Reassessing Banana Phylogeny and Organelle Inheritance Modes Using Genome Skimming Data

Abstract

Bananas (Musa spp.) are some of the most important fruit crops in the world, contributing up to US$10 billion in export values annually. In this study, we use high-throughput sequencing to obtain genomic resources of high-copy DNA molecules in bananas. We sampled 13 wild species and eight cultivars that represent the three genera (Ensete, Musa, and Musella) of the banana family (Musaceae). Their plastomic, 45S rDNA, and mitochondrial scaffolds were recovered from genome skimming data. Two major clades (Clades I & II) within Musa are strongly supported by the three genomic compartment data. We document, for the first time, that the plastomes of Musaceae have expanded inverted repeats (IR) after they diverged from their two close relatives, Heliconiaceae (the lobster-claws) and Strelitziaceae (the traveler's bananas). The presence/absence of rps19 within IR regions reinforces the two intra-generic clades within Musa. Our comparisons of the bananas' plastomic and mitochondrial DNA sequence trees aid in identifying hybrid bananas' parentage. As the mitochondrial genes of Musa have elevated substitution rates, paternal inheritance likely plays an influential role on the Musa mitogenome evolution. We propose genome skimming as a useful method for reliable genealogy tracing and phylogenetics in bananas.

Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships

“…In addition, M. coccinea lost one copy of the trnH gene. This result is congruent with previous investigations [ 23 ]. The different copy numbers of trnH and rps19 genes may hint at their gene substitution on nuclear and/or functional redundancy in the plastid [ 63 ].…”

“…M. ingens distributes in the tropical montane forests of New Guinea, Indonesia. Our study sampled more Australimusa species than earlier phylogenetic studies [ 6 , 17 , 18 , 23 ]. Six species ( M. jackeyi , M. johnsii , M. lolodensis , M. maclayi , M. peekelii , M. troglodytarum ) were sampled from the 12 Australimusa species [ 2 ] and formed one single cluster.…”

“…Their resulting phylogeny also encompassed multiple low-support branches. In contrast, studies using multiple low copy nuclear genes or even whole-genome sequences on Musaceae phylogeny have in-depth gene coverage and strong internal support, but their taxonomic coverage was often sparse [ 20 – 23 ] since their sampled species did not even exceed 20. Thus, it is worthwile to investigate phylogenetic relationships of Musaceae in more detail with both expanded taxonomic coverage and gene sampling.…”

“…Some highly variable regions in the plastome have been identified as “hotspots” and employed as useful molecular markers for phylogenetic studies [ 32 , 33 ]. In recent years, although some plastome sequences ofMusaceae have been reported [ 23 , 34 – 36 ], most species studied concentrated on a few wild bananas cultivated at botanical gardens and did not propose a comprehensive plastome analysis for the Musaceae family. In this study, we used the genome skimming approach for the assembly of the plastomes of a large panel of Musaceae species.…”

Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

“…DNA barcoding success generally is reached if there is a clear barcode gap or if conspecific samples are reciprocally monophyletic. However, species‐level paraphyly and polyphyly are commonly observed in recently diverged plant groups (van Velzen et al, 2012; Wu et al, 2021). Despite having been pointed out many times in previous studies (Mutanen et al, 2016; Ross, 2014), the prevalence of nonmonophyly has not yet inspired a solution and is rarely discussed in the plant science community.…”