Allopolyploid origin in Rubus (Rosaceae) inferred from nuclear granule-bound starch synthase I (GBSSI) sequences

Abstract

Background Polyploidy and hybridization are ubiquitous in Rubus L., a large and taxonomically challenging genus. Chinese Rubus are mainly concentrated into two major sections, the diploid Idaeobatus and the polyploid Malachobatus . However, it remains unclear to be auto- or allo- polyploid origin of polyploids in Rubus . We investigated the homoeologs and the structure of the GBSS I-1 (granule-bound starch synthase I) gene in 140 Rubus individuals representing 102 taxa in 17 (out of the total 24) subsections of 7 (total of 12) sections at different ploidy levels. Results Based on the gene structure and sequence divergence, we defined three gene variants, GBSS I-1a, GBSS I-1b, and GBSS I-1c. When compared with GBSS I-1a, both GBSS I-1b and GBSS I-1c have a shorter fourth intron, and GBSS I-1c had an additional deletion in the fifth intron. For diploids, either GBSS I-1a or GBSS I-1b was detected in 56 taxa consisting of 82 individuals from sect. Idaeobatus , while both alleles existed in R. pentagonus and R. peltatus . Both homoeologs GBSS I-1a and GBSS I-1b were identified in 39 taxa (48 individuals) of Malachobatus polyploids. They were also observed in two sect. Dalibardastrum taxa, in one sect. Chamaebatus taxon, and in three taxa from sect. Cylactis . Interestingly, all three homoeologs were observed in the three tetraploid taxa. Phylogenetic trees and networks suggested two clades (I and II), corresponding to GBSS I-1a, and GBSS I-1b/1c sequences, respectively. GBSS I-1 homoeologs from the same polyploid individual were resolved in different well-supported clades, and some of these homoelogs were more closely related to homoelogs in other species than they were to each other. This implied that the homoeologs of these polyploids were donated by different ancestral taxa, indicating their allopolyploid origin. Two kinds of diploids hybridized to form most allotetraploid species. The early-divergent diploid species with GBSS I-1a or -1b emerged before polyploid formation in the evolutionary history of Rubus . Conclusion This study provided new insights into allopolyploid origin and evolution from diploid to polyploid within the genus ...

Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

“…700 species, is distributed worldwide and is abundant in the Northern Hemisphere, with very few species occurring in the Southern Hemisphere 7 . Focke established the widely adopted Rubus infrageneric classification system that recognizes 12 subgenera [8][9][10] , and several attempts have been made to unravel the overall phylogeny within the genus as well as the role of hybridization events [11][12][13][14][15][16] . Approximately 41 species from three subgenera are currently recognized in Taiwan; i.e., Chamaebatus (3 species), Idaoeobatus (27 species), and Malochobatus (11 species).…”

The Low Copy Nuclear Gene Region, Granule Bound Starch Synthase (GBSS1), as a Novel Mini-DNA Barcode for the Identification of Different Sage (Salvia) Species

“…This study found that the exon 9 – 14 region of the low-copy nuclear gene called WAXY gene ( GBSS1 ) has been used for plantsʼ phylogenetic assignment 28 , 29 , 30 but not for DNA barcoding as a potential barcode region. For Salvia species, only 19 GBSS1 sequences were available in NCBI GenBank (as of November 15, 2020).…”

“…The major advantage of single-copy genes from the nuclear genome is their high rate of variation that helped in easy species identification 27 . The granule bound starch synthase ( GBSS1 ) region from any nuclear genome is a single copy gene that has been useful for the phylogenetic assignment of several plant taxa 28 , 29 , 30 . However, to the best of our knowledge, there have been no reports of the GBSS1 gene region being tested to identify species using DNA barcoding.…”

Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision

“…(2008), and Wang & al. (2016) sequenced a few other nuclear and chloroplast loci, including GBSSI‐1 and GBSSI‐2 (Evans & al., 2000; Wang & al., 2016, 2019), LEAFY (Yang & al., 2012), ndhF (Howarth & al., 1997; Morden & al., 2003; Zhang & al., 2015), PEPC (Wang & al., 2016), rbcL (Imanishi & al., 2008; Wang & al., 2016), rpl16 (Alice & al., 2008; Wang, 2011), rpl32 ‐ ndhF (Wang, 2011); rpl20 ‐ rps12 (Wang & al., 2016), trnK intron (Wang, 2011); trnL‐trnF (Alice & al., 2008; Wang, 2011; Yang & Pak, 2006), trnG‐trnS (Michael, 2006; Wang, 2011; Wang & al., 2016), and trnV ‐ ndhC (Wang, 2011). Individual and combined analyses of nuclear and chloroplast loci indicated that Rubus plus Dalibarda form a monophyletic group, but of the subgenera with more than one species sampled, only R .…”

“…Additionally, single‐gene trees may not represent species trees due to hybridization, intra‐ and interspecific polyploidization, incomplete lineage sorting, and gene duplication (Bammi & Olmo, 1966; Pamilo & Nei, 1988; Maddison, 1997; Alice & al., 2001; Nichols, 2001; Mimura & al., 2014; Szöllősi & al., 2015; Pfeil & al., 2017; Carter & al., 2019; Gonçalves & al., 2019; Boussau & Scornavacca, 2020). Conflicting gene trees in Rubus were found frequently using either maternally inherited chloroplast markers or bi‐parentally inherited ribosomal DNA markers (Yang & Pak, 2006; Yang & al., 2012; Wang & al., 2016, 2019). Therefore, in order to tackle the problem of incomplete lineage sorting effectively, either phylogenetic insights into Rubus from chloroplast genomes and nuclear DNAs are necessary, or alternatively a species tree under the multispecies coalescent framework could be adopted (Jones & al., 2015; Jones, 2016).…”