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Revealing The Genomic Code For The Earliest Forms Of Terrestrial Plant Life – Astrobiology – Astrobiology News

Revealing The Genomic Code For The Earliest Forms Of Terrestrial Plant Life

a, Heatmap of 45 conserved microexon-tags predicted by MEPmodeler. Microexon rate is the rate of true microexons among all predicted results in the cluster. For example, green cells indicate that 100% microexons with two flanking introns are present, orange indicates all microexon sequences are parts of large exons and none of them could be considered as microexons, and the others are between 0 and 1. A gray cell indicates missing data (a microexon-tag could not be found). The numbers on the right column indicate the predicted clusters containing at least one true microexon (see ref. 80 for more detail). b, RNA-seq evidence of the 1 bp microexon in cluster 2 (x axis the genomic location, and y axis the read count). c, RNA-seq evidence of two adjacent microexons, 5 (cluster 7) and 12 bp (cluster 28). In b and c, the RNA-seq of condition p881sControl2 was used; RNA-seq read depth (blue numbers) and gene annotation are shown; blue arcs indicate introns (exon–exon junctions), and the numbers indicate the junction read counts supporting the introns. The pink arrows point to microexons. d, Exon–intron structures of microexon-tag clusters 7 and 28 in 14 plant genomes. The structure was predicted by relaxing the stringency in M. viride genome and by doing TBLASTX search in S. muscicola genome (all three copies are intronless in this microexon-tag), respectively. The others are predicted with default parameters. — Nature Genetics

Plant life first emerged on land about 550 million years ago, and an international research team co-led by University of Nebraska–Lincoln computational biologist Yanbin Yin has cracked the genomic code of its humble beginnings, which made possible all other terrestrial life on Earth, including humans.

The team — about 50 scientists in eight countries – has generated the first genomic sequence of four strains of Zygnema algae, the closest living relatives of land plants. Their findings shed light on the ability of plants to adjust to the environment and provide a rich basis for future research.

The study was published May 1 in the journal Nature Genetics.

“This is an evolutionary story,” said Yin, who led the research team with a scientist from Germany. “It answers the fundamental question of how the earliest land plants evolved from aquatic freshwater algae.”

Yin’s lab in the Nebraska Food for Health Center and the Department of Food Science and Technology has a long history of studying plant cell wall carbohydrates, a major component of dietary fibers for humans and farm animals; lignocelluloses for biofuel production; and natural barriers to protect crops from pathogens and environmental stresses.

All current plant life on land burst from a one-off evolutionary event known as plant terrestrialization from ancient freshwater algae. The first land plants, known as embryophyta within the clade of streptophyta, emerged on land about 550 million years ago — their arrival fundamentally changing the surface and atmosphere of the planet. They made all other terrestrial life, including humans and animals, possible by serving as an evolutionary foundation for future flora and food for fauna.

The researchers worked with four algal strains from the genus Zygnema — two from a culture collection in the United States and two from Germany. Scientists combined a range of cutting-edge DNA sequencing techniques to determine the entire genome sequences of these algae. These methods enabled scientists to generate complete genomes for these organisms at the level of whole chromosomes — something that had never been done before on this group of algae. Comparing the genomes with those of other plants and algae led to the discovery of specific overabundances of cell wall enzymes, signalling genes and environmental response factors.

A unique feature of these algae revealed by microscopic imaging — performed at the University of Innsbruck in Austria, the Universität Hamburg in Germany and UNL’s Center for Biotechnology — is a thick and highly sticky layer of carbohydrates outside the cell walls, called the mucilage layer. Xuehuan Feng, the first author of the paper and a Husker postdoctoral research associate, developed a new and effective DNA extraction method to remove this mucilage layer for high purity and high molecular DNAs.

“It is fascinating that the genetic building blocks, whose origins predate land plants by millions of years, duplicated and diversified in the ancestors of plants and algae and, in doing so, enabled the evolution of more specialized molecular machinery,” said Iker Irisarri of the Leibniz Institute for the Analysis of Biodiversity Change and co-first author of the paper.

The team’s other co-leader, Jan de Vries of the University of Göttingen, said, “Not only do we present a valuable, high-quality resource for the entire plant scientific community, who can now explore these genome data, our analyses uncovered intricate connections between environmental responses.”

The four multicellular Zygnema algae belong to the class Zygnematophyceae, the closest living relatives of land plants; it is a class of freshwater and semi-terrestrial algae with more than 4,000 described species. Zygnematophyceae possess adaptations to withstand terrestrial stressors, such as desiccation, ultraviolet light, freezing and other abiotic stresses. The key to understanding these adaptations is the genome sequences. Before this paper, genome sequences were only available for four unicellular Zygnematophyceae.

Yin said this research aligns with one of the National Science Foundation’s 10 Big Ideas — “Understanding the Rules of Life” — to address societal challenges, from clean water to climate resilience. The discovery also holds significance in applied sciences, such as bioenergy, water sustainability and carbon sequestration.

“Our gene network analyses reveal co-expression of genes, especially those for cell wall synthesis and remodifications that were expanded and gained in the last common ancestor of land plants and Zygnematophyceae,” Yin said. “We shed light on the deep evolutionary roots of the mechanism for balancing environmental responses and multicellular cell growth.”

The international research collaboration includes about 50 researchers from 20 research institutions in eight countries — the United States, Germany, France, Austria, Canada, China, Israel and Singapore. Other Husker researchers on the team are Chi Zhang, professor of biological sciences, and Jeffrey Mower, professor of agronomy and horticulture.

Funding for UNL’s portion of the research came primarily from Yin’s NSF CAREER award, the Nebraska Tobacco Settlement Biomedical Research Enhancement Fund, the National Institutes of Health, and the U.S. departments of Agriculture and Energy.

a, Three cells of a vegetative filament of SAG 698-1b (top) compared with one cell of a vegetative filament of SAG 698-1a (bottom, both samples of 1 month old cultures). Scale bar, 20 μm. C, chloroplast; N, nucleus; P, pyrenoid. One-cell filament contains two chloroplasts and one nucleus. b, Chromosome counting on light micrographs of SAG 698-1b fixed and stained with acetocarmine at prophase (0.5 months old); count was also performed in metaphase and telophase (Supplementary Fig. 1). The green dots represent the 20 chromosomes that were counted after rendering a stack of ~100 images. Scale bar, 10 μm. See Supplementary Fig. 1 for the original images. A minimum of ten cells each from three independent cell cultures were analyzed. c, A confocal laser scanning image of one SAG 698-1b cell (0.5 months). Scale bar, 20 μm. d, Transmission electron micrographs illustrating the filamentous nature of Z. circumcarinatum (SAG 698-1b). Left: overview showing that the cells are connected by extremely thin cross cell walls (cCW), while the outer cell wall (CW) is surrounded by a pectinous extracellular matrix (ECM); within the individual cells, pyrenoids (Py) and the nucleus (N) are clearly depictable. Scale bar, 5 µm. e, A detailed view of the cross wall separating two cells where chloroplast lobes are visible. Scale bar, 0.5 µm. Transmission electron micrographs (d and e) derived from the analysis of ≥15 algal filaments each for two independent cell cultures. f, Chromosome-level assembly of the SAG 698-1b genome. Concentric rings show chromosome (Chr) numbers, gene density (blue), repeat density (yellow), RNA-seq mapping density log10(fragments per kilobase of transcript per million mapped reads) (dark green) and guanine-cytosine content density (violet). The red and green links show respectively intra- and interchromosomal syntenic blocks. g, A comparison of genome properties for 13 algal and 3 land plant species. The time-calibrated species tree was built from 493 low-copy genes (all nodes supported by >97% nonparametric bootstrap; numbers at branches are estimated divergence times in million years (mean ± standard deviation) (see Supplementary Table 1f for details). Data for the bar plot can be found in Supplementary Table 1i,j. — Nature Genetics

Genomes of multicellular algal sisters to land plants illuminate signaling network evolution, Imaging analysis (open access)

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LSU student moves to eliminate socio-economic challenges – NewsDay

Bongani Tshuma said the socio-economic challenges faced in the village are the root causes of the problems faced by the youths.

A LUPANE State University (LSU) student who was struggling to pay fees has made waves in Khafa village under Chief Madhliwa, in Nkayi, Matabeleland North province with his project to eliminate the crippling socio-economic challenges faced by the youth.

After getting help from well-wishers, Bongani Tshuma, a second-year applied biotechnology student has formed an organisation aimed at offering free online lessons to students and mentorship programmes to the youth in Nkayi.

He formed the organisation called Zim Inclusive Leaning Trust with his colleague Melulwazi Dlamini.

“Professional life coaches and teachers volunteer to teach for free, we have managed to reach many students and also got sponsors to help a few academically gifted students. We want to expand the number of students to get sponsorship so that they attend school. As the representative of Nkayi in the organisation, I am working very hard to see our youths in Nkayi doing great,” Tshuma told Southern Eye.

This latest development comes after Tshuma observed, through his research, that people from his village were battling with early marriages, child pregnancies, school dropouts, high crime rates and other related social issues in the community.

Tshuma said the socio-economic challenges faced in the village are the root causes of the problems faced by the youths.

“Nkayi is grappling with persistent social and economic challenges, including early pregnancies and a high crime rate, which can be attributed to limited access to secondary education,” Tshuma said.

“The schools are approximately 12km away, forcing students to walk long distances, resulting in a high dropout rate. In fact, fewer than 3% of students have passed their O’ Levels in the past five years.”

He also observed that boys abandon their education to work as illegal miners, which ultimately harms the community with the police not adequately addressing the issues that arise.

“We have underprivileged learners in Nkayi who are academically gifted but they don’t get access to education,” he said.

Tshuma pleaded with the government to address these challenges by increasing the number of secondary schools in the area.

“We also seek assistance from individuals in the diaspora to invest in our community; introducing manual work programmes can help reduce youth unemployment,” he said.

“We must prioritise affordable education for every girl child in our community, many dropouts occur because parents or guardians are unable to fund school fees. We advocate a law that targets support for girls in rural areas and holds culprits accountable for their actions. We need stricter law enforcement to address the issues in our villages.”

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Mangwe villagers fight devastating drought – The Southern Eye – NewsDay

The communities since November last year have been receiving US$54 where some have been able to do projects and generated more income.

VILLAGERS in ward 3 of Madabe village, Plumtree in Mangwe District, Matabeleland South, are grappling with the devastating effects of a severe drought induced by climate change, but have taken it on themselves to survive.

Despite the challenges, the villagers persevered thanks to the emergency social cash transfer (ESCT) programme introduced by  the government and Unicef, which has enabled them to sustain themselves through various home projects.

While they continue to navigate the challenging recovery process, the communities are, however, calling on the government to maintain the crucial support provided by the ESCT, emphasising its vital role in their ongoing survival and resilience.

Under the ESCT programme, vulnerable families get monthly payments to alleviate poverty.

Goal Zimbabwe are the implementing partners with financial support from the Government of Germany through their KfW Development Bank.

The communities since November last year have been receiving US$54 where some have been able to do projects and generated more income.

A beneficiary from the programme, Mkhumbulo Mpofu (66), said the project came at a time when the area had been hit by drought.

“This programme has helped the community we had nothing at all. We last received the rains the past two years and we have been hit by severe drought. But through the introduction of this programme, we have managed to start up different projects.

“I have managed to pay school fees for my grandchildren, buy uniforms and food at home. This is a good initiative and we don’t want it to end. As you can see I am an old man and now it’s difficult for me to fend for the family,” he said.

Mpofu added: “We had nothing but then with this help from Goal, it has brought a little hope otherwise we would be dead by now. I am happy and appreciate this programme.

Sipho Moyo (57) said the programme had assisted her including taking care of her grandchildren.

“This programme started in November and the funds have helped me and my family because I was in a crisis.”

“But then after, I saw a change. I am able to get something which I can give to my grandchildren. I have my grandchild who is at high school, this money has helped me pay fees.

“Even our life has changed a bit because things seem to be going on well for me. I took the other money and invested in a club. We are contributing US$10 a month and that money we are able to lend it to a member who repays inclusive of an interest of 10%. Goal really helped me with my family.”

The ESCT helps provide support to families to deal with reduced income and scarcity of access to water and food. Cash transfer positively impacts household’s ability to ensure continued education of their children and feed their children.

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Zanu PF youths disrupt PVO Bill hearings – NewsDay

In Harare, police had to be called in after suspected ruling party youths disrupted the public hearing held at Ambassador Hotel.

ZANU PF youths yesterday disrupted public hearings on the Private Voluntary Organisations Amendment Bill in Gweru and Harare.

In Gweru, the meeting was  abandoned after the ruling party youths turned rowdy shouting at the officials led by Senator Sisasenkosi Ndebele who had to leave the venue in a huff.

In her welcome remarks Ndebele had said the meeting was non-political and participants were “free to air their views”.

After disrupting the meeting the youths started singing in support of President Emmerson Mnangagwa asking why “people hated him”.

During the meeting, Zanu PF youths would occasionally disrupt the proceedings when they booed other participants’ contributions as well as clapping when fellow party members were making their submissions.

In their support of the Bill, the youths unanimously said it would “curb terrorism” by monitoring the activities of non-profit organisations which they accused of allegedly harbouring a “regime change agenda” through support from “hostile Western countries”.

When other participants gave different thoughts against the Bill, the youths would occasionally boo them, interrupting proceedings.

In Harare, police had to be called in after suspected ruling party youths disrupted the public hearing held at Ambassador Hotel.

The hearing ended prematurely after participants largely from Zanu PF and some religious sects started singing  party songs.

This was after a young woman had criticised the Bill as giving the responsible minister overarching powers to interfere in the work of civic groups.

The woman was booed by alleged Zanu PF youths and she bolted out of the room fearing for her life.

The commotion left the committee leading the hearings with no choice, but to abandon the proceedings

Prior to the disruptions, participants expressed concerns that the Bill gave too much power to the line minister.

Civic society groups have condemned the Bill saying it undermines freedoms of expression and association and gives the government unjustifiable control over their operations.

The Bill allows the State to interfere with civil society organisations’ governance and activities

Penalties for breaching provisions of the Bill range from heavy fines to imprisonment.

President Emmerson Mnangagwa referred the Bill back to Parliament during the 9th Parliament for reconsideration and now returns when Zanu PF now has the two-thirds majority.

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