Wooo!! Congrats!!

Most importantly, big thanks to everyone involved--the co-1st authors I highlighted in the thread and co-last authors @andrassimon.bsky.social and @maxyunlab.bsky.social. It was a huge effort from many and this work opens the door to approaches we could only dreamed about a few years ago!
(15/x)

We now have some leads to key components of newts regenerative ability. Now it's time to dig into the functional relevance of these findings and whether they indeed underpin the remarkable regenerative capacity of newts 🦎!
(14/x)

Continuing evaluation of RNAs, previous work had indicated an expansion of embryonic stem cell-specific miRNAs in P. waltl. Ketan went on to confirm this expansion in this new higher contiguity assembly, perform a genome-wide annotation of miRs, and define 4 novel P. waltl miR groups.
(13/x)

Ketan noted that TEs can create circRNA. These have recently emerged as RNA molecules with roles in processes like transcription and stemness. Sleuthing the newt genome for circRNA, TEs appeared to facilitate circRNA genesis. Importantly, some circRNA were enriched during regeneration!
(12/x)

TEs ability to jump around the genome means they can have a major influence on genomic architecture. PhD student and co-first author Ketan Mishra dug into how TEs may be changing the newt genome.
(11/x)

So, it seems that salamanders are unable to control TE accumulation in their genomes, so could this accumulation be beneficial?
(10/x)

Now back to the TEs…co-first author Svetlana Iarovenko found that unlike other giant genomes, the TE-driven expansion of the newt genome appears due to more DNA elements as compared to RNA elements that have driven expansion in other species with giant genomes (like the axolotl).
(9/x)

Though the newt genome is massive, newts lose genes over evolution. We found that Fgf5 was lost in newts and lost in other species with giant genomes. This suggests that giant genomes may be susceptible to disruptions at this locus or that disruptions at this locus facilitate genome expansion.
(8/x)

Before we dive into the TEs, annotation efforts from co-first authors Ahmed Elewa and Tom confirmed that though their genome size is massive, the # of protein-coding genes is similar to other vertebrates. We also found that the general layout of their genome matched well with related species.
(7/x)

So how did the newt genome get so big? Similar to #axolotl our findings indicate that the P. waltl has an expanded genome due to a massive accumulation of transposable elements (TEs). An amazing ¾ of the genome is repeat elements!
(6/x)

Enter long-read DNA sequencing; now we can dramatically increase the size of each puzzle piece and make each piece more unique. A manageable puzzle to solve, at least for co-first author Thomas Brown—the genome assembler behind the this newt genome!
(5/x)

Due to technical limitations imposed by short read DNA sequencing, the highly repetitive nature of salamander genomes has made them notoriously difficult to assemble. Imagine a puzzle with millions of tiny pieces that are all the same color—this would be a nearly impossible puzzle.
(4/x)

While there are different means by which genomes expand over evolutionary time, salamanders have long been noted to have highly repetitive genomes. This massive accumulation of transposable (repeat) elements drove the expansion of the #axolotl salamander genome. www.nature.com/articles/nat...
(3/x)

Creating high-quality genome assemblies has been challenging for salamanders due to their enormous genomes.

Salamander genomes are 4-43X larger than the human genome!

How did salamander genomes get so big?

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