Jane L. Doyle

Multiple Independent Losses of Two Genes and One Intron from Legume Chloroplast Genomes

The losses of genes or introns from the chloroplast genome are of potential utility as phylogenetic characters. Previous broad surveys of angiosperms, along with sequencing studies in Pisum sativum, uncovered several instances of variation for such characters within the Legumi- nosae. Using a slot blot hybridization method that did not require high molecular weight DNA, probes for six genes and three introns typically found in angiosperm chloroplast genomes were used to screen 392 legume genera, representing all three subfamilies and 50 out of 51 tribes, and 48 genera from 26 other families of dicots. Few cases of chloroplast gene or intron loss from chloroplast genomes were observed among nonlegumes or within the legume subfamilies Mimo- soideae and Caesalpinioideae, but numerous apparent losses were observed in the large subfamily Papilionoideae. Certain cases of suspected losses were tested by polymerase chain reaction. The genes rpl2 and rbcL appear to be present in all taxa surveyed, and virtually all possess accD. In contrast, ORF184 and rpsl6 each appear to have been lost multiple, independent times within Leguminosae, while all members of the family appear to lack rp122. The intron of rpl2 has likely been lost at least four times within the family, and its absence is a synapomorphy for a core group of the papilionoid tribe Desmodieae. No convincing evidence of loss was observed among legumes for the introns of trnI and rpll6. These results indicate that gene or intron loss characters may often be homoplastic. Intron losses are a more reliable and valuable class of phylogenetic characters than are gene losses.

Chloroplast DNA Phylogeny of the Papilionoid Legume Tribe Phaseoleae

Restriction map variation has been assayed in the slowly evolving chloroplast DNA (cpDNA) inverted repeat regions of 43 genera of the large and economically important legume tribe Phaseoleae and representatives of several allied tribes. Cladistic analyses of these data indicate that several plastome groups correspond well to subtribes recognized largely on the basis of mor- phological variation. Based on these cpDNA data, the tribe as a whole does not appear to be monophyletic, a result in accordance with current, morphologically-based hypotheses. Plastomes of several genera belonging to subtribes considered basal within Phaseoleae have as their sister groups plastomes of non-Phaseoleae tribes, notably Millettieae, the tribe considered to represent the ancestral stock from which diverse elements of Phaseoleae were derived. More unexpectedly, plastomes of the tribe Desmodieae fall within the clade that includes the most derived chloroplast genomes of Phaseoleae.

GENOMES, MULTIPLE ORIGINS, AND LINEAGE RECOMBINATION IN THE GLYCINE TOMENTELLA (LEGUMINOSAE) POLYPLOID COMPLEX: HISTONE H3-D GENE SEQUENCES

Abstract Relationships among the various diploid and polyploid taxa that comprise Glycine tomentella have been hypothesized from crossing studies, isozyme data, and repeat length variation for the 5S nuclear ribosomal gene loci. However, several key questions have persisted, and detailed phylogenetic evidence from homoeologous nuclear genes has been lacking. The histone H3‐D locus is single copy in diploid Glycine species and has been used to elucidate relationships among diploid races of G. tomentella, providing a framework for testing genome origins in the polyploid complex. For all six G. tomentella polyploid races (T1—T6), alleles at two homoeologous histone H3‐D loci were isolated and analyzed phylogenetically with alleles from diploid Glycine species, permitting the identification of all of the homoeologous genomes of the complex. Allele networks were constructed to subdivide groups of homoeologous alleles further, and two‐locus genotypes were constructed using these allele classes. Results suggest that some races have more than one origin and that interfertility within races has led to lineage recombination. Most alleles in polyploids are identical or closely related to alleles in diploids, suggesting recency of polyploid origins and spread beyond Australia. These features parallel the other component of the Glycine subgenus Glycine polyploid complex, G. tabacina, one of whose races shares a diploid genome with a G. tomentella polyploid race.

Chloroplast-Expressed Glutamine Synthetase in Glycine and Related Leguminosae: Phylogeny, Gene Duplication, and Ancient Polyploidy

Abstract The nuclear gene encoding the chloroplast-expressed isozyme of glutamine synthetase (ncpGS) is single copy in diploid angiosperms but is duplicated in species of Glycine, a paleopolyploid genus. The two Glycine paralogues are sister to one another in phylogenetic analyses, a pattern that suggests that this ncpGS duplication occurred subsequent to the divergence of Glycine from extant Glycininae. This pattern does not support an allopolyploid hypothesis in which genomes from close relatives of extant genera combined to form the polyploid, 2n = 40 genome of Glycine, nor with an ancient gene duplication shared with other Glycininae. Rather, it is consistent with autopolyploidy or with a simple gene duplication. Teramnus ncpGS was the closest relative of the two Glycine paralogues, supporting a sister-group relationship between these two genera. In contrast, ncpGS results suggested that Sinodolichos, a genus that has been suggested as a possible congener of Glycine, is more closely related to Pseueminia and Pseudovigna. Both paralogues of ncpGS identify known genome groups among species of Glycine subg. Glycine, but neither strongly resolves relationships among these groups. Incongruence between the two paralogues in the placement of G. falcata mirrors incongruence between the chloroplast genome and other nuclear genes for this species.

Molecular phylogenetic relationships within and among diploid races of Glycine tomentella (Leguminosae)

DNA-sequence variation at the single-copy nuclear locus histone H3-D was surveyed in 35 accessions of diploid Glycine tomentella Hayata (2n = 38, 40) and samples of the closely related new species Glycine aphyonota B.Pfeil and Glycine pullenii B.Pfeil, Tindale & Craven. The objective was a thorough analysis of the infraspecific variation in this complex species as a prelude to the analysis of the evolutionary origin of its tetraploid races. The shortest trees found by a heuristic search employing parsimony all grouped the accessions into five wellsupported clades that related closely to infraspecific taxa previously recognised from cytogenetic, isozyme and ITSsequence studies. The most-differentiated race (isozyme label D4) is related to the so-called A-genome species G. clandestina Wendl., G. canescens F.J.Herm., G. latrobeana (Meissn.) Benth. and G. argyrea Tind. This race is restricted to the central uplands of Queensland. The two common races from Queensland are the aneuploid (2n = 38) race and the euploid form from north-east coastal regions (D3). Remarkably, an isolated population of this race was found in the northern wetter fringes of the Kimberley District, Western Australia. The remaining two races (D5A and D5B) are centred on the monsoonal tropics of Kimberley and Top End, Northern Territory. These two groups have distinctive isozyme and morphological features that support the recognition of such divergence, at least at subspecific level.

Confirmation of shared and divergent genomes in the Glycine tabacina polyploid complex (Leguminosae) using histone H3-D sequences.

Abstract Glycine tabacina, a wild perennial relative of soybean, comprises a widespread polyploid complex in Australia and islands of the Pacific Ocean. Data from a single-copy nuclear locus, histone H3-D, confirm the existence of two polyploid races. Plants of one of these (AAB′B′) are nonstoloniferous and have linear leaflets. One of the genomes of this race is that of an A-genome diploid, identified by the histone data most closely with a race of G. tomentella. Its other genome (B′B′) was donated by a nonstoloniferous diploid species that is sister to all of the remaining B-genome species, which are stoloniferous. Plants of the second race of polyploid G. tabacina (BBB′B′) are stoloniferous, have ovate leaflets, and combine a B′ genome with a genome of the core B-genome diploid group. The likely source of the shared B′ genome is a species previously referred to as G. sp. aff tabacina, that is here formally named Glycine stenophita. Communicating Editor: Alan Whittemore

Analysis of a polyploid complex in Glycine with chloroplast and nuclear DNA.

Studies of chloroplast DNA and nuclear 18s–25s ribosomal genes have revealed considerable variation in Glycine subgenus Glycine, the perennial relatives of the cultivated annual soybean. We have used these molecular characters to investigate the origins and evolution of G. tabacina, a species that comprises a widespread polyploid complex in Australia and the islands of the southern and west-central Pacific. Two principal groups of accessions were detected in this species using molecular characters. These two types also differ morphologically and have distinct, though overlapping, geographic ranges; comparison with results of artificial hybridisation studies showed that sterility barriers exist between the two groups. Both types are fixed hybrids for nuclear rDNA, and share one rDNA repeat class, presumably derived from a common diploid progenitor. The two types had different maternal progenitors, based on cpDNA variation. One of the two polyploid types is polymorphic for cpDNA, and shares nearly all of its plastome variants with diploid accessions, suggesting multiple, independent origins of the polyploid from a pool of diploid progenitors. Molecular data suggest that polyploids have originated recently, and that dispersal from Australia to the islands of the Pacific has occurred several times.

The wild side of a major crop: soybean's perennial cousins from Down Under.

The accumulation of over 30 years of basic research on the biology, genetic variation, and evolution of the wild perennial relatives of soybean (Glycine max) provides a foundation to improve cultivated soybean. The cultivated soybean and its wild progenitor, G. soja, have a center of origin in eastern Asia and are the only two species in the annual subgenus Soja. Systematic and evolutionary studies of the ca. 30 perennial species of subgenus Glycine, native to Australia, have benefited from the availability of the G. max genomic sequence. The perennial species harbor many traits of interest to soybean breeders, among them resistance to major soybean pathogens such as cyst nematode and leaf rust. New species in the Australian subgenus continue to be described, due to the collection of new material and to insights gleaned through systematic studies of accessions in germplasm collections. Ongoing studies in perennial species focus on genomic regions that contain genes for key traits relevant to soybean breeding. These comparisons also include the homoeologous regions that are the result of polyploidy in the common ancestor of all Glycine species. Subgenus Glycine includes a complex of recently formed allopolyploids that are the focus of studies aimed at elucidating genomic, transcriptomic, physiological, taxonomic, morphological, developmental, and ecological processes related to polyploid evolution. Here we review what has been learned over the past 30 years and outline ongoing work on photosynthesis, nitrogen fixation, and floral biology, much of it drawing on new technologies and resources.

Chloroplast DNA Phylogenetic Affinities of Newly Described Species in Glycine (Leguminosae: Phaseoleae)

Chloroplast DNA variation was used as a simple and rapid means to produce phy- logenetic hypotheses for three newly described species of Glycine subg. Glycine. The presence or absence of 43 restriction site characters previously described in a cpDNA survey of the entire subgenus, and five new characters reported here, was determined for seven accessions representing G. albicans, G. hirticaulis, and G. lactovirens, and two accessions of G. falcata, a species to which two of these new species are thought to be related. All of the new species are shown to belong to the A chloroplast genome (plastome) group, one of three major clades in the subgenus, among whose species are G. falcata. However, within this major clade none of the new species shared their closest affinities with chloroplast DNAs of G. falcata, but rather with plastomes of a group of five species forming a separate clade within the A genome. These results, if indicative of organismal phylogenies, suggest that habitual amphicarpy has developed independently in G. falcata and G. albicans. Chlo- roplast DNA polymorphism, common elsewhere in the subgenus, was observed in G. hirticaulis, G. lactovirens, and G. falcata.

DNA and Higher Plant Systematics: Some Examples from the Legumes

In the last few years, the DNA revolution has begun to have a dramatic impact on the field of plant systematics. Access to the various plant genomes--chloroplast, mitochondrial, and nuclear--has provided the systematist with a virtually inexhaustible source of characters for phylogenetic analysis. The interaction of DNA technology and cladistic analysis has been particularly powerful: the tools for producing empirical data relevant to phylogenetic relationship have been complemented by a rigorous theoretical framework on which to build explicit hypotheses of homology and phylogeny. This potent combination has led to a rapid acceptance of molecular approaches in “mainstream” plant systematics, which has been manifested in a large number of publications and papers at plant systematics meetings (at least in the USA) involving DNA phylogenies. Not all of the three genomes have received equal attention, however, nor have the tools that are currently most widely used been shown to be useful at all taxonomic levels. Furthermore, the role of polymorphism, of confidence in phylogenies, and in general of the difference between gene trees and species trees is only slowly becoming appreciated among plant systematists and clearly should have some impact on the development of the field.