cultivation seasons, increasing their susceptibility to soilborne pathogens. Among devastating soilborne plant pathogens, <em>Fusarium oxysporum</em> f. sp., the causal agent of corm rot, poses a significant threat to saffron cultivation globally. The development of effective management strategies against <em>F. oxysporum</em> is impeded by the absence of resistant genotypes and a limited understanding of its pathogenicity. To assess and find genes associated with the response to <em>F. oxysporum</em> infection, the corm transcriptome was analyzed following <em>F. oxysporum</em> inoculation by RNA-seq. More than 294,520 and 243,328 transcripts were documented. Out of 168,448 identified unigenes, 34,862, 15,234 and 27,213 unigenes were annotated in NCBI non-redundant (Nr) protein database, GO and UniProtKB/Swiss-Prot databases, respectively. Out of 38,643 annotated genes, 2169 genes exhibited differential expression in response to <em>F. oxysporum.</em> Among these, 1832 genes showed decreased expression, whereases 337 genes displayed increased expression. Quantitative RT-PCR analysis confirmed the expression patterns of 10 hub genes, including chitinase, a serine/threonine kinase and a WRKY transcription factor gene. In contrast, the relative expression of a pectin methylesterase, a Flavodoxin-like quinone oxidoreductase and HSP genes were found to be down-regulated. The findings of this study clearly demonstrate that <em>F. oxysporum</em> infection significantly perturbs the expression of corms R-genes, suggesting that such genes can be used to improve saffron plant resistance to fungal and oomycetes soilborne pathogens in future breeding programs.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100488"},"PeriodicalIF":2.2,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143177774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary dynamics of Senna: Perspectives from plastome evolution and phylogenomics","authors":"Samaila Samaila Yaradua ,&nbsp;Faten Zubair Filimban","doi":"10.1016/j.plgene.2024.100486","DOIUrl":"10.1016/j.plgene.2024.100486","url":null,"abstract":"<div><div>Genus <em>Senna</em> (Caesalpinioideae, <em>Fabaceae</em>) comprises about 350 species mainly distributed in the American continent. Despite the sequencing and assembly of the chloroplast genome of some of the species in the genus, the chloroplast genome sequence and structural variation have not been evaluated, and the evolutionary relationship within the genus is still lacking. In this study, we sampled different species of the genus representing the six sections to examine the variation in the genome and phylogenetic relationships. The chloroplast genome of <em>Senna</em> has a typical quadripartite structure with a size ranging from 148, 437 bp to 162, 426 bp. There are gene losses in some species of the genus, the earliest diverged species lost 9 protein-coding genes which were recovered in the latter diverged lineages. No inversion was detected in the genome but there is a significant level of sequence variation, gene number, and genome size, that provide valuable information on the evolution of the genus. The following regions are the most variable regions in the genus and can be used as DNA barcodes for the identification of the species: <em>Psba, ndhH, trnT-trnL</em>, <em>trnG-trnR</em>, <em>rps18</em>-<em>rpl20</em>, and <em>trnI-rrn16</em>. The phylogenomic analysis revealed a well-resolved phylogenetic relationship of the genus, supporting the monophyly of the genus. The phylogenetic tree reported the phylogenetic positions and sister relationships of some species for the first time. Our result revealed that section Chameafistula is paraphyletic and calls for the revision of the infrageneric classification of the genus.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100486"},"PeriodicalIF":2.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143176480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}