The genetics of convergent evolution: insights from plant photosynthesis

Heyduk, Karolina; Moreno-Villena, Jose J; Gilman, Ian S.; Christin, Pascal‐Antoine; Edwards, Erika J.

doi:10.1038/s41576-019-0107-5

Cited by 114 publications

(119 citation statements)

References 122 publications

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“…To support this analysis, the 2∆LnL value of rpl20 is zero and the p-value of LRT is greater than 0.05 (Tables 2 and 3). All these highly positive selection genes are involved in the functions of the plant genetic system or photosynthesis process [27][28][29][30][31]. Besides, these seven genes have undergone positive selection, which might be the result of adaptation to their diverse habitats.…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Raman¹,

Park²

2020

Agronomy

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The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

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Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Raman¹,

Park²

2020

Agronomy

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“…Alloteropsis may be the finest model clade yet for identifying the very early stages of C 4 emergence, as there is a full C 3 to C 4 physiological spectrum found within a single species, Alloteropsis semialata (Lundgren et al ., ). One potentially new realization is that the C 4 optimization stage may be longer and more elaborate than we have thought, and that many of the differences between distantly related C 3 and C 4 species evolved later in C 4 lineages, long after the first emergence of the pathway – and thus are not necessary components, but rather are optimizations of the pathway (Heyduk et al ., ). In Alloteropsis , for example, several populations received several fully optimized C 4 genes via lateral gene transfer from co‐occurring C 4 grass species (Christin et al ., ), which they preferentially utilize, and their vertically inherited genes show very low levels of expression.…”

Section: The C4 Evolutionary Trajectory: Anatomy First Biochemistry mentioning

confidence: 97%

Evolutionary trajectories, accessibility and other metaphors: the case of C₄ and CAM photosynthesis

2019

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Summary Are evolutionary outcomes predictable? Adaptations that show repeated evolutionary convergence across the Tree of Life provide a special opportunity to dissect the context surrounding their origins, and identify any commonalities that may predict why certain traits evolved many times in particular clades and yet never evolved in others. The remarkable convergence of C4 and Crassulacean Acid Metabolism (CAM) photosynthesis in vascular plants makes them exceptional model systems for understanding the repeated evolution of complex phenotypes. This review highlights what we have learned about the recurring assembly of C4 and CAM, focusing on the increasingly predictable stepwise evolutionary integration of anatomy and biochemistry. With the caveat that we currently understand C4 evolution better than we do CAM, I propose a general model that explains and unites C4 and CAM evolutionary trajectories. Available data suggest that anatomical modifications are the ‘rate‐limiting step’ in each trajectory, which in large part determines the evolutionary accessibility of both syndromes. The idea that organismal structure exerts a primary influence on innovation is discussed in the context of other systems. Whether the rate‐limiting step occurs early or late in the evolutionary assembly of a new phenotype may have profound implications for its distribution across the Tree of Life.

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“…According to current models, an initial C 4 pathway can evolve via enzyme upregulation and limited modifications of the proteins (Sage et al, 2012;Heckmann et al, 2013;Dunning et al, 2019;Heyduk et al, 2019), as observed in C 3 -C 4 intermediates (Svensson et al, 2003;Dunning et al, 2017). Once a C 4 pathway is in place, selection will act to improve its efficiency (Heckmann et al, 2013), and variation among members of the same C 4 lineage indicates that such process can take protracted periods of selection on novel mutations (Heyduk et al, 2019). Because these are likely necessary for a function of PEPC in C 4 cells with high concentrations of metabolites, we suggest that relaxed sensitivity to inhibitors happens early during the evolution of C 4 PEPC.…”

Section: Moody Et Almentioning

confidence: 99%

Kinetic Modifications of C4 PEPC Are Qualitatively Convergent, but Larger in Panicum Than in Flaveria

2020

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C 4 photosynthesis results from a set of anatomical features and biochemical components that act together to concentrate CO 2 within the leaf and boost productivity. This complex trait evolved independently many times, resulting in various realizations of the phenotype, but in all C 4 plants the primary fixation of atmospheric carbon is catalyzed by phosphoenolpyruvate carboxylase. Comparisons of C 4 and non-C 4 PEPC from a few closely related species suggested that the enzyme was modified to meet the demands of the C 4 cycle. However, very few C 4 groups have been investigated, hampering general conclusions. To test the hypothesis that distant C 4 lineages underwent convergent biochemical changes, we compare the kinetic variation between C 4 and non-C 4 PEPC from a previously assessed young lineage (Flaveria, Asteraceae) with those from an older lineage found within the distantly related grass family (Panicum). Despite the evolutionary distance, the kinetic changes between the non-C 4 and C 4 PEPC are qualitatively similar, with a decrease in sensitivity for inhibitors, an increased specificity (k cat /K m) for bicarbonate, and a decreased specificity (k cat /K m) for PEP. The differences are more pronounced in the older lineage Panicum, which might indicate that optimization of PEPC for the C 4 context increases with evolutionary time.

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The genetics of convergent evolution: insights from plant photosynthesis

Cited by 114 publications

References 122 publications

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Evolutionary trajectories, accessibility and other metaphors: the case of C₄ and CAM photosynthesis

Kinetic Modifications of C4 PEPC Are Qualitatively Convergent, but Larger in Panicum Than in Flaveria

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The genetics of convergent evolution: insights from plant photosynthesis

Cited by 114 publications

References 122 publications

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Evolutionary trajectories, accessibility and other metaphors: the case of C4 and CAM photosynthesis

Kinetic Modifications of C4 PEPC Are Qualitatively Convergent, but Larger in Panicum Than in Flaveria

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Evolutionary trajectories, accessibility and other metaphors: the case of C₄ and CAM photosynthesis