The Banana Genome Hub

One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splicefactor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.

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“…mpob.gov.my). Reference genome and annotation for banana (Musa acuminata) were retrieved from the banana genome hub (Droc et al 2013).…”

Section: Genome Assemblies and Annotationsmentioning

confidence: 99%

Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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“…malaccensis 'DH-Pahang' and M. balbisiana 'PKW' to map the exact loci position on designated 11 Musa chromosomes and plastid genome. The searching was accessed via The Banana Genome Hub database (Droc et al 2013) which is available at the following URL: http://banana-genome.cirad.fr. The ClustalW2 program was used to perform the sequence alignment between SSR loci and the corresponding loci on DH-Pahang and PKW genomes.…”

Section: Ssr Clones Identification and Primers Designmentioning

confidence: 99%

Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas

et al. 2016

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Bananas in Thailand have been surveyed by our team to be at least 140 cultivars in the plantations, 10 wild species and, 4 introduced species. To characterize the genetic relationship of species and cultivars, a set of novel SSR markers was developed. Totaling 53 clones containing SSR motifs were isolated from SSR-enriched library of wild Musa balbisiana Colla 'Tani' (BB). Selected positive clones were used to design 28 primer pairs for amplification of 12 wild and 82 cultivar accessions with genome designations AA, AB, AAA, AAB, ABB, and BBB. These SSR markers loci were homology searched to the banana genomes to map their locations. The seven-sets multiplex PCR approach using four fluorescent-labeled universal primers were utilized for cost effectiveness. Capillary fragment analysis yielded the accurate size of amplicons for evaluation of particular patterns for each cultivar. Phylogram and Structure analysis presented the specific genotype of genome groups (A and B genotypes, polyploid hybrid genomes) and cultivar groups. By A:B specific alleles ratio, accurate genome designations of hybrids can be determined. Additionally, a marker, characterized to be partial plastid ycf2 gene, indicated the maternal identification of hybrid cultivars. One SSR marker was also preliminary tested with some wild species and advised to be the candidate fingerprinting marker for species identification. In conclusion, SSR marker sets developed here proved their exploitation in detailed identity and relationship of cultivated bananas, which would be useful for genetic conservation and ongoing breeding programs in Thailand and other areas.

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“…Therefore, FeR could serve as a sensor of cell wall changes in plant induced by pathogen and in turn trigger downstream defense responses in the host cell. In the Banana Genome Hub database, around ten loci of FeR were found which are present on the chromosomes namely, Chr 3, 8, 9, 10, 11 and ChrUn_random (Droc et al 2013). Fox invasion is through roots and as FeRONIA also helps in root hair development as discussed, its interaction and involvement in signaling in banana during pathogen infection as observed in the case of powdery mildew will open a new area and help to understand the communication among ROS, FeR and other unknown components.…”

Section: Auxinmentioning

confidence: 99%