Origin and evolution of the triploid cultivated banana genome

Abstract

Eleven genome assemblies of diploid banana publicly available were downloaded to perform comparative analysis in our study (Supplementary Table 10). In total, 58 RNA-seq samples representing five tissues from Cavendish cultivar Baxi were aligned to Cavendish, DH-Pahang and Banksii assemblies, and the mapping rate of RNA-seq reads to Cavendish assembly showed the highest alignment rate of an average of 91.5% at 48 RNA-seq samples (Supplementary Table 11). We downloaded 148 known M. acuminata AAA group mRNA sequences from GenBank and aligned them to our Cavendish and Gros Michel assemblies, and found their average identity to be 99.2% and 99.1%, with 87.7% and 88.5% of the mRNA sequences covered by our Cavendish and Gros Michel assemblies, respectively (Supplementary Table 12).We found >70% of 128 mRNA sequences from Cavendish with at least 96% identity and 80% covered by our Cavendish assembly (Supplementary Table 12). All six mRNA sequences from Gros Michel were found with at least 98% identity and 100% covered our Gros Michel assembly (Supplementary Table 12). These results indicate a high base accuracy and completeness of our assembled sequences.

Identification of the Loci Associated with Resistance to Banana Xanthomonas Wilt (Xanthomonas vasicola pv. musacearum) Using DArTSeq Markers and Continuous Mapping

“…Zebrina is one of the three M. acuminata subspecies that are the main contributors to edible bananas, together with banksii, and malaccensis [61][62][63][64]. In the evaluation of various accessions for their response to Xvm, zebrina was found to be partially resistant, while banksii and malaccensis were found to be highly susceptible [18].…”

Chromosome-level genome assembly of autotetraploidSelenicereus megalanthusand gaining genomic insights into the evolution of trait patterning in diploid and polyploid pitaya species

“…From the assembled genome, nonredundant protein-coding genes were functionally annotated using the MAKER 98 (v.2.31.11) pipeline by combining de novo , homologous searches, and transcriptome data. The transposable elements were predicted de novo method TE annotator (EDTA) (1.9.6) 99 .…”

“…TE library derived from EDTA, de novo transcriptome assembly of 3 tissues (stem, pericarp, and pulp), and gene predictions were generated by the fast and accurate algorithm of AUGUSTUS (v.3.4.0) 100 and GeneMark-EP + (v.4.6.3) (http://topaz.gatech.edu/GeneMark/license_download.cgi) 101 . The final new yellow pitaya transcripts were merged with MAKER gene models to produce the final set of transcripts, by combining all the data sets and eliminating the transposable elements related domains, and redundant elements 98 . Selenicereus undatus (http://www.pitayagenomic.com/download.php) 3,26,75 , Carnegiea gigantea (GCA_029747015.1_UA_SGP5p_2), Arabidopsis thaliana (GCA_000001735.1_TAIR10) 102,103 , Oryza sativa (GCF_001433935.1_IRGSP-1.0) 104 , Solanum lycopersicum (GCF_000188115.5_SL3.1), and Solanum tuberosum (GCF_000226075.1_SolTub_3.0) 105 species were used for homology prediction in yellow pitaya ( Supplementary Table 32 ).…”

“…The length of 11 chromosomes ranged from 115.62-204. 98 Mb, and unanchored genomic sequences of 40.69 Mb. The assembly had contig N50 13Mb, and we applied Hi-C data to order and orient the resulting contigs.…”

“…From the assembled genome, nonredundant protein-coding genes were functionally annotated using the MAKER 98 98 .…”