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Xiaoquan Wang - One of the best experts on this subject based on the ideXlab platform.
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the complete mitochondrial genome of taxus cuspidata taxaceae eight protein coding genes have transferred to the nuclear genome
BMC Evolutionary Biology, 2020Co-Authors: Shenglong Kan, Tingting Shen, Ping Gong, Jinhua Ran, Xiaoquan WangAbstract:Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six Gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in Gymnosperms. Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released Gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of Gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in Gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four Gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of Gymnosperm mitogenomes, which are different from angiosperm mitogenomes.
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revisiting the phosphatidylethanolamine binding protein pebp gene family reveals cryptic flowering locus t gene homologs in Gymnosperms and sheds new light on functional evolution
New Phytologist, 2016Co-Authors: Kezhen Yang, Xiaoquan WangAbstract:Summary Angiosperms and Gymnosperms are two major groups of extant seed plants. It has been suggested that Gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released Gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three Gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of Gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that Gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of Gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that Gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of Gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.
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Revisiting the phosphatidylethanolamine‐binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in Gymnosperms and sheds new light on functional evolution
New Phytologist, 2016Co-Authors: Kezhen Yang, Xiaoquan WangAbstract:Summary Angiosperms and Gymnosperms are two major groups of extant seed plants. It has been suggested that Gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released Gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three Gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of Gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that Gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of Gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that Gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of Gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.
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Evolution and biogeography of Gymnosperms
Molecular phylogenetics and evolution, 2014Co-Authors: Xiaoquan Wang, Jinhua RanAbstract:Living Gymnosperms comprise only a little more than 1000 species, but represent four of the five main lineages of seed plants, including cycads, ginkgos, gnetophytes and conifers. This group has huge ecological and economic value, and has drawn great interest from the scientific community. Here we review recent advances in our understanding of Gymnosperm evolution and biogeography, including phylogenetic relationships at different taxonomic levels, patterns of species diversification, roles of vicariance and dispersal in development of intercontinental disjunctions, modes of molecular evolution in different genomes and lineages, and mechanisms underlying the formation of large nuclear genomes. It is particularly interesting that increasing evidence supports a sister relationship between Gnetales and Pinaceae (the Gnepine hypothesis) and the contribution of recent radiations to present species diversity, and that expansion of retrotransposons is responsible for the large and complex nuclear genome of Gymnosperms. In addition, multiple coniferous genera such as Picea very likely originated in North America and migrated into the Old World, further indicating that the center of diversity is not necessarily the place of origin. The Bering Land Bridge acted as an important pathway for dispersal of Gymnosperms in the Northern Hemisphere. Moreover, the genome sequences of conifers provide an unprecedented opportunity and an important platform for the evolutionary studies of Gymnosperms, and will also shed new light on evolution of many important gene families and biological pathways in seed plants.
Conrad C Labandeira - One of the best experts on this subject based on the ideXlab platform.
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false blister beetles and the expansion of Gymnosperm insect pollination modes before angiosperm dominance
Current Biology, 2017Co-Authors: David Peris, Ricardo Perezde La Fuente, Xavier Delclòs, Eduardo Barrón, Conrad C Labandeira, Enrique PeñalverAbstract:Summary During the mid-Cretaceous, angiosperms diversified from several nondiverse lineages to their current global domination [1], replacing earlier Gymnosperm lineages [2]. Several hypotheses explain this extensive radiation [3], one of which involves proliferation of insect pollinator associations in the transition from Gymnosperm to angiosperm dominance. However, most evidence supports Gymnosperm–insect pollinator associations, buttressed by direct evidence of pollen on insect bodies, currently established for four groups: Thysanoptera (thrips), Neuroptera (lacewings), Diptera (flies), and now Coleoptera (beetles). Each group represents a distinctive pollination mode linked to a unique mouthpart type and feeding guild [4–9]. Extensive indirect evidence, based on specialized head and mouthpart morphology, is present for one of these pollinator types, the long-proboscid pollination mode [10], representing minimally ten family-level lineages of Neuroptera, Mecoptera (scorpionflies), and Diptera [8, 10, 11]. A recurring feature uniting these pollinator modes is host associations with ginkgoalean, cycad, conifer, and bennettitalean Gymnosperms. Pollinator lineages bearing these pollination modes were categorized into four evolutionary cohorts during the 35-million-year-long angiosperm radiation, each defined by its host-plant associations (Gymnosperm or angiosperm) and evolutionary pattern (extinction, continuation, or origination) during this interval [12]. Here, we provide the first direct evidence for one cohort, exemplified by the beetle Darwinylus marcosi , family Oedemeridae (false blister beetles), that had an earlier Gymnosperm (most likely cycad) host association, later transitioning onto angiosperms [13]. This association constitutes one of four patterns explaining the plateau of family-level plant lineages generally and pollinating insects specifically during the mid-Cretaceous angiosperm radiation [12].
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false blister beetles and the expansion of Gymnosperm insect pollination modes before angiosperm dominance
Current Biology, 2017Co-Authors: David Peris, Ricardo Perezde La Fuente, Xavier Delclòs, Eduardo Barrón, Conrad C Labandeira, Enrique PeñalverAbstract:Summary During the mid-Cretaceous, angiosperms diversified from several nondiverse lineages to their current global domination [1], replacing earlier Gymnosperm lineages [2]. Several hypotheses explain this extensive radiation [3], one of which involves proliferation of insect pollinator associations in the transition from Gymnosperm to angiosperm dominance. However, most evidence supports Gymnosperm–insect pollinator associations, buttressed by direct evidence of pollen on insect bodies, currently established for four groups: Thysanoptera (thrips), Neuroptera (lacewings), Diptera (flies), and now Coleoptera (beetles). Each group represents a distinctive pollination mode linked to a unique mouthpart type and feeding guild [4–9]. Extensive indirect evidence, based on specialized head and mouthpart morphology, is present for one of these pollinator types, the long-proboscid pollination mode [10], representing minimally ten family-level lineages of Neuroptera, Mecoptera (scorpionflies), and Diptera [8, 10, 11]. A recurring feature uniting these pollinator modes is host associations with ginkgoalean, cycad, conifer, and bennettitalean Gymnosperms. Pollinator lineages bearing these pollination modes were categorized into four evolutionary cohorts during the 35-million-year-long angiosperm radiation, each defined by its host-plant associations (Gymnosperm or angiosperm) and evolutionary pattern (extinction, continuation, or origination) during this interval [12]. Here, we provide the first direct evidence for one cohort, exemplified by the beetle Darwinylus marcosi , family Oedemeridae (false blister beetles), that had an earlier Gymnosperm (most likely cycad) host association, later transitioning onto angiosperms [13]. This association constitutes one of four patterns explaining the plateau of family-level plant lineages generally and pollinating insects specifically during the mid-Cretaceous angiosperm radiation [12].
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why did terrestrial insect diversity not increase during the angiosperm radiation mid mesozoic plant associated insect lineages harbor clues
2014Co-Authors: Conrad C LabandeiraAbstract:Several studies provided evidence that family-level insect diversity remained flat throughout the initial mid-Cretaceous angiosperm radiation 125–90 million years ago. As this result has engendered considerable commentary, a reanalysis was done of a new dataset of 280 plant-associated insect families spanning the 174 million year interval of the Jurassic–Paleogene periods from 201 to 23 million years ago. Lineage geochronologic ranges were determined, and feeding attributes were characterized by: (i) dominant feeding guild (herbivore, pollinator, herbivore–pollinator, pollinator–mimic, xylophage); (ii) membership in one of eight functional feeding groups; and (iii) dominant plant host or host transition (cryptogam/fern only, cryptogam/fern → angiosperm, Gymnosperm only, Gymnosperm → angiosperm, angiosperm only). A time-series plot of insect lineages and their dominant plant–host affiliations resulted in four conclusions. First, insect lineages with dominant Gymnosperm hosts reached a level of 95 families in the 35 million years preceding the initial angiosperm radiation. Second, earlier insect lineages with Gymnosperm → angiosperm host transitions and newly originated insect lineages that developed dominant associations with emerging angiosperms rapidly diversified during the angiosperm radiation, later establishing a plateau of 110 families during a 20 million year interval after the initial angiosperm radiation. Third, these two diversity maxima were separated during the angiosperm radiation by a diversity minimum, the Aptian–Albian gap, indicating major turnover and time-lag effects associated with the extirpation and acquisition of plant associations. Last, insect lineages most affected during this interval were herbivores and pollinators, exophagous feeders, and those hosting Gymnosperms, angiosperms and Gymnosperm → angiosperm transitions. These data largely explain the flat or even decreased level of insect diversity immediately before, during, and after the initial angiosperm radiation.
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a probable pollination mode before angiosperms eurasian long proboscid scorpionflies
Science, 2009Co-Authors: Conrad C Labandeira, Jorge A Santiagoblay, Alexandr P Rasnitsyn, Chungkun Shih, Alexei S Bashkuev, Amelia M V Logan, Carol L Hotton, David L DilcherAbstract:The head and mouthpart structures of 11 species of Eurasian scorpionflies represent three extinct and closely related families during a 62-million-year interval from the late Middle Jurassic to the late Early Cretaceous. These taxa had elongate, siphonate (tubular) proboscides and fed on ovular secretions of extinct Gymnosperms. Five potential ovulate host-plant taxa co-occur with these insects: a seed fern, conifer, ginkgoopsid, pentoxylalean, and gnetalean. The presence of scorpionfly taxa suggests that siphonate proboscides fed on Gymnosperm pollination drops and likely engaged in pollination mutualisms with Gymnosperms during the mid-Mesozoic, long before the similar and independent coevolution of nectar-feeding flies, moths, and beetles on angiosperms. All three scorpionfly families became extinct during the later Early Cretaceous, coincident with global Gymnosperm-to-angiosperm turnover.
Günter Theissen - One of the best experts on this subject based on the ideXlab platform.
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MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants.
Annals of botany, 2014Co-Authors: Lydia Gramzow, Lisa Weilandt, Günter TheissenAbstract:BACKGROUND AND AIMS MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for Gymnosperms. METHODS The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for Gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. KEY RESULTS Type I MADS-box genes are under-represented in Gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in Gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In Gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant Gymnosperms had at least 14-16 Type II MADS-box genes. CONCLUSIONS The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that Gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of Gymnosperms. This study is the first that provides a comprehensive overview of MADS-box genes in conifers and thus will provide a framework for future work on MADS-box genes in seed plants.
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The naked and the dead: the ABCs of Gymnosperm reproduction and the origin of the angiosperm flower.
Seminars in cell & developmental biology, 2009Co-Authors: Rainer Melzer, Yong-qiang Wang, Günter TheissenAbstract:20 years after establishment of the ABC model many of the molecular mechanisms underlying development of the angiosperm flower are relatively well understood. Central players in the gene regulatory network controlling flower development are SQUA-like, DEF/GLO-like, AG-like and AGL6/SEP1-like MIKC-type MADS-domain transcription factors. These provide class A, class B, class C and the more recently defined class E floral homeotic functions, respectively. There is evidence that the floral homeotic proteins recognize the DNA of target genes in an organ-specific way as multimeric protein complexes, thus constituting 'floral quartets'. In contrast to the detailed insights into flower development, how the flower originated during evolution has remained enigmatic. However, while orthologues of all classes of floral homeotic genes appear to be absent from all non-seed plants, DEF/GLO-like, AG-like, and AGL6-like genes have been found in diverse extant Gymnosperms, the closest relatives of the angiosperms. While SQUA-like and SEP1-like MADS-box genes appear to be absent from extant Gymnosperms, reconstruction of MADS-box gene phylogeny surprisingly suggests that the most recent common ancestor of Gymnosperms and angiosperms possessed representatives of both genes, but that these have been lost in the lineage that led to extant Gymnosperms. Expression studies and genetic complementation experiments indicate that both angiosperm and Gymnosperm AG-like and DEF/GLO-like genes have conserved functions in the specification of reproductive organs and in distinguishing male from female organs, respectively. Based on these findings novel models about the molecular basis of flower origin, involving changes in the expression patterns of DEF/GLO-like or AGL6/SEP1/SQUA-like genes in reproductive structures, were developed. While in angiosperms SEP1-like proteins play an important role in floral quartet formation, preliminary evidence suggests that Gymnosperm DEF/GLO-like and AG-like proteins alone can already form floral quartet-like complexes, further corroborating the view that the formation of floral quartet-like complexes predated flower origin during evolution.
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distinct mads box gene expression patterns in the reproductive cones of the Gymnosperm gnetum gnemon
Development Genes and Evolution, 2003Co-Authors: Annette Becker, Heinz Saedler, Günter TheissenAbstract:Expression patterns from in situ hybridization of four MADS-box genes (GGM7, GGM9, GGM11, and GGM15) from the Gymnosperm species Gnetum gnemon are presented. Together with previously published data about putative orthologs of floral homeotic genes from G. gnemon (GGM2, GGM3, GGM13), we describe seven temporally and spatially distinct expression patterns in male, female or both types of reproductive units which very likely reflect the diversity of MADS-box gene function in Gymnosperm cones. There is evidence that some aspects of the observed differential expression have been conserved since the last common ancestor of extant angiosperms and Gymnosperms about 300 million years ago.
Kezhen Yang - One of the best experts on this subject based on the ideXlab platform.
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revisiting the phosphatidylethanolamine binding protein pebp gene family reveals cryptic flowering locus t gene homologs in Gymnosperms and sheds new light on functional evolution
New Phytologist, 2016Co-Authors: Kezhen Yang, Xiaoquan WangAbstract:Summary Angiosperms and Gymnosperms are two major groups of extant seed plants. It has been suggested that Gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released Gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three Gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of Gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that Gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of Gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that Gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of Gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.
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Revisiting the phosphatidylethanolamine‐binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in Gymnosperms and sheds new light on functional evolution
New Phytologist, 2016Co-Authors: Kezhen Yang, Xiaoquan WangAbstract:Summary Angiosperms and Gymnosperms are two major groups of extant seed plants. It has been suggested that Gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released Gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three Gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of Gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that Gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of Gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that Gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of Gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.
Amanda R De La Torre - One of the best experts on this subject based on the ideXlab platform.
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Comparative Genomics of Spruce and Other Gymnosperms
Compendium of Plant Genomes, 2020Co-Authors: Amanda R De La TorreAbstract:In contrast to flowering plants, the genomes of Gymnosperms are still poorly understood. Current knowledge on the genomic architecture, gene space, and macrostructure of Gymnosperm genomes mainly comes from Pinaceae species, in which spruce species (genera with most sequenced genomes to date) had played a significant role. Whereas the accumulation of nuclear genomes’ sequence information has followed a slow pace, the sequencing of chloroplast genomes skyrocketed in the last 10 years, with many spruce species sequenced so far. From the comparison of nuclear, mitochondrial, and chloroplast genomes, we can conclude that they all differ in their genomic macrostructure and rates of sequence evolution. The high structural conservation among species, genera, and families is characteristic of nuclear genomes, whereas chloroplast and mitochondrial genomes show less conserved structures due to genomic arrangements. Finally, Picea species follow trends observed in other Gymnosperms and angiosperms, in which rates of sequence evolution are the highest in nuclear DNA, followed by chloroplast and then mitochondrial DNA.
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Functional and morphological evolution in Gymnosperms: a portrait of implicated gene families
Evolutionary applications, 2019Co-Authors: Amanda R De La Torre, Anthony Piot, Bobin Liu, Benjamin Wilhite, Matthew Weiss, Ilga PorthAbstract:Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several Gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within Gymnosperms, and between angiosperms and Gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in Gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus Gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants.
Molecular biology and evolution, 2017Co-Authors: Amanda R De La Torre, Yves Van De Peer, Par K IngvarssonAbstract:The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (Gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and Gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of Gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that Gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and Gymnosperms differ considerably in their rates of molecular evolution per unit time, with Gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in Gymnosperms. In contrast to their slow rates of molecular evolution, Gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in Gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
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insights into conifer giga genomes
Plant Physiology, 2014Co-Authors: Amanda R De La Torre, Stefan Jansson, Ove Nilsson, John Mackay, Inanc Birol, Par K Ingvarsson, Christopher I Keeling, Steven J.m. Jones, Jean Bousquet, Kermit RitlandAbstract:Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of Gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of Gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and Gymnosperm genomes.