Quantification of new and archived Diaphorina citri transcriptome data using a chromosomal length D. citri genome assembly reveals the vector’s tissue-specific transcriptional response to citrus greening disease

BackgroundHuanglongbing (HLB) is the most serious disease of citrus. HLB is caused by the obligate, intracellular bacterium “Candidatus Liberibacter asiaticus” (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid. Development of transmission blocking strategies to manage HLB relies on knowledge of CLas-D. citri interactions at the molecular level. Prior transcriptome analyses of CLas-infected and un-infected D. citri point to changes in psyllid biology due to CLas-infection. These studies relied on incomplete versions of the D. citri genome, lacked proper host plant controls, and/or were analyzed using different statistical approaches. Therefore, we used standardized experimental and computational approaches to identify differentially expressed genes in both CLas (+) and CLas (-) D. citri. The comparative analysis utilized the newest chromosomal length D. citri genome assembly Diaci_v3. In this work, we present a quantitative transcriptome analysis of excised heads, salivary glands, midguts and bacteriomes from CLas (+) and CLas (-) insects.ResultsEach organ had unique transcriptome profiles and responses to CLas infection. Though most psyllids were infected with CLas, CLas-derived transcripts were not detected in all organs. By analyzing the midgut dataset using both the Diaci_v1.1 and v3.0 D. citri genomes, we showed that improved genome assembly led to significant and quantifiable differences in RNAseq data interpretation.ConclusionsOur results support the hypothesis that future transcriptome studies on circulative, vector-borne pathogens should be conducted at the tissue specific level using complete, chromosomal-length genome assemblies for the most accurate understanding of pathogen-induced changes in vector gene expression.

Orcein and DAPI-stained karyotype analysis of Alocasia macrorrhizos (L.) G. Don

Karyotype analyses are required for the identification, characterization, and genetic improvement of any organism. Alocasia macrorrhizos (L.) G. Don. was investigated cytogenetically to determine the karyotypic features. Complex chromocenter type, of interphase nuclei, and gradient type of prophase chromosomes were found in this study. Alocasia macrorrhizos was found to possesses 2n=28 chromosomes. The total length of the 2n chromosome complement was recorded as 98.83±1.39 μm. The range of chromosomal length was 2.50±0.10-4.70±0.10 μm. A gradual decrease in chromosomal length was observed. The total form (TF%) value was found to be 43.58%, Karyotype symmetry index (Syi %) was 77.00 % and karyotype asymmetry index (AsK %) was 56.66%. The centromeric formula was 18m+4sm+2ac, representing asymmetric karyotype. In DAPI banding, the 1.48% positive banded region indicates the lower amount of AT rich repeats in this material. Therefore, Alocasia macrorrhizos could be authentically characterized through karyotype analysis. J. Bangladesh Acad. Sci. 45(1); 27-35: June 2021

Comparative karyomorphological analysis of two varieties of Brassica campestris from Bangladesh

Two varieties of the oilseed plant viz. Brassica campestris var. Tori-7 and Brassica campestris var. BARI Sarisha-9 were karyomorphologically investigated following orcein staining. Presence of “Round Pro-chromosome Type” of interphase nuclei and “Continuous Type” of prophase chromosomes indicating that both Tori-7 and BARI Sarisha-9 were originated from common ancestor. Moreover, both the varieties were found to possess 2n=20 chromosomes with almost similar range of length i.e.; 0.90±0.04-2.51±0.05μm for Tori-7 and 0.99±0.06-2.60±0.06μm for BARI Sharisha-9. The total length of 2n chromosome complement was recorded as 29.61±0.76μm for Tori-7 and 29.75±0.80μm for BARI Sharisha- 9 where a slight gradual decrease of chromosomal length was observed in both cases. Average chromosomal length, range of individual chromosomal length, relative length and centromeric index of both varieties were more or less similar. Karyotype symmetry index and Karyotype asymmetry index indicating the symmetric nature of both varieties. All metacentric chromosomes were found in Tori-7 representing strictly symmetric karyotype. Beside metacentric, 2 sub-metacentric chromosomes were found in BARI Sharisha-9 representing almost symmetric karyotype. Thus the two varieties of Brassica campestris -were plants of primitive nature. However, BARI Sharisha-9 can be considered comparatively advanced than Tori-7 based on different cytogenetical features. Therefore, the compilation of these karyomorphological information will be useful for authentic identification and characterization of the two varieties of Brassica campestris which are very basic and important information for breeding in crop improvement programme. Jahangirnagar University J. Biol. Sci. 9(1 & 2): 69-77, 2020 (June & December)

Utilizing a chromosomal-length genome assembly to annotate the Wnt signaling pathway in the Asian citrus psyllid, Diaphorina citri

The Asian citrus psyllid, Diaphorina citri, is an insect vector that transmits Candidatus Liberibacter asiaticus, the causal agent of the Huanglongbing (HLB), or citrus greening disease. This disease has devastated Florida’s citrus industry, and threatens California’s industry as well as other citrus producing regions around the world. To find novel solutions to the disease, a better understanding of the vector is needed. The D. citri genome has been used to identify and characterize genes involved in Wnt signaling pathways. Wnt signaling is utilized for many important biological processes in metazoans, such as patterning and tissue generation. Curation based on RNA sequencing data and sequence homology confirms 24 Wnt signaling genes within the D. citri genome, including homologs for beta-catenin, Frizzled receptors, and seven Wnt-ligands. Through phylogenetic analysis, we classify D. citri Wnt ligands as Wg/Wnt1, Wnt5, Wnt6, Wnt7, Wnt10, Wnt11, and WntA. The D. citri version 3.0 genome with chromosomal length scaffolds reveals a conserved Wnt1-Wnt6-Wnt10 gene cluster with a gene configuration like that in Drosophila melanogaster. These findings provide greater insight into the evolutionary history of D. citri and Wnt signaling in this important hemipteran vector. Manual annotation was essential for identifying high quality gene models. These gene models can be used to develop molecular systems, such as CRISPR and RNAi, which target and control psyllid populations to manage the spread of HLB. Manual annotation of Wnt signaling pathways was done as part of a collaborative community annotation project.

Evaluation of Chromosomal Structural Anomalies in Fertility Disorders

Background and objectives: Reproductive disorders may occur not only due to environmental factors (air pollution, stressful lifestyle, previous abortions or the use of contraceptives) but also due to genetic factors. Materials and Methods: The aim of the study was to identify the range and frequency of chromosomal aberrations in couples (n = 99) with infertility or recurrent miscarriages in Lithuania. The data were collected from the out-patient medical histories. The couples were divided into three groups based on pregnancy, childbirth and the number of miscarriages. The Chi-square test was used to carry out the statistical analysis, and the statistical significance was (p < 0.05). Results: There were 6.6% (n = 13) structural changes observed in the karyotype tests. Chromosomal aberrations were found in 3% (n = 6) of the subjects, while 3.6% (n = 7) of them had chromosomal length polymorphisms. No difference was found between the aberration frequency in the karyotypes of men and women (p > 0.05). The most common aberrations were balanced translocations (23.1%, n = 3) which accounted for 15.4% of the reciprocal (n = 2) and 7.7% of the Robertsonian type (n = 1) of translocations. The most frequent aberrations were found in couples with the inability to conceive (42.9% (n = 3), p = 0.031). The childless couples and those with recurrent miscarriages showed an aberration rate of 8.2% (n = 5), while in the couples with at least one child it was 16.1% (n = 5). The group of couples unable to conceive had a significantly higher aberration rate of 28.6% (n = 2), p = 0.029. Miscarriages in partners’ families accounted for 8.1%. Miscarriages on the female side of the family accounted for 4.5% (n = 9), on the male side it accounted for 2.5% (n = 5) and on both sides it accounted for 1.1% (n = 2). There were no statistically significant differences observed between the female and male sides (p > 0.05). The miscarriages observed in the second group of couples (childless with ≥2 miscarriages) were more frequent at 18.1% (n = 11), in the third group (having children ≥2 miscarriages) they were less frequent at 12.9% (n = 4), while no miscarriages were recorded in the first group of infertile couples. In total, 3% of the identified significant chromosomal aberrations were likely to trigger miscarriages or the inability to conceive. Conclusions: In couples with reproductive disorders, chromosomal mutations and chromosomal length polymorphisms were found at similar rates: 3% vs. 3.6%. The highest aberration rate was found in couples that were unable to conceive, a lower one was found in a group with children and ≥2 miscarriages, and the lowest one was found in a childless group of subjects with ≥2 miscarriages. The miscarriage rate in partner families was 8.1%; however, no difference was found between the male and female sides.

Chromosomal length reference assembly for Diaphorina citri using single-molecule sequencing and Hi-C proximity ligation with manually curated genes in developmental, structural and immune pathways

Hemipterans include some of the most important insect pests of agricultural systems and vectors of plant pathogens. The vector, Diaphorina citri (Asian citrus psyllid) belonging to the Psylloidae superfamily, is the primary target of approaches to stop the spread of the pathogen Ca. Liberibacter asiaticus that causes Huanglongbing or citrus greening disease. High quality genomic resources enable rapid functional discovery that can target disease transmission and control. The previous psyllid genome (Diaci v1.1) available in NCBI is missing 25% of the single copy markers conserved in other Hemipterans. Manual genome curation helped to identify a significant number of genome anomalies including misassemblies and missing genes. We present an improved and highly contiguous de novo assembly based on PacBio long reads followed by Dovetail Chicago and Hi-C based scaffolding. The current assembly (Diaci v3) has 13 chromosomal length scaffolds with a genome size of 475 Mb. This is the first report of a chromosomal length assembly in the Hemiptera order according to our knowledge. Full-length cDNA transcripts were sequenced with PacBio Iso-Seq technology from diseased and healthy tissue at multiple life stages. Iso-Seq along with diverse Illumina RNA-Seq expression data were used to predict 19,049 protein-coding genes in psyllid using MAKER annotation pipeline. We also generated a genome independent transcriptome with a comprehensive catalog of all genes in the psyllid.Gene-targeting technologies like RNAi, antisense oligos and CRISPR require accurate annotation of genes. Lack of closely related and well characterized model organisms coupled with the diversity of insect genomes impacts the quality of predicted gene models. We used the improved genomic resources to create a high-quality manually curated gene set for developmental, structural and immune pathways. All resources are available on https://citrusgreening.org/, a portal for all omics resources for the citrus greening disease research community. The high quality ACP genome assembly, annotation based on transcriptomics evidence, manual curation of critical pathways and a genome independent de novo transcriptome will provide a foundation for comparative analysis among genomes of agricultural pests and vectors in the Hemiptera.

Chromosome Nomenclature and Cytological Characterization of Sacred Lotus

Sacred lotus is a basal eudicot plant that has been cultivated in Asia for over 7,000 years for its agricultural, ornamental, religious, and medicinal importance. A notable characteristic of lotus is the seed longevity. Extensive endeavors have been devoted to dissect its genome assembly, including the variety China Antique, which germinated from a 1,300-year-old seed. Here, cytogenetic markers representing the 10 largest megascaffolds, which constitute approximately 70% of the lotus genome assembly, were developed. These 10 megascaffolds were then anchored to the corresponding lotus chromosomes by fluorescence in situ hybridization using these cytogenetic markers, and a set of chromosome-specific cytogenetic markers that could unambiguously identify each of the 8 chromosomes was generated. Karyotyping was conducted, and a nomenclature based on chromosomal length was established for the 8 chromosomes of China Antique. Comparative karyotyping revealed relatively conserved chromosomal structures between China Antique and 3 modern cultivars. Interestingly, significant variations in the copy number of 45S rDNA were detected between China Antique and modern cultivars. Our results provide a comprehensive view on the chromosomal structure of sacred lotus and will facilitate further studies and the genome assembly of lotus.

Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects

Faithful chromosome segregation in all eukaryotes relies on centromeres, the chromosomal sites that recruit kinetochore proteins and mediate spindle attachment during cell division. The centromeric histone H3 variant, CenH3, is the defining chromatin component of centromeres in most eukaryotes, including animals, fungi, plants, and protists. In this study, using detailed genomic and transcriptome analyses, we show that CenH3 was lost independently in at least four lineages of insects. Each of these lineages represents an independent transition from monocentricity (centromeric determinants localized to a single chromosomal region) to holocentricity (centromeric determinants extended over the entire chromosomal length) as ancient as 300 million years ago. Holocentric insects therefore contain a CenH3-independent centromere, different from almost all the other eukaryotes. We propose that ancient transitions to holocentricity in insects obviated the need to maintain CenH3, which is otherwise essential in most eukaryotes, including other holocentrics.

Karyological studies in Brazilian species of Lippia L. (Verbenaceae)

The genus Lippia (Verbenaceae) comprise around 160 species spread out mainly in South and Central Americas with few African species, some of them with potential medicinal use. Brazil is one the most important centers of diversity with approximately 75% of the species described so far. Innumerous species are endemic and poorly studied especially at a cytological level. Here, chromosomal length, karyomorphology and chromosome asymmetry of twelve Brazilian species of Lippia were evaluated [L. alba (Miller) N.E.Brown, L. diamantinensis Glaz., L. florida Cham., L. hermanioides Cham., L. lacunosa Mart. & Schauer, L. lupulina Cham., L. pohliana Schauer, L. pseudothea (St. Hil) Schauer, L. rosella Moldenke, L. rotundifolia Cham., L. rubella Moldenke and L. sidoides Cham.]. The analysis suggested that the genus has a variable chromosome number (from 2n = 20 to 2n = 56) originated by dysploidy and polyploidy. This is the first description of chromosome morphology for 11 of the 12 Lippia species studied.