Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diversification of mandarin citrus by hybrid speciation and apomixis.

ABSTRACT: The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.

SUBMITTER: Wu GA

PROVIDER: S-EPMC8313541 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Structural variation and parallel evolution of apomixis in citrus during domestication and diversification.

Project description:Apomixis, or asexual seed formation, is prevalent in Citrinae via a mechanism termed nucellar or adventitious embryony. Here, multiple embryos of a maternal genotype form directly from nucellar cells in the ovule and can outcompete the developing zygotic embryo as they utilize the sexually derived endosperm for growth. Whilst nucellar embryony enables the propagation of clonal plants of maternal genetic constitution, it is also a barrier to effective breeding through hybridization. To address the genetics and evolution of apomixis in Citrinae, a chromosome-level genome of the Hongkong kumquat (Fortunella hindsii) was assembled following a genome-wide variation map including structural variants (SVs) based on 234 Citrinae accessions. This map revealed that hybrid citrus cultivars shelter genome-wide deleterious mutations and SVs into heterozygous states free from recessive selection, which may explain the capability of nucellar embryony in most cultivars during Citrinae diversification. Analyses revealed that parallel evolution may explain the repeated origin of apomixis in different genera of Citrinae. Within Fortunella, we found that apomixis of some varieties originated via introgression. In apomictic Fortunella, the locus associated with apomixis contains the FhRWP gene, encoding an RWP-RK domain-containing protein previously shown to be required for nucellar embryogenesis in Citrus. We found the heterozygous SV in the FhRWP and CitRWP promoters from apomictic Citrus and Fortunella, due to either two or three miniature inverted transposon element (MITE) insertions. A transcription factor, FhARID, encoding an AT-rich interaction domain-containing protein binds to the MITEs in the promoter of apomictic varieties, which facilitates induction of nucellar embryogenesis. This study provides evolutionary genomic and molecular insights into apomixis in Citrinae and has potential ramifications for citrus breeding.

| S-EPMC9671666 | biostudies-literature

Citrus hybrid cultivar cultivar:Ponkan mandarin

Project description:Citrus hybrid cultivar cultivar:Ponkan mandarin Raw sequence reads

| PRJNA545864 | ENA

Citrus hybrid cultivar cultivar:Ponkan mandarin

Project description:Ponkan mandarin methylation

| PRJNA545866 | ENA

High incidence of citrus tristeza virus in mandarin (Citrus reticulata) in North-East states of India.

Project description:Khasi mandarin is one of the most remunerative crop in North Eastern Hills region of India playing a very critical role in the socio-economic upliftment of the people. The orchards of this region were found to express the typical symptoms of citrus tristeza virus (CTV). An extensive survey of the Khasi mandarin orchard for six North Eastern states of India namely Arunachal Pradesh, Meghalaya, Assam, Nagaland, Sikkim and Tripura, was carried out to establish the identity of these viruses using ELISA and PCR/RT-PCR techniques. Out of 300 Khasi mandarin tree samples collected from the six states, 172 were found to be positive for CTV infection by DAS-ELISA indicating 57.33% overall CTV disease incidence. Results revealed presence of CTV in all the surveyed states showing a maximum incidence of 66.00% in Arunachal Pradesh followed by 62.00% in Assam, 60.00% in Meghalaya and Nagaland, 54.00% in Sikkim and 42.33% in Tripura. Higher CTV concentration was recorded in the age group > 15 years (69.09%) followed by 10-15 (57%) and 5-10 years (43.33%). However, this study, to the best of our knowledge, is the first report for the detection of CTV in Khasi mandarin from Arunachal Pradesh, Nagaland and Tripura and also the first authentic survey of overall disease incidence of CTV Khasi mandarins from the six major mandarin growing North Eastern states of India.

| S-EPMC5747839 | biostudies-other

The complete chloroplast genome of Korean popular Citrus hybrid Hallabong mandarin [(Citrus unshiu×C. sinensis)×C. reticulate] (Rutaceae).

Project description:A Citrus hybrid, Hallabong mandarin, is a major Citrus tree largely cultivated in Korea. The complete chloroplast genome sequence of Hallabong mandarin was characterized by de novo assembly using whole genome next generation sequences. The chloroplast genome was 160 703 bp in length and separated into four distinct regions such as large single copy region (87 922 bp), small single copy region (18 801 bp) and a pair of inverted repeat regions (26 990 bp). The genome contained a total of 114 genes including 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic inference using chloroplast genome sequences revealed that Hallabong mandarin was close to Citrus aurantiifolia (Omani lime) and Citrus sinensis (sweet orange).

| S-EPMC7799927 | biostudies-literature

Citrus reticulata cultivar:Mandarin

Project description:Citrus reticulata cultivar:Mandarin Genome sequencing and assembly

| PRJNA942351 | ENA

Citrus reticulata cultivar:Mandarin

Project description:Citrus reticulata cultivar:Mandarin Genome sequencing and assembly

| PRJNA951226 | ENA

Synthetic apomixis transfers stably over multiple generations in hybrid rice

Project description:we reproduced the clonal plants of Fix (Fixation of rice heterozygosity) to T4 generation with 1.9~3.2% clonal seeds rate of Fix-T01th, T12th, T23th and T34th. The descendant clonal plants Fix-T0, T1, T2, T3 and T4 exhibited no discernible differences on plant morphology, clonal seeds rate (3.7~4.3%), genome, methylome and transcriptome. Unexpectedly, few aneuploids were identified in each generation. The visible morphology changes of aneuploids might be caused by chromosome segments elimination. Together, the synthetic apomixis was heritable through multiple generations and few aneuploids were induced when using the synthetic apomixis system.

2022-09-28 | GSE214179 | GEO

Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis.

Project description:Nucellar embryony (NE) is an adventitious form of apomixis common in citrus, wherein asexual embryos initiate directly from nucellar cells surrounding the embryo sac. NE enables the fixation of desirable agronomic traits and the production of clonal offspring of virus-free rootstock, but impedes progress in hybrid breeding. In spite of the great importance of NE in citrus breeding and commercial production, little is understood about the underlying molecular mechanisms. In this study, the stages of nucellar embryo initiation (NEI) were determined for two polyembryonic citrus cultivars via histological observation. To explore the genes and regulatory pathways involved in NEI, we performed mRNA-seq and sRNA-seq analyses of ovules immediately prior to and at stages during NEI in the two pairs of cultivars. A total of 305 differentially expressed genes (DEGs) were identified between the poly- and monoembryonic ovules. Gene ontology (GO) analysis revealed that several processes are significantly enriched based on DEGs. In particular, response to stress, and especially response to oxidative stress, was over-represented in polyembryonic ovules. Nearly 150 miRNAs, comprising ~90 conserved and ~60 novel miRNAs, were identified in the ovules of either cultivar pair. Only two differentially expressed miRNAs (DEMs) were identified, of which the novel miRN23-5p was repressed whereas the targets accumulated in the polyembryonic ovules. This integrated study on the transcriptional and post-transcriptional regulatory profiles between poly- and monoembryonic citrus ovules provides new insights into the mechanism of NE, which should contribute to revealing the regulatory mechanisms of plant apomixis.

| S-EPMC5066493 | biostudies-literature

Antibiotic use in mandarin production (Citrus reticulata Blanco) in major mandarin-producing areas in Thailand: A survey assessment.

Project description:BACKGROUND:Antimicrobial resistance (AMR), one of the major global threats to human security, has serious negative consequences for both health and economies. Excessive and inappropriate uses of antibiotics are the main drivers of the emergence of resistant bacterial strains. In Thailand, antibiotics have been used in citrus production since 2012 to treat citrus greening disease or Huanglongbing disease, despite no antibiotics being registered for use in mandarin. This raises concerns about irrational use of antibiotics, which can cause AMR. OBJECTIVE:To assess the status of greening disease and the use of antibiotics in mandarin production. METHOD:A face-to-face interview survey in 2017 with 221 mandarin growers in two major mandarin-producing areas. FINDINGS:Greening disease is one of the most serious diseases in mandarins and farmers in the two major mandarin-producing areas in Thailand used ampicillin, amoxicillin, tetracycline and penicillin to treat it. As no antibiotics are registered for use in plants, farmers used antibiotics (registered with the Thai Food and Drug Administration) for human use, either active pharmaceutical ingredients or finished products. They commonly purchased them from retail pharmacies or agrochemical suppliers. Farmers were influenced to use antibiotics by their orchard neighbours and advice from a few academics. The farmers injected antibiotics into the tree trunks approximately three to four times a year and stopped for more than two months before harvesting for in-season fruits. CONCLUSION:Antibiotics registered for human use are being applied to control greening diseases. We recommend scaling up sustainable disease control measures and curtail the use of antibiotics through close and effective dialogue among 'One Health' partners.

| S-EPMC6853317 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data