Genic regions of a large salamander genome contain long introns and novel genes

Smith, Jeramiah J.; Putta, Srikrishna; Zhu, Wei; Pao, Gerald M.; Verma, Inder M.; Hunter, Tony; Bryant, Susan V.; Gardiner, David M.; Harkins, Timothy T.; Voss, S. Randal

doi:10.1186/1471-2164-10-19

Cited by 82 publications

(98 citation statements)

References 65 publications

(53 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3a, Supplementary Information section 4.3), a trend that was previously observed in five genes obtained from selective bacterial artificial chromosome sequencing of the axolotl genome 13 . Figure 3b shows a typical gene organization in axolotl compared to its human orthologue.…”

Section: Expansion Of Long Terminal Repeat Retroelementsmentioning

confidence: 59%

The axolotl genome and the evolution of key tissue formation regulators

Nowoshilow

Schloissnig

Fei

et al. 2018

Nature

450

478

View full text Add to dashboard Cite

Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3. However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3 −/− and Pax7 −/− mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies.

show abstract

Section: Expansion Of Long Terminal Repeat Retroelementsmentioning

confidence: 59%

The axolotl genome and the evolution of key tissue formation regulators

Nowoshilow

Schloissnig

Fei

et al. 2018

Nature

450

478

View full text Add to dashboard Cite

show abstract

“…It is also the rationale behind the new global bioinformatic and systems biology approaches that integrate the molecular elements of large genomic and proteomic databases into functional networks and pathways from which hypotheses about mechanisms emerge (Nabel, 2009). For example, global genomic and proteomic data on blastema formation in regenerating anuran and urodele limbs has been generated by a number of laboratories Habermann et al, 2004;Putta et al, 2004;Grow et al, 2006;Pearl et al, 2008;Smith et al, 2009;Monaghan et al, 2009;Rao et al, 2009) and in one case transcription factor pathways have been subjected to a systems biology analysis (Jhamb et al, 2011).…”

Section: New Approaches and Challengesmentioning

confidence: 99%

Looking proximally and distally: 100 years of limb regeneration and beyond

Stocum

Cameron

2011

Developmental Dynamics

106

View full text Add to dashboard Cite

The experimental study of amphibian limb regeneration spans most of the 20 th century and the first decade of the 21 st century. We first review the major questions investigated over this time span: (1) the origin of regeneration blastema cells, the mechanism of tissue breakdown that liberates cells from their tissue organization to participate in blastema formation, (3) the mechanism of dedifferentiation of these cells, (4) how the blastema grows, (5) how the blastema is patterned to restore the missing limb structures, and (6) why adult anurans, birds and mammals do not have the regenerative powers of urodele salamanders. We then look forward in a perspective to discuss the many unanswered questions raised by investigations of the past century, what new approaches can be taken to answer them, and what the prospects are for translation of basic research on limb regeneration into clinical means to regenerate human appendages. Developmental Dynamics 240:943-968,

show abstract

“…As the majority of publicly available axolotl genomic data comes from expressed sequence tag (EST) sequencing, and as the average intron length in the axolotl genome is greater than 10 kb (Smith et al, 2009), only a subset of targets found within EST sequences are spaced sufficiently far from intron-exon boundaries to be reliably detected with PCR-based methods. Rapid, endonuclease-based methods of screening pooled PCR products cannot be used to assess mutation frequency when putative mutation sites are near the edges of small PCR products.…”

Section: Rgn Target Selection and Detection Of Indels In The Axolotlmentioning

confidence: 99%

“…The axolotl is not widely adopted as a genetic model organism due to its slow development, its late age of sexual maturity (>1 year), and its exceptionally large (∼3.2×10 10 bp) and currently unsequenced genome (Smith et al, 2009). To overcome these drawbacks, the ideal practical system for investigating gene function in this organism must meet several seemingly daunting requirements.…”

Section: Introductionmentioning

confidence: 99%

Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease

et al. 2014

View full text Add to dashboard Cite

Among tetrapods, only urodele salamanders, such as the axolotl Ambystoma mexicanum, can completely regenerate limbs as adults. The mystery of why salamanders, but not other animals, possess this ability has for generations captivated scientists seeking to induce this phenomenon in other vertebrates. Although many recent advances in molecular biology have allowed limb regeneration and tissue repair in the axolotl to be investigated in increasing detail, the molecular toolkit for the study of this process has been limited. Here, we report that the CRISPR-Cas9 RNA-guided nuclease system can efficiently create mutations at targeted sites within the axolotl genome. We identify individual animals treated with RNA-guided nucleases that have mutation frequencies close to 100% at targeted sites. We employ this technique to completely functionally ablate EGFP expression in transgenic animals and recapitulate developmental phenotypes produced by loss of the conserved gene brachyury. Thus, this advance allows a reverse genetic approach in the axolotl and will undoubtedly provide invaluable insight into the mechanisms of salamanders' unique regenerative ability.

show abstract

Genic regions of a large salamander genome contain long introns and novel genes

Cited by 82 publications

References 65 publications

The axolotl genome and the evolution of key tissue formation regulators

The axolotl genome and the evolution of key tissue formation regulators

Looking proximally and distally: 100 years of limb regeneration and beyond

Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease

Contact Info

Product

Resources

About