Abstract
BackgroundComparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW).ResultsSequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes.ConclusionsA large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.
Highlights
Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level
This indicates that we have identified two large resistance gene analog (RGA) clusters corresponding to the MaRGA08 probe
We have identified two sequence haplotypes in wild M. balbisiana Pisang Klutuk Wulung” (PKW) in the region of the RGA08 cluster which allowed us to assess their degree of sequence divergence
Summary
Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. Limited genetic variation in the most economically important banana cultivars, which are clonally propagated sterile polyploids, has resulted in a crop lacking resistance to some major fungal, bacterial and viral pathogens and to several pests. Wild M. balbisiana is native to South Asia with a geographical distribution ranging from India to south China [3,4]. It grows in forest clearings and produces nonpulpy, non-edible bananas. Plants of this species are immune to several diseases and pests such as Fusarium wilt and Black leaf streak disease and represent excellent sources of natural resistance [5,6]. A better knowledge of the genome structure and diversity of M. balbisiana should help exploiting this resource to increase the genetic basis of cultivated bananas
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