The Secret to a 1,000-Year Life: Scientists Decode the Genome of Welwitschia, the World's Most Extraordinary Desert Plant

Table of Contents

• Key Points
• A Plant Like No Other
• What Makes Welwitschia So Special?
• How the Research Was Conducted
• The Welwitschia Genome at a Glance
• An Ancient Whole-Genome Duplication
• Jumping Genes: The Retrotransposon Burst
• DNA Methylation: Epigenetic Secrets of Survival
• What These Findings Mean for Science
• Limitations of the Study
• What's Next? Future Research Directions
• Frequently Asked Questions
• Source Information

Key Points

• Welwitschia is an ancient desert plant that lives thousands of years with only two continuously growing leaves.
• Its genome is over twice the size of the human genome and is mostly repetitive DNA.
• An ancient whole-genome duplication about 86 million years ago provided extra genes, followed by genome downsizing.
• Welwitschia shows extremely high CHH DNA methylation, potentially the highest in any plant, likely silencing jumping genes.
• Findings may inform future crop improvement for drought tolerance, but functional experiments are still needed.

A Plant Like No Other

When Joseph Dalton Hooker, director of the Royal Botanic Gardens at Kew in the United Kingdom from 1865 to 1885, first encountered Welwitschia, he reportedly declared that "it is out of the question the most wonderful plant ever brought to this country and one of the ugliest."

That verdict from one of the most respected botanists of the Victorian era has proven remarkably durable. More than 150 years later, Welwitschia continues to astonish scientists with its bizarre appearance, extraordinary lifespan, and almost supernatural ability to survive conditions that would kill nearly any other plant.

The species grows only in the Kaokoveld Centre of Africa, an arid coastal desert spanning northern Namibia and southern Angola, where annual precipitation is less than 50 millimeters (about 2 inches) per year. It belongs to the Gnetophyta, an ancient lineage of gymnosperms—seed plants that also includes the genera Gnetum and Ephedra. Genetic evidence suggests Welwitschia and Gnetum diverged from a common ancestor more than 110 million years ago, during the early Cretaceous period, when dinosaurs still roamed the Earth. A fossilized Welwitschia seedling, Cratonia cotyledon, was found in early Cretaceous beds of Brazil, confirming the lineage's ancient origins.

What Makes Welwitschia So Special?

Welwitschia's most striking feature is its morphology: throughout its entire life—which can last several thousand years—the plant produces just two leaves. These leaves grow continuously from a basal meristem (a region of actively dividing cells at the base), resulting in what scientists describe as the longest-lived leaves in the plant kingdom.

The plant is dioecious, meaning individual plants are either male or female, and both produce cones for reproduction. Recent molecular data suggest there are two genetically and geographically distinct populations that may correspond to subspecies.

For centuries, scientists have debated where gnetophytes fit in the tree of life. Their conflicting phylogenetic placement, unique morphological features, and the extinction of critical seed plant groups have fueled speculation. However, the current consensus—based predominantly on gene sequences—is that gnetophytes are more closely related to conifers than to other gymnosperms, a hypothesis known as the "Gnepine," "Gnecup," or "Gnetifer" hypothesis.

How the Research Was Conducted

To uncover the genetic basis of Welwitschia's remarkable biology, an international team of researchers—led by scientists from the Chinese Academy of Sciences, Ghent University in Belgium, Queen Mary University of London, and the Gobabeb Research and Training Centre in Namibia—undertook a comprehensive genomic analysis.

They combined two powerful sequencing technologies to assemble the Welwitschia genome:

• Oxford Nanopore sequencing at 108× coverage (a long-read technology that can read very long stretches of DNA)
• Illumina sequencing at 134× coverage (a short-read technology known for high accuracy)

This dual approach allowed the team to generate a chromosome-level assembly comprising 6.86 gigabases (Gb) of DNA—that's 6.86 billion base pairs—covering 98% of the estimated genome size of 7.0 Gb. For context, the human genome is about 3.2 Gb, so Welwitschia's genome is more than twice the size of ours.

The researchers also produced an improved, high-quality genome assembly of Gnetum montanum (hereafter "Gnetum"), a related gnetophyte, using 10× Genomics and BioNano Genomics platforms to extend the scaffolds of a previous assembly. This allowed direct comparison between the two lineages.

To anchor and order the DNA sequences into chromosomes, the team used optical mapping and Hi-C (chromosome contact) maps, ultimately generating 21 pseudo-chromosomes for Welwitschia and 22 for Gnetum. These pseudo-chromosomes represent 93.65% (6.43 Gb) of the Welwitschia assembly and 86.47% (3.57 Gb) of the Gnetum assembly.

A total of 26,990 protein-coding genes were predicted in Welwitschia, of which 89.11% were validated by RNA sequencing transcript evidence from multiple tissues or by orthology with genes in other species. The BUSCO analysis—a standard benchmark for assessing genome assembly completeness—suggested that 83.47% of genes had been recovered. For Gnetum, the improved assembly showed a substantial enhancement over the previous release, with scaffold N50 lengths of 157.93 Mb, 27,354 genes identified, and 84.6% of BUSCO genes recovered.

In addition to genome sequencing, the researchers conducted extensive analysis of the methylome (patterns of DNA methylation, a chemical modification that can turn genes on or off) and transcriptome (the complete set of RNA transcripts) across different tissue types, including basal meristems and young leaves from both wild and greenhouse-grown plants.

The Welwitschia Genome at a Glance

The assembled Welwitschia genome is striking in several respects. The longest chromosome was approximately 551.97 Mb—a remarkable 3.3 times longer than the shortest chromosome. This observation agrees with previous cytogenetic studies showing that Welwitschia has telocentric chromosomes (chromosomes where the centromere is located very close to the end) that differ considerably in total length.

Perhaps the most dramatic finding is the sheer abundance of repetitive DNA. A staggering 86.85% of the Welwitschia genome consists of repetitive elements distributed across all chromosomes. The most abundant repeats are long terminal repeat retrotransposons (LTR-RTs)—a type of "jumping gene" that copies itself and inserts elsewhere in the genome—which alone comprise 55.26% of the genome.

Interestingly, unlike many other plant genomes, Welwitschia shows no indication of where centromeric regions lie based on repeat density, and it lacks the subtelomeric tandem repeats that are found in Gnetum.

An Ancient Whole-Genome Duplication

One of the most important discoveries concerns the evolutionary history of the genome. By analyzing the distribution of synonymous substitutions per synonymous site (K_S)—a molecular clock that measures how much duplicate genes have diverged—the researchers found clear evidence of an ancient whole-genome duplication (WGD) event unique to Welwitschia.

In simple terms, a whole-genome duplication means that at some point in the past, the entire genetic material of the plant was duplicated, providing a vast reservoir of extra genes that evolution could repurpose for new functions. Such events are known to have driven major evolutionary innovations in plants.

The data revealed:

• A signature peak of duplicate genes with a K_S value close to 1, indicating a relatively ancient duplication event
• 198 pairs of paralogous genes (duplicate genes derived from the same ancestral gene) located in 47 collinear duplicated regions
• An additional 773 paralogous genes in 222 syntenic regions (regions where paralogs are retained but gene order has been disrupted)

Cross-species comparisons provided even stronger evidence. When comparing the two gnetophyte genomes, researchers identified 21 genomic segments in Gnetum, each corresponding to two orthologous segments in Welwitschia—a pattern expected if Welwitschia's genome had been duplicated in its entirety while Gnetum's had not.

Absolute dating of the WGD placed it at approximately 86 million years ago, with a 90% confidence interval of 78–96 million years ago. This timing coincides with the late Cretaceous period, a time of major geological and climatic upheaval.

Despite the WGD, Welwitschia's genome is relatively small for a gymnosperm. At ~6.8 Gb, it is only about one-third of the mean genome size of 18 Gb/1C calculated from 421 gymnosperm species. This suggests that although Welwitschia experienced a genome duplication, it also underwent substantial genome downsizing—a topic the researchers explored further through their analysis of retrotransposons.

Jumping Genes: The Retrotransposon Burst

Retrotransposons are genetic elements that can "copy and paste" themselves throughout the genome, and they are major drivers of genome size and evolution. The researchers' analysis revealed a fascinating recent chapter in Welwitschia's genomic history.

By measuring the divergence between adjacent 5′ and 3′ LTRs (long terminal repeats) of the same retrotransposon, they discovered a burst of LTR-RT activity within the last 1–2 million years. This recent activity involved both:

• Autonomous elements (which encode the proteins needed for their own mobilization): 13,893 copies of Ty1-copia and 9,999 copies of Ty3-gypsy
• Non-autonomous elements (which lack these proteins and need to "borrow" them from autonomous elements): 10,589 copies

This pattern of recent non-autonomous element bursts has been observed in two angiosperm species (Camellia sinensis and Oryza species) and may be a common phenomenon that becomes more apparent as genome assembly quality improves. The hypothesis is that non-autonomous retrotransposons may inhibit the retrotransposition frequency of complete elements by competing for the proteins needed for amplification.

Evolutionary analysis of reverse transcriptase (RT) genes from complete retrotransposons across Welwitschia, Gnetum, Amborella trichopoda (hereafter, Amborella), and Ginkgo biloba (hereafter, Ginkgo) revealed that Welwitschia lacks numerous species-specific repeat clades. Instead, multiple deeply diverging clades contained elements from Welwitschia, Gnetum, and sometimes Amborella. This contrasts sharply with Ginkgo, which has many species-specific clades derived from activity peaks around 15 million years ago, and which has many more complete autonomous elements (4,237) than the other species.

The ratio of solo LTRs (remnants of recombination events) to intact LTRs was notably higher in Welwitschia:

• Welwitschia: 3.87 (4,610 solo-LTRs : 1,191 intact LTRs)
• Gnetum: 2.07 (971 : 470)
• Amborella: 2.35 (214 : 91)
• Ginkgo: 4.26 (60,623 : 14,128)

Solo-LTRs arise through excision-based DNA recombination that removes the internal portion of the retrotransposon, leading to genome downsizing. The higher frequency of solo-LTRs in Welwitschia compared with Gnetum suggests an elevated rate of recombination-based removal of retroelements—a mechanism that helps explain how Welwitschia kept its genome relatively compact despite the ancient WGD and recent retrotransposon bursts.

DNA Methylation: Epigenetic Secrets of Survival

Beyond the static DNA sequence, the researchers investigated the epigenome—specifically, patterns of DNA methylation, a chemical tag added to DNA that can influence gene activity without changing the underlying sequence. This is particularly relevant because Welwitschia lives for millennia, and epigenetic mechanisms likely help the plant respond to environmental stress over its extraordinarily long life.

The study's methylation analysis revealed several striking findings:

First, the overall methylation levels in CG and CHG sequence contexts (where H represents A, T, or C) were very high in both meristems and leaves, reaching an average of 78.32% for CG and 76.11% for CHG of all cytosines. These values are similar to those observed in the conifer Norway spruce (Picea abies) but considerably higher than typically reported for angiosperms, where about 50% of cytosines are methylated on average.

Second, and most remarkably, the average methylation level of cytosines in the CHH context was 35.7% in both meristem and leaf tissue. This is described by the authors as "considerably higher than previously reported for angiosperms and gymnosperms" and is potentially the highest value recorded for any plant to date. To put this in perspective:

• An analysis of 34 angiosperm species found that 85% had CHH methylation levels below 10%, with the highest value being 18.8% in sugar beet (Beta vulgaris)
• In Norway spruce, only ~1.5% of cytosines in CHH trinucleotides were methylated in cultured tissues

Third, CHH methylation levels varied dramatically between tissues. Levels were consistently lower in leaves (24%) than in basal meristems, but even within meristems there were substantial differences between wild-collected plants (58.72%) and greenhouse-grown plants (31.42%). This suggests that environmental conditions strongly influence methylation patterns, and the high methylation in wild plants might reflect a response to the harsh desert environment.

Fourth, the differentially methylated regions (DMRs) at CHH sites were overwhelmingly concentrated in intergenic regions (regions between genes) and transposable elements. Of the regions differentially methylated between individuals, over 97% of the sites occurred within intergenic regions, and 89% of these were within transposable elements. This is significant because methylation of transposable elements is a well-known defense mechanism that keeps these "jumping genes" silenced—preventing them from causing harmful mutations by inserting themselves into functional genes.

The researchers also analyzed genes involved in the RNA-directed DNA methylation (RdDM) pathway—the molecular machinery that establishes and maintains DNA methylation. Most of these genes showed increased transcript abundance in meristematic tissues compared with young leaves, indicating active regulation of the methylation machinery in the growth zones of the plant.

What These Findings Mean for Science

This study provides the first chromosome-level genome assembly for Welwitschia and offers profound insights into the biology of extreme longevity and stress tolerance in plants.

The combination of an ancient whole-genome duplication and lineage-specific genome downsizing paints a picture of a genome that has been shaped by both expansion and contraction forces over 86 million years of evolution. The WGD likely provided duplicated genes that could evolve new functions, while the elevated rate of solo-LTR formation helped prevent the genome from becoming unmanageably large.

The extraordinary levels of CHH methylation—the highest seen in any plant—suggest that epigenetic silencing of transposable elements is particularly important in Welwitschia. By keeping these genomic parasites in check, the plant may protect the integrity of its functional genes over millennia. The variation in methylation between wild and greenhouse-grown plants also hints that epigenetic mechanisms could play a role in the plant's ability to acclimate to environmental stress, including extreme temperature fluctuations, nutrient scarcity, and water deficit.

Changes in copy number and/or expression of gene families and transcription factors—particularly R2R3MYB and SAUR (Small Auxin-Up RNA)—that control cell growth, differentiation, and metabolism are likely to underpin the plant's longevity and its tolerance to stress. These are exactly the kinds of genes that plant breeders and biotechnologists might target in efforts to improve stress tolerance in crop species.

Limitations of the Study

While this study is comprehensive, it has several limitations that should be acknowledged.

First, although the genome assembly is high-quality, the BUSCO analysis recovered 83.47% of genes in Welwitschia, meaning a portion of the gene space was not captured. This is not unusual for large, repeat-rich genomes, but it means some genes remain to be discovered.

Second, the function of the exceptional CHH methylation levels remains to be fully explained. The researchers report correlations, but experimental validation—for example, by manipulating methylation levels and observing the effects—would be needed to establish causation.

Third, the study compared methylation patterns in a limited number of tissue types and individuals. The substantial differences observed between wild and greenhouse-grown plants suggest environmental effects are important, but the sample size (7 biologically independent samples) is small.

Fourth, the precise mechanisms by which the identified gene families (R2R3MYB, SAUR) and transcription factors contribute to longevity and stress tolerance are not yet functionally characterized. Genomic analysis can identify candidate genes, but direct experiments are required to confirm their roles.

Finally, the long-term deamination of methylated cytosines leading to an exceptionally GC-poor genome is noted, but the full implications of this nucleotide composition bias for genome function and stability are not yet clear.

What's Next? Future Research Directions

This groundbreaking study opens many avenues for future research:

1. Functional characterization of candidate genes: Researchers should experimentally test the roles of R2R3MYB, SAUR, and other identified gene families in cell growth, longevity, and stress tolerance, potentially using model plants like Arabidopsis as test systems.
2. Population genomics: With two genetically and geographically distinct Welwitschia populations identified, comparative population studies could reveal ongoing adaptation and genetic diversity within the species—information critical for conservation planning.
3. Epigenetic studies across environments: The striking differences in CHH methylation between wild and greenhouse plants warrant larger-scale studies examining how methylation patterns change with environmental conditions, seasons, and plant age.
4. Conservation applications: Understanding the genetic and epigenetic basis of Welwitschia's adaptations can inform conservation strategies for this vulnerable species in the face of climate change and habitat disturbance.
5. Crop improvement: The genes and regulatory mechanisms that confer extreme drought tolerance and longevity in Welwitschia could potentially be harnessed to improve stress tolerance in agricultural crops.
6. Comparative genomics across gnetophytes: The improved Gnetum genome assembly provides a valuable resource for further comparative studies across this ancient and enigmatic plant lineage.

Frequently Asked Questions

What is Welwitschia and why is it so unusual?

Welwitschia is a desert plant that lives thousands of years and grows only two leaves that never stop elongating. It survives on less than 50 millimeters of rain per year in the Kaokoveld desert of Namibia and Angola. Scientists consider it one of the most extraordinary plants on Earth.

What are jumping genes and what role did they play in Welwitschia?

Jumping genes, or retrotransposons, are DNA sequences that can copy and insert themselves elsewhere in the genome. In Welwitschia, there was a burst of activity within the last 1–2 million years. These elements make up over half of its genome and contribute to its large size.

What is DNA methylation and why was it remarkable in Welwitschia?

DNA methylation is a chemical modification that can turn genes on or off without changing the DNA sequence. Welwitschia had extremely high levels of a specific type called CHH methylation, potentially the highest recorded in any plant. This may help silence jumping genes and protect the plant over its long life.

How could Welwitschia's genetics help improve crop plants?

Researchers identified genes and regulatory mechanisms that may underlie Welwitschia's extreme drought tolerance and longevity. These include certain gene families like R2R3MYB and SAUR that control cell growth and stress responses. In the future, scientists might use these to improve stress tolerance in agricultural crops.

What were the limitations of this genome study?

The genome assembly captured about 83% of the expected genes, so some genes remain undiscovered. The high CHH methylation levels were observed, but experimental proof of their function is lacking. Only a small number of samples and tissues were studied, and the roles of many candidate genes have not been directly tested.

Source Information

Original Article: "The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts"

Authors: Tao Wan, Zhiming Liu, Ilia J. Leitch, Haiping Xin, Gillian Maggs-Kölling, Yanbing Gong, Zhen Li, Eugene Marais, Yiying Liao, Can Dai, Fan Liu, Qijia Wu, Chi Song, Yadong Zhou, Weichang Huang, Kai Jiang, Qi Wang, Yong Yang, Zhixiang Zhong, Ming Yang, Xue Yan, Guangwan Hu, Chen Hou, Yingjuan Su, Shixiu Feng, Ji Yang, Jijun Yan, Jinfang Chu, Fan Chen, Jinhua Ran, Xiaoquan Wang, Yves Van de Peer, Andrew R. Leitch, and Qingfeng Wang

Journal: Nature Communications (2021), Volume 12, Article 4247

DOI: https://doi.org/10.1038/s41467-021-24528-4

Institutions: Wuhan Botanical Garden (Chinese Academy of Sciences), Fairy Lake Botanical Garden, Royal Botanic Gardens Kew, Gobabeb Research and Training Centre (Namibia), Ghent University, Queen Mary University of London, and collaborating institutions in China and South Africa.

Note: This patient-friendly article is based on peer-reviewed research published in Nature Communications. It has been written for a general audience and does not constitute medical advice. The original research can be accessed via the DOI link above.