Journal of Heredity

Experiments with Digital Organisms on the Origin and Maintenance of Sex in Changing Environments.

Publication Date: 2010 Mar 8 PMID: 20200140
Authors: Misevic, D. - Ofria, C. - Lenski, R. E.
Journal: J Hered

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Extensive MHC Class II B Gene Duplication in a Passerine, the Common Yellowthroat (Geothlypis trichas).

Publication Date: 2010 Mar 3 PMID: 20200139
Authors: Bollmer, J. L. - Dunn, P. O. - Whittingham, L. A. - Wimpee, C.
Journal: J Hered

The major histocompatibility complex (MHC) is characterized by a birth and death model of evolution involving gene duplication, diversification, loss of function, and deletion. As a result, gene number varies across taxa. Birds have between one and 7 confirmed MHC class II B genes, and the greatest diversity appears to occur in passerines. We used multiple primer sets on both genomic DNA (gDNA) and complementary DNA (cDNA) to characterize the range of class II B genes present in a passerine, the common yellowthroat (Geothlypis trichas). We confirmed 39 exon 2 sequences from gDNA in a single individual, indicating the presence of at least 20 class II B loci. From a second individual, we recovered 16 cDNA sequences belonging to at least 8 transcribed loci. Phylogenetic analysis showed that common yellowthroat sequences fell into subgroups consisting of classical loci, as well as at least 4 different clusters of sequences with reduced sequence variability that may represent pseudogenes or nonclassical loci. Data from 2 additional common yellowthroats demonstrated high interindividual variability. Our results reveal that some passerines possess an extraordinary diversity of MHC gene duplications, including both classical and nonclassical loci.

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Complementation, genetic conflict, and the evolution of sex and recombination.

Publication Date: 2010 Mar 8 PMID: 20200138
Authors: Archetti, M.
Journal: J Hered

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Fitness Epistasis among 6 Biosynthetic Loci in the Budding Yeast Saccharomyces cerevisiae.

Publication Date: 2010 Mar 8 PMID: 20194517
Authors: Hall, D. W. - Agan, M. - Pope, S. C.
Journal: J Hered

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Female reproductive success variation in a Pseudotsuga menziesii seed orchard as revealed by pedigree reconstruction from a bulk seed collection.

Publication Date: 2010 Mar-Apr PMID: 20080805
Authors: El-Kassaby, Y. A. - Funda, T. - Lai, B. S.
Journal: J Hered

The impact of female reproductive success on the mating system, gene flow, and genetic diversity of the filial generation was studied using a random sample of 801 bulk seed from a 49-clone Pseudotsuga menziesii seed orchard. We used microsatellite DNA fingerprinting and pedigree reconstruction to assign each seed's maternal and paternal parents and directly estimated clonal reproductive success, selfing rate, and the proportion of seed sired by outside pollen sources. Unlike most family array mating system and gene flow studies conducted on natural and experimental populations, which used an equal number of seeds per maternal genotype and thus generating unbiased inferences only on male reproductive success, the random sample we used was a representative of the entire seed crop; therefore, provided a unique opportunity to draw unbiased inferences on both female and male reproductive success variation. Selfing rate and the number of seed sired by outside pollen sources were found to be a function of female fertility variation. This variation also substantially and negatively affected female effective population size. Additionally, the results provided convincing evidence that the use of clone size as a proxy to fertility is questionable and requires further consideration.

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The alpha glycerophosphate cycle in Drosophila melanogaster V. molecular analysis of alpha glycerophosphate dehydrogenase and alpha glycerophosphate oxidase mutants.

Publication Date: 2010 Mar-Apr PMID: 19995806
Authors: Carmon, A. - Chien, J. - Sullivan, D. - MacIntyre, R.
Journal: J Hered

Two enzymes, alpha glycerophosphate dehydrogenase (GPDH-1) in the cytoplasm and alpha glycerophosphate oxidase (GPO-1) in the mitochondrion cooperate in Drosophila flight muscles to generate the ATP needed for muscle contraction. Null mutants for either enzyme cannot fly. Here, we characterize 15 ethyl methane sulfonate (EMS)-induced mutants in GPDH-1 at the molecular level and assess their effects on structural and evolutionarily conserved domains of this enzyme. In addition, we molecularly characterize 3 EMS-induced GPO-1 mutants and excisions of a P element insertion in the GPO-1 gene. The latter represent the best candidate for null or amorphic mutants in this gene.

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The alpha glycerophosphate cycle in Drosophila melanogaster VI. structure and evolution of enzyme paralogs in the genus Drosophila.

Publication Date: 2010 Mar-Apr PMID: 19995805
Authors: Carmon, A. - MacIntyre, R.
Journal: J Hered

The genome sequences of 12 Drosophila species contain 3 paralogs for alpha glycerophosphate dehydrogenase (GPDH) and for the mitochondrial alpha glycerophosphate oxidase (GPO). These 2 enzymes participate in the alpha glycerophosphate cycle in the adult thoracic flight muscles. The flight muscle enzymes are encoded by gpdh-1 at 26A2 and gpo-1 at 52C8. In this paper, we show that the GPDH paralogs share the same evolutionarily conserved functional domains and most intron positions, whereas the GPO paralogs share only some of the functional domains of mitochondrial oxidoreductases. The GPO paralogs not expressed in the flight muscles essentially lack introns. GPDH paralogs encoded by gpdh-2 and gpdh-3 and the GPO paralogs encoded by gpo-2 and gpo-3 are expressed only in the testes. Gene trees for the GPDH and GPO paralogs indicate that the genes expressed in the flight muscles are evolving very slowly presumably under strong purifying selection whereas the paralogs expressed in the testes are evolving more rapidly. The concordance between species and gene trees, d(N)/d(S) ratios, phylogenetic analysis by maximum likelihood-based tests, and analyses of radical and conservative substitutions all indicate that the additional GPDH and GPO paralogs are also evolving under purifying selection.

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Analysis of STR markers reveals high genetic structure in Portuguese native cattle.

Publication Date: 2010 Mar-Apr PMID: 19965912
Authors: Ginja, C. - Telo Da Gama, L. - Penedo, M. C.
Journal: J Hered

Genetic structure and diversity of 13 Portuguese native and 3 imported cattle breeds were assessed with 39 microsatellites. Allelic richness per locus was high, with an overall average of 8.3 +/- 2.5. The mean observed and expected heterozygosities were 0.673 +/- 0.043 and 0.691 +/- 0.034, respectively. The mean number of alleles per breed ranged between 5.36 +/- 1.27 and 7.87 +/- 2.66. Brava de Lide and Mirandesa breeds had the lowest genetic diversity, whereas Minhota, Arouquesa, and Mertolenga had the highest. Significant (P < 0.05) heterozygote deficit was detected in all breeds except Garvonesa, Marinhoa, Minhota, and Limousin. Hardy-Weinberg deviations are most probably due to inbreeding, particularly in Alentejana, Brava de Lide, Mertolenga, and Ramo Grande (F(is) > 0, P < 0.0001). Based on the principal component and the Neighbor-Net analyses, Mirandesa was the most genetically distinct breed. Even though admixture was detected across all breeds (6.7%, q < 0.800), the molecular structure was consistent with original breed designations, with the exception of Cachena that had a clear influence of Barrosa (K = 15). Mertolenga showed substructure with independent clustering of red speckled animals. The percentage animals correctly assigned was >or=90 in all breeds except Cachena, Garvonesa, and Preta (q >or= 0.800). The results obtained here confirmed that high levels of genetic diversity exist within Portuguese native cattle and that the breeds are highly structured. Conservation measures should be implemented for all native breeds to minimize inbreeding.

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QTL mapping for photoperiod insensitivity of a Japanese soybean landrace Sakamotowase.

Publication Date: 2010 Mar-Apr PMID: 19959597
Authors: Liu, B. - Abe, J.
Journal: J Hered

The insensitivity of flowering to long daylength is an important characteristic which soybeans have used to adapt to environments at higher latitude. The objective of this study was to map the novel gene(s) for photoperiod insensitivity in the Japanese soybean landrace Sakamotowase. A previous study suggested that Sakamotowase possessed the genotype e1e1e3e3E4E4. The progeny of testcrosses with the Harosoy isoline for e3 (L62-667) produced the roughly expected segregation pattern for the monogenic inheritance, suggesting the major involvement of a single gene in photoperiod insensitivity of Sakamotowase. By mapping analysis for 6 linkage groups (LGs) harboring the known major genes and quantitative trait loci (QTLs) for flowering, we detected a major QTL for the insensitivity near an simple sequence repeat marker (Satt577) in LG C2 and a minor QTL in LG L. Our results therefore suggest that a novel gene for photoperiod insensitivity of Sakamotowase was located in LG C2. It was estimated from the position of the tagging marker that the novel gene may be an allele at the E1 or E7 loci or a novel gene tightly linked to the E1 locus.

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SPAGHETTI: simulation software to test genetic mapping programs.

Publication Date: 2010 Mar-Apr PMID: 19959595
Authors: Tinker, N. A.
Journal: J Hered

SPAGHETTI is a computer program to simulate genetic populations with segregating molecular markers that are influenced by "real-life" complications such as duplicated loci and segregation distortion. It produces output that is readable by popular mapping software, and it can be used to demonstrate or test methods for constructing genetic linkage maps. The source code, sample files, instructions for use, and an executable version compatible with MS Windows are available for free from http://gnomad.agr.ca/software/spaghetti.

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Genealogical relationship among members of selection and production populations of yellow cedar (Callitropsis nootkatensis [D. Don] Oerst.) in the absence of parental information.

Publication Date: 2010 Mar-Apr PMID: 19945992
Authors: Massah, N. - Wang, J. - Russell, J. H. - Van Niejenhuis, A. - El-Kassaby, Y. A.
Journal: J Hered

We used DNA fingerprinting and pedigree reconstruction to determine the genetic relationship among members of 3 yellow-cedar (Callitropsis nootkatensis [D. Don] Oerst.) selection populations in the absence of their parental genotypes. Selection population members consisted of the tallest individuals within seedling crops originated from natural stand seed collected from multiple seed donors covering wide areas within 3 distinct locations (phenotypic mass selection). Pairwise relative kinship estimates indicated the presence of extensive coancestry among the selected seedlings, and pedigree reconstruction grouped each selection members into multiple full-sib families of different sizes (1-10) nested within several half-sib families (19-21). The "STRUCTURE" program (Pritchard JK, Stephens M, Donnelly P. 2000. "Inference of population structure using multilocus genotype data." Genetics. 155:945-959.) provided a pictorial classification of the 3 selection populations and grouped their individuals into multiple cohorts (9-10). The STRUCTURE program's results corresponded with that of the pedigree reconstruction, indicating that members of the selection populations originated from a subset of the seed donors forming the natural stand seed collections. The species' silvics, reproductive biology, methods of natural stand seed collection and seedling production, and the high selection intensity applied to form the selection populations contributed to limiting the selection to a subset of the original donor trees. The associated buildup of coancestry in selection and production populations is expected to result in inaccurate estimation of genetic parameters and an unintentional reduction in genetic diversity in reforestation stocks.

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The impact of landscape disturbance on spatial genetic structure in the Guanacaste tree, Enterolobium cyclocarpum (Fabaceae).

Publication Date: 2010 Mar-Apr PMID: 19945990
Authors: Gonzales, E. - Hamrick, J. L. - Smouse, P. E. - Trapnell, D. W. - Peakall, R.
Journal: J Hered

We examined spatial genetic structure (SGS) in Enterolobium cyclocarpum (the Guanacaste tree), a dominant tree of Central American dry forests in 4 sites in Guanacaste Province, Costa Rica. In disturbed dry forest sites (e.g., pastures), E. cyclocarpum is primarily dispersed by cattle and horses, whose movements are restricted by pasture boundaries. The study sites varied in tree densities and disturbance. Allozyme analyses of adult trees demonstrated significant levels of SGS in 3 of 4 sites. SGS was primarily due to clusters of young adults located along seasonal streams, rocky areas, and in abandoned pastures. SGS was highest in the first distance class in the least disturbed population, which also had the lowest density of large adults. Low, but significant SGS characterized the site with the highest number of large adults located in individual pastures. The semiurban site, had no clusters of young adults and, probably as a result, failed to exhibit SGS. Our results demonstrate that disturbance can strongly influence SGS patterns and are consistent with a landscape model in which the location of potential recruitment sites, restricted seed disperser movements, and the number and location of maternal individuals dictate the level and pattern of SGS.

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Tracking mtDNA heteroplasmy through multiple generations in the North Atlantic right whale (Eubalaena glacialis).

Publication Date: 2010 Mar-Apr PMID: 19939969
Authors: McLeod, B. A. - White, B. N.
Journal: J Hered

Mitochondrial heteroplasmy has been identified in a variety of species and can result from either paternal leakage, whereby sperm mitochondria enter the ova during fertilization, or more commonly by the "survival" and proliferation of mutant variants within an organism. From an evolutionary perspective, this process represents the generation of new mitochondrial diversity within a species. Although this has been documented in some mammalian species, it has been reported from relatively few wild mammalian populations and in no wild nonhuman population has the transfer and segregation of mitochondrial heteroplasmy been tracked through multiple generations. We report on the first case of the identification and tracking of mitochondrial control region heteroplasmy through 3 generations in the North Atlantic right whale, Eubalaena glacialis. We also identify the full segregation to the mutant variant within a single generation and thus the development of a new haplotype (haplotype G) in a maternal lineage of this endangered species. Witnessed here is the generation of mitochondrial diversity in a genetically depauperate species.

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Characterization of a minimal microsatellite set for whole genome scans informative in warmblood and coldblood horse breeds.

Publication Date: 2010 Mar-Apr PMID: 19939968
Authors: Mittmann, E. H. - Lampe, V. - Momke, S. - Zeitz, A. - Distl, O.
Journal: J Hered

The availability of a high-quality draft sequence of the horse makes known the physical location of microsatellites. The aim of the present study was to establish a highly polymorphic minimal screening set of microsatellite markers for horses (MSSH) annotated on the horse genome assembly EquCab2.0. We have used the previously reported linkage and radiation hybrid maps and have extended these marker sets by filling in gaps as noted from annotation on the horse sequence. This MSSH covers all autosomes and the X chromosome with 322 evenly spaced microsatellites whose positions were determined on the horse genome assembly (EquCab2.0). The average chromosomal distance among markers amounts to 7.44 Mb. The characteristics established for this microsatellite set were the number of alleles, the observed heterozygosity (HET), and the polymorphism information content (PIC) for Hanoverian warmblood (HW) and several German coldblood horse breeds (CB). The average number of alleles was 7.3 and 8.0 in HW and CB, respectively. HET was at 71% for HW and CB, PIC at 65% (HW) and 67% (CB). This MSSH allows scanning of the whole horse genome at close to 7- to 10-Mb resolution.

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Probabilistic expert systems for forensic inference from DNA markers in horses: applications to confirm genealogies with lack of genetic data.

Publication Date: 2010 Mar-Apr PMID: 19939967
Authors: Dobosz, M. - Bocci, C. - Bonuglia, M. - Grasso, C. - Merigioli, S. - Russo, A. - De Iuliis, P.
Journal: J Hered

Microsatellites have been used for parentage testing and individual identification in forensic science because they are highly polymorphic and show abundant sequences dispersed throughout most eukaryotic nuclear genomes. At present, genetic testing based on DNA technology is used for most domesticated animals, including horses, to confirm identity, to determine parentage, and to validate registration certificates. But if genetic data of one of the putative parents are missing, verifying a genealogy could be questionable. The aim of this paper is to illustrate a new approach to analyze complex cases of disputed relationship with microsatellites markers. These cases were solved by analyzing the genotypes of the offspring and other horses' genotypes in the pedigrees of the putative dam/sire with probabilistic expert systems (PESs). PES was especially efficient in supplying reliable, error-free Bayesian probabilities in complex cases with missing pedigree data. One of these systems was developed for forensic purposes (FINEX program) and is particularly valuable in human analyses. We applied this program to parentage analysis in horses, and we will illustrate how different cases have been successfully worked out.

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Reciprocal translocations in grass pea (Lathyrus sativus L.): pattern of transmission, detection of multiple interchanges and their independence.

Publication Date: 2010 Mar-Apr PMID: 19939966
Authors: Talukdar, D.
Journal: J Hered

Grass pea (Lathyrus sativus L.) is a diploid crop having 2n = 14 chromosomes. Four different plant types, heterozygous for reciprocal translocation (RT), RT-1, RT-2, RT-3, and RT-4 showing pollen semisterility, were isolated in induced mutant population of three varieties of grass pea. Transmission rate of these 4 translocations was studied in advanced selfed and intercrossed progenies, whereas multiple chromosomal interchanges were detected by the pattern of chromosomal ring formation at meiosis I in the F(1) progeny of RTxRT. RT transmitted at an average of 48.89% in selfed progeny and along with normal plants, RT and translocation homozygotes produced some trisomic plants in the segregation progeny. RT-3 showing maximum frequency (68.20%) of zig-zag or alternate chromosome orientation exhibited highest transmission (55.20%). Presence of a ring of 6 or 2 rings of 4 chromosomes in F(1) double heterozygotes obtained from RTxRT suggested involvement of one common chromosome in translocations of RT-1, RT-2, and RT-4 but a different one in common between RT-2 and RT-3. No common chromosome, however, was shared by RT-3 and RT-4. Thus, 5 out of 7 chromosomes are involved in the present RTs, and one of the translocated chromosomes in RT-1 line was always associated with nucleolar organizing region.

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Association study of cobalamin deficiency in the Chinese Shar Pei.

Publication Date: 2010 Mar-Apr PMID: 19926684
Authors: Grutzner, N. - Bishop, M. A. - Suchodolski, J. S. - Steiner, J. M.
Journal: J Hered

Cobalamin deficiency is a common disorder in Chinese Shar Peis (Shar Peis) and is thus suspected to be hereditary. The objective of this study was to identify a genomic region or locus that cosegregates with the phenotype of cobalamin deficiency in Shar Peis. Serum cobalamin concentrations were measured, and blood for genomic DNA extraction was collected from 14 cobalamin-deficient Shar Peis and 28 Shar Peis with a serum cobalamin concentration in the reference range. The 327 microsatellite markers from the canine minimal screening set 2 and 4 additional markers were amplified by polymerase chain reaction and genotyped by automated capillary electrophoresis. Two microsatellite markers, DTR13.6 (P = 1.4 x 10(-6)) and REN13N11 (P = 1.5 x 10(-5)), both on canine chromosome 13, showed evidence of linkage disequilibrium. These findings indicate that the region of chromosome 13 near these markers should be mapped and closely examined for potential mutations associated with this disease in Shar Peis.

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Microsatellite genetic characterization of the humpback whale (Megaptera novaeangliae) breeding ground off Brazil (breeding stock A).

Publication Date: 2010 Mar-Apr PMID: 19889721
Authors: Cypriano-Souza, A. L. - Fernandez, G. P. - Lima-Rosa, C. A. - Engel, M. H. - Bonatto, S. L.
Journal: J Hered

The Southwestern Atlantic Ocean humpback whales wintering ground (breeding stock A) are distributed along the Brazilian coast (5-23 degrees S), and their main mating and calving ground is in the Abrolhos Bank. We investigated genetic diversity, population structure, and relatedness of individuals sampled from the entire Southwest Atlantic humpback whale population. A total of 275 individuals sampled from 2 subregions (Abrolhos Bank, n = 229 and Praia do Forte, n = 46) were screened for 9 microsatellite loci. This population showed a high level of allelic diversity (A = 12.1) and a high mean observed heterozygosity (H(O) = 0.733). No signal of significant genetic bottleneck was detected in accordance with the mitochondrial DNA data. We find no evidence of temporal (between years) genetic structure as well as no genetic differentiation between whales from the 2 subregions of the Brazilian breeding ground. We observed that the proportion of males and females in this population was approximately 1:1, which differs from the male-biased sex ratio observed in other breeding grounds. The data obtained through this study provided no evidence of kinship associations within social groups. Finally, a female sampled off South Georgia Islands showed a putative parent-offspring relationship with a female off Abrolhos Bank, supporting the migratory link between these 2 areas.

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Simultaneous evaluation of paternal and maternal immigrant gene flow and the implications for the overall genetic composition of Pinus densiflora dispersed seeds.

Publication Date: 2010 Mar-Apr PMID: 19889720
Authors: Iwaizumi, M. G. - Takahashi, M. - Watanabe, A. - Ubukata, M.
Journal: J Hered

When considering the genetic implications of immigrant gene flow, it is important to evaluate both the proportions of immigrant gametes and their genetic composition. We simultaneously investigated paternal and maternal gene flow in dispersed seeds in a natural population of Pinus densiflora located along a ridge. The paternity and maternity of a total of 454 dispersed seeds (in 2004 and 2005) were accurately and separately assigned to 454 candidate adult trees, by analyzing the nuclear DNA of both diploid biparentally derived embryos and haploid maternally derived megagametophytes of the seeds. The relative genetic diversities and differences between within-population and immigrant groups of both paternally and maternally derived gametes (4 groups) that formed the genotypes of the seeds were evaluated. Using 8 microsatellite markers, we found that 64.0-72.6% of paternally derived gametes, and 17.8-20.2% of maternally derived gametes, were from other populations. Principal coordinate analysis showed that the 4 gamete groups tended to be plotted at different locations on the scattergram, indicating that they each have different genetic compositions. Substantial paternal and maternal immigrant gene flow occurred in this population, and therefore, the overall genetic variation of dispersed seeds is enhanced by both paternally and maternally derived immigrant gametes.

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Phylogenetic analysis of subgenus vigna species using nuclear ribosomal RNA ITS: evidence of hybridization among Vigna unguiculata subspecies.

Publication Date: 2010 Mar-Apr PMID: 19861637
Authors: Vijaykumar, A. - Saini, A. - Jawali, N.
Journal: J Hered

Molecular phylogeny among species belonging to subgenus Vigna (genus Vigna) was inferred based on internal transcribed spacer (ITS) sequences of 18S-5.8S-26S ribosomal RNA gene unit. Analysis showed a total of 356 polymorphic sites of which approximately 80% were parsimony informative. Phylogenetic reconstruction by neighbor joining and maximum parsimony methods placed the 57 Vigna accessions (belonging to 15 species) into 5 major clades. Five species viz. Vigna heterophylla, Vigna pubigera, Vigna parkeri, Vigna laurentii, and Vigna gracilis whose position in the subgenus was previously not known were placed in the section Vigna. A single accession (Vigna unguiculata ssp. tenuis, NI 1637) harbored 2 intragenomic ITS variants, indicative of 2 different types of ribosomal DNA (rDNA) repeat units. ITS variant type-I was close to ITS from V. unguiculata ssp. pubescens, whereas type-II was close to V. unguiculata ssp. tenuis. Transcript analysis clearly demonstrates that in accession NI 1637, rDNA repeat units with only type-II ITS variants are transcriptionally active. Evidence from sequence analysis (of 5.8S, ITS1, and ITS2) and secondary structure analysis (of ITS1 and ITS2) indicates that the type-I ITS variant probably does not belong to the pseudogenic rDNA repeat units. The results from phylogenetic and transcript analysis suggest that the rDNA units with the type-I ITS may have introgressed as a result of hybridization (between ssp. tenuis and ssp. pubescens); however, it has been epigenetically silenced. The results also demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. unguiculata.

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