Explore the vast range of titles available.

Lavandula maroccana Murb., an endemic species of the western Mediterranean, is classified as vulnerable and was added to the International Union for Conservation of Nature (IUCN) Red List in 2020. We assembled and annotated the chloroplast genome and compared it with chloroplast genomes of five previously published Lavandula species. The assembled chloroplast genome of L. maroccana , spans 151,323 bp, and exhibits a typical quadripartite structure, consisting of an 82,861 bp large single-copy (LSC) region, a 17,452 bp small single-copy (SSC) region, and two 25,505 bp inverted repeat (IR) regions. The genome has a GC content of 38% and contains 110 unique genes, 37 tRNA genes, and 4 rRNA genes. A total of 37 perfect SSR motifs were identified, with most being mononucleotide repeats. Pentanucleotide and hexanucleotide repeats were absent as perfect motifs but were present as imperfect motifs at a lower frequency than other repeat types. AT-rich SSRs were more prevalent than GC-rich motifs. Palindromic and forward repeats were more frequent than complementary and reverse repeats. Nucleotide sequence diversity (Pi) values ranged from 0.004 ( atpH ) to 0.035 ( matK ), with protein-coding genes found to be under purifying selection. Phylogenomic analyses, based on the complete plastome sequences and the matK + trnL genes, revealed that intra- and inter-species diversity within Lavandula species. We compared the genomes, and their evolutionary relationships, and genetic structures with published chloroplast genomes from other species- L. maroccana , L. angustifolia , and L. dentata .

Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

Banana (Musa spp.) is an important tropical crops. Low temperature is one of the key environmental stresses, which greatly affects the global banana production. Different varieties of banana exhibit a high degree of genetic variability for cold tolerance. Compared with Cavendish banana, Dajiao has superior cold tolerance. Cloning of Dajiao cold-tolerant genes and characterization of their functions could reveal the molecular mechanism of cold tolerance in Dajiao. Our previous comparative transcriptome analysis of cold-sensitive Cavendish banana and cold-tolerant Dajiao identified several cold-tolerance candidate genes in Dajiao. In this study, a Dajiao candidate gene, MpMYBS3 (homolog of MYBS3 in rice), encoding a transcription factor, was cloned and characterized. Amino acid sequence alignments showed that MpMYBS3 belongs to the R1-type MYB transcription factors. Subcellular localization analysis indicated that MpMYBS3 is located in the nucleus. Heterologous overexpression of MpMYBS3 in banana showed that the transgenic lines had significantly higher cold tolerance than the wild-type, which might be associated with the increased accumulation of proline, and a reduction in malondialdehyde content and electrolyte leakage. Surprisingly, MYBS3 repressed the well-known ICE1–CBF-dependent cold signaling pathway in banana: the MaCBF1 and MaCBF2 genes were repressed at the transcriptional level after cold treatment. However, MaMKRY46 was significantly induced in transgenic bananas overexpressing MpMYBS3 under cold stress. These findings suggest that MYBS3-mediated cold signaling as a key player in cold adaptation of banana.

Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

Background Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance. PDI family genes are among of them. Results We have identified 32 PDI genes from the Br135K microarray dataset, NCBI and BRAD database, and in silico characterized their sequences. Expression profiling of those genes was performed using cDNA of plant samples imposed to abiotic stresses; cold, salt, drought and ABA (Abscisic Acid) and biotic stress; Fusarium oxysporum f. sp. conglutinans infection. The Chinese cabbage PDI genes were clustered in eleven groups in phylogeny. Among them, 15 PDI genes were ubiquitously expressed in various organs, while 24 PDI genes were up-regulated under salt and drought stress. By contrast, cold and ABA stress responsive gene number were ten and nine, respectively. In case of F. oxysporum f. sp. conglutinans infection 14 BrPDI genes were highly up-regulated. Interestingly, BrPDI1–1 gene was identified as putative candidate against abiotic (salt and drought) and biotic stresses, BrPDI5–2 gene for ABA stress, and BrPDI1–4, 6–1 and 9–2 were putative candidate genes for both cold and chilling injury stresses. Conclusions Our findings help to elucidate the involvement of PDI genes in stress responses, and they lay the foundation for functional genomics in future studies and molecular breeding of Brassica rapa crops. The stress-responsive PDI genes could be potential resources for molecular breeding of Brassica crops resistant to biotic and abiotic stresses.

Ensete ventricosum is a morphologically gigantic, monocot, diploid sister to the banana plant species. It is commercially cultivated as a starch source, only in Ethiopia, where it feeds twenty million people. Here, the complete chloroplast (CP) genomes of 15 diverse landraces of E. ventricosum were assembled and annotated, for comparative genomics, genetic diversity analysis, and molecular marker development. The assembled E. ventricosum CP genomes ranged between 168,388 and 168,806 bp. The sampled CP genomes were quadripartite in structure and had two single-copy regions, a large single-copy region (LSC, average length 88,657 bp), and a small single-copy region (SSC, average length 11,098 bp) separated by inverted repeat regions (IR, average length 34,437 bp). The total number of annotated genes varies between 135 and 138, including 89–92 protein-coding genes, 38 tRNA genes, and 4 rRNA genes. All CP genes, including non-functional ones and intergenic regions, were transcribed with the transcriptome, covering almost 92% of the E. ventricosum CP genome. Codon usage, amino acid frequency, GC contents, and repeat nucleotides were similar among the 15 landraces. Mono- and tetranucleotide simple sequence repeats (SSRs) were found more frequently than other SSRs. An average of 71% of these SSRs were located in the LSC region, and the majority of the SSR motifs were composed of A/T nucleotides. A phylogenetic analysis of the 15 Ensete landraces indicated a common evolutionary origin, while the China sample was positioned separately, suggesting notable genetic differences. This study presents a comparative analysis of the chloroplast genomes of 15 E. ventricosum landraces, providing valuable insights into their genetic diversity and evolution. The identified SSR markers and conserved genomic features offer essential resources for future research and an improvement in Ensete conservation and breeding.

Homozygous genotypes are valuable for genetic and genomic studies in higher plants. However, obtaining homozygous perennial plants using conventional breeding techniques is currently a challenge because of a long juvenile period, high heterozygosity and the substantial inbreeding depression. In vitro androgenesis has been used to develop haploid and doubled haploid plants. In this study, we report the regeneration of doubled haploid lines of Valencia sweet orange cv. Rohde Red (Citrus sinensis [L.] Osbeck) via anther culture. Anthers at the uninucleate stage were induced and two embryogenic calli were obtained that further regenerated to embryoids (2/400). Plantlets were obtained after transferring the embryoids to a shoot regeneration medium, but were short-lived. Ploidy analysis via both flow cytometry and chromosome counting verified that these two lines were diploids. Additionally, 43 simple sequence repeat (SSR) markers which showed to be heterozygous in the Valencia sweet orange donor line confirmed homozygosity and doubled haploids in the anther-derived lines. Furthermore, analysis of the doubled haploids via cleaved amplified polymorphic sequence (CAPS) markers and target region sequencing confirmed the allelic state of two genes (LCYE and LCYB) involved in the carotenoid biosynthesis of sweet oranges.

In this study, two different hybrids of Easter lily ( Lilium longiflorum) , obtained from two cross combinations, along with their four parents were sequenced by high–throughput RNA–sequencing (RNA–Seq) to find out differentially expressed gene in parent-hybrid combinations. The leaf mRNA profiles of two hybrids and their four parents were RNA–sequenced with a view to identify the potential candidate genes related to plant height heterosis. In both cross combinations, based to morphological traits mid–parent heterosis (MPH) was higher than high–parent heterosis (HPH) for plant height, leaf length, and number of flowers whereas HPH was higher than MPH for flowering time. A total of 4,327 differentially expressed genes (DEGs) were identified through RNA–Seq between the hybrids and their parents based on fold changes (FC) ≥ 2 for up– and ≤ –2 for down–regulation. Venn diagram analysis revealed that there were 703 common DEGs in two hybrid combinations, those were either up– or down–regulated. Most of the commonly expressed DEGs exhibited higher non–additive effects especially overdominance (75.9%) rather than additive (19.4%) and dominance (4.76%) effects. Among the 384 functionally annotated DEGs identified through Blast2GO tool, 12 DEGs were up–regulated and 16 of them were down–regulated in a similar fashion in both hybrids as revealed by heat map analysis. These 28 universally expressed DEGs were found to encode different types of proteins and enzymes those might regulate heterosis by modulating growth, development and stress–related functions in lily. In addition, gene ontology (GO) analysis of 260 annotated DEGs revealed that biological process might play dominant role in heterotic expression. In this first report of transcriptome sequencing in Easter lily, the notable universally up-regulated DEGs annotated ABC transporter A family member–like, B3 domain–containing, disease resistance RPP13/1, auxin–responsive SAUR68–like, and vicilin–like antimicrobial peptides 2–2 proteins those were perhaps associated with plant height heterosis. The genes expressed universally due to their overdominace function perhaps influenced MPH for greater plant height― largely by modulating biological processes involved therein. The genes identified in this study might be exploited in heterosis breeding for plant height of L. longiflorum .

Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, and ILP markers from Musa and its sister species, creating a comprehensive molecular marker repository for the improvement of Musa species. This database contains 2,115,474 SSR, 63,588 SNP, and 91,547 ILP markers developed from thirteen Musa species and two of its relative species. We found that 77% of the SSR loci are suitable for marker development; 38% of SNP markers originated from the genic region, and transition mutations (C↔T; A↔G) were more frequent than transversion. The database is freely accessible and follows a ‘three-tier architecture,’ organizing marker information in MySQL tables. It has a user-friendly interface, written in JavaScript, PHP, and HTML code. Users can employ flexible search parameters, including marker location in the chromosome, transferability, polymorphism, and functional annotation, among others. These distinctive features distinguish the Musa Marker Database (MMdb) from existing marker databases by offering a novel approach that is tailored to the precise needs of the Musa research community. Despite being an in silico method, searching for markers based on various attributes holds promise for Musa research. These markers serve various purposes, including germplasm characterization, gene discovery, population structure analysis, and QTL mapping.

Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense (Foc), is one of the most destructive diseases of banana. Toxins produced by Foc have been proposed to play an important role during the pathogenic process. The objectives of this study were to investigate the contamination of banana with toxins produced by Foc, and to elucidate their role in pathogenesis. Twenty isolates of Foc representing races 1 and 4 were isolated from diseased bananas in five Chinese provinces. Two toxins were consistently associated with Foc, fusaric acid (FA) and beauvericin (BEA). Cytotoxicity of the two toxins on banana protoplast was determined using the Alamar Blue assay. The virulence of 20 Foc isolates was further tested by inoculating tissue culture banana plantlets, and the contents of toxins determined in banana roots, pseudostems and leaves. Virulence of Foc isolates correlated well with toxin deposition in the host plant. To determine the natural occurrence of the two toxins in banana plants with Fusarium wilt symptoms, samples were collected before harvest from the pseudostems, fruit and leaves from 10 Pisang Awak 'Guangfen #1' and 10 Cavendish 'Brazilian' plants. Fusaric acid and BEA were detected in all the tissues, including the fruits. The current study provides the first investigation of toxins produced by Foc in banana. The toxins produced by Foc, and their levels of contamination of banana fruits, however, were too low to be of concern to human and animal health. Rather, these toxins appear to contribute to the pathogenicity of the fungus during infection of banana plants.