A community annotation system for Musa genomes

Poster presented at ISHS/ProMusa Banana Symposium Global Perspectives on Asian Challenges. Guangzhou (China), 14-18 Sep 200

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods

Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata)

Genome structure and chromosome segregation in triploid interspecific plantain bananas (AAB) and breeding accessions (AAAB)

Many banana cultivars are triploid interspecific hybrids between M. acuminata (Genome A, 2n=22) and M. balbisiana (Genome B, 2n=22). They included the important group of Plantain cooking bananas classified as AAB that account for almost 20% of the bananas produced worldwide. Previous molecular analysis suggested that this group is genetically homogeneous but diversified phenotypically through somatic variations. To progress on the understanding of chromosome composition and segregation of the breeding material used to improve plantain bananas, we performed several analysis based on Genotyping By Sequencing (GBS) technologies. We analyzed the A/B chromosomes composition of a few plantain cultivars and discovered chromosome segments with AAA composition and one entire chromosome with ABB composition instead of the supposed general 'AAB' composition. We compared the global chromosome structure of A and B genomes through the construction a high density M. balbisiana genetic map and its comparison with the M. acuminata reference sequence assembly. We identified a large reciprocal translocation between a region of 0.6Mb at the beginning of chromosome 1 and a 8 Mb region at the end of chromosome 3. We also identified a large inversion of 9Mb within chromosome 5. We analyzed the A/B chromosomes segregation in a progeny from an 'AAAB' tetraploid breeding accession derived from a plantain. We revealed frequent recombination between A and B all along the genomes with a few exceptions. The exceptions consisted in the absence of recombination recorded in the inverted segment between A and B on chromosome 5 and a reduced recombination rate near the translocated regions on chromosome 1 and 3. We also observed 62% of aneuploids in the progeny involving mainly the three chromosomes that differed in their global structure between A and B genomes. Implication of these results on the origin of plantain banana cultivars and on breeding of allopolyploid bananas will be discussed based on the patterns of recombination revealed

Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees

Musa balbisiana genome reveals subgenome evolution and functional divergence

Banana cultivars (Musa ssp.) are diploid, triploid and tetraploid hybrids derived from Musa acuminata and Musa balbisiana. We presented a high-quality draft genome assembly of M. balbisiana with 430 Mb (87%) assembled into 11 chromosomes. We identified that the recent divergence of M. acuminata (A-genome) and M. balbisiana (B-genome) occurred after lineage-specific whole-genome duplication, and that the B-genome may be more sensitive to the fractionation process compared to the A-genome. Homoeologous exchanges occurred frequently between A- and B-subgenomes in allopolyploids. Genomic variation within progenitors resulted in functional divergence of subgenomes. Global homoeologue expression dominance occurred between subgenomes of the allotriploid. Gene families related to ethylene biosynthesis and starch metabolism exhibited significant expansion at the pathway level and wide homoeologue expression dominance in the B-subgenome of the allotriploid. The independent origin of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) homoeologue gene pairs and tandem duplication-driven expansion of ACO genes in the B-subgenome contributed to rapid and major ethylene production post-harvest in allotriploid banana fruits. The findings of this study provide greater context for understanding fruit biology, and aid the development of tools for breeding optimal banana cultivars

Gene annotation, orthogroups and gene trees in Musa acuminata subspecies

Gene annotation was performed on the obtained de novo assembly for ‘Banksii’, ‘Maia Oa’ and ‘Calcutta 4,’ as well as on the draft Musa balbisiana ‘PKW’ assembly. Gene families were identified using OrthoFinder v1.1.4 with default parameters based on BLASTp (e-value 1e-5). Single-copy OGs (i.e. orthogroups with one copy of a gene in each of the five genotypes) from protein, coding DNA sequence (CDS), and genes (including introns and UTRs) were aligned with MAFFT v7.271 (Katoh & Standley 2013), and gene trees were constructed using PhyML v3.1 (Guindon et al. 2009) with ALrT branch support. All trees were rooted using Musa balbisiana as outgroup using Newick utilities v1.6 (Junier & Zdobnov 2010)

Mosaic genome structure and chromosome segregation in polyploid interspecific plantain bananas and derived breeding accessions

Almost 40% of the world banana production relies on triploid interspecific cultivars deriving from hybridization between Musa. acuminata (Genome A, 2n=22) and M. balbisiana (Genome B, 2n=22). These cultivars were classified based on morphological characteristics in genomic groups (AAB and ABB) subdivided into various subgroups. They include the cooking banana Plantain group (classified as AAB) that represents 18% of the banana production worldwide. The origin of these cultivars, their chromosome structure as well as its impact on chromosome recombination and segregation are still poorly known. We analyzed using Genotyping By Sequencing (GBS), the A/B chromosomes composition of a few cultivars and showed that it deviates in several regions from the conventional genomic classification. For example Plantain, classified as 'AAB,' has six genomic regions with an AAA chromosome composition and one entire chromosome set with an ABB composition. We compared the global chromosome structure of A and B genomes through the construction a high density SNP genetic map of M. balbisiana and its comparison with the M. acuminata reference sequence assembly. We identified a large reciprocal translocation between chromosome 1 and chromosome 3 and a large inversion on chromosome 5. We analyzed the A/B chromosomes recombination and segregation in a progeny from an 'AAAB' Plantain-derived tetraploid breeding accession. This revealed frequent recombination between A and B chromosomes all along the genome to the main exception of the inverted segment on chromosome 5. We observed 62% of aneuploids in the progeny that mainly involved the three chromosomes displaying large structural variations between A and B genomes. Implication of these results will be discussed

Genomics of Banana and Plantain (Musa spp.), Major Staple Crops in the Tropics

This chapter on Musa (banana and plantain) genomics covers the latest information on activities and resources developed by the Global Musa Genomics Consortium. Section 4.1 describes the morphology of the plant, its socio-economical importance and usefulness as an experimental organism. Section 4.2 describes the complexity of Musa taxonomy and the importance of genetic diversity. Section 4.3 details the genetic maps which have recently been developed and those that are currently being developed. Section 4.4 presents the five BAC libraries which are now publicly available from the Musa Genome Resource Centre and can be distributed in various forms under a material transfer agreement. Section 4.5 gives an overview of cytogenetics and genome organization, showing that the genus Musa has a quite high proportion of repetitive DNA; the discovery of the first para-retrovirus integrated in the genome makes it unique. Section 4.6 explains the first attempts to sequence the genome by BAC end sequencing, whole BAC sequencing, and reduced representation sequencing. Section 4.7 addresses functional genomics with the description of cDNA libraries, gene validation using gene trapping, mutation induction and tilling techniques, as well as genetic transformation. Section 4.8 draws overall conclusions. This chapter demonstrates that by organizing the Global Musa Genomics Consortium (currently comprising 33 member institutions from 23 countries), duplication of effort can be minimized and the results of Musa genomics research are rapidly made accessible to taxonomists, breeders and the biotechnology communit

Evolution of the banana genome (Musa acuminata) is impacted by large chromosomal translocations

Most banana cultivars are triploid seedless parthenocarpic clones derived from hybridization between Musa acuminata subspecies and sometimes M. balbisiana. M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations in inter-subspecies hybrids. We searched for large chromosomal rearrangements in a seedy M. acuminata ssp. malaccensis banana accession through mate-pair sequencing, BAC-FISH, targeted PCR and marker (DArTseq) segregation in its progeny. We identified a heterozygous reciprocal translocation involving two distal 3 Mb and 10 Mb segments from chromosomes 01 and 04, respectively, and showed that it generated high segregation distortion, reduced recombination and linkage between chromosomes 01 and 04 in its progeny. The two chromosome structures were found to be mutually exclusive in gametes and the rearranged structure was preferentially transmitted to the progeny. The rearranged chromosome structure was frequently found in triploid cultivars but present only in wild malaccensis ssp. accessions, thus suggesting that this rearrangement occurred in M. acuminata ssp. malaccensis. We propose a mechanism for the spread of this rearrangement in Musa diversity and suggest that this rearrangement could have played a role in the emergence of triploid cultivars