Comparative analysis of pseudogenes across three phyla.

نویسندگان

  • Cristina Sisu
  • Baikang Pei
  • Jing Leng
  • Adam Frankish
  • Yan Zhang
  • Suganthi Balasubramanian
  • Rachel Harte
  • Daifeng Wang
  • Michael Rutenberg-Schoenberg
  • Wyatt Clark
  • Mark Diekhans
  • Joel Rozowsky
  • Tim Hubbard
  • Jennifer Harrow
  • Mark B Gerstein
چکیده

Pseudogenes are degraded fossil copies of genes. Here, we report a comparison of pseudogenes spanning three phyla, leveraging the completed annotations of the human, worm, and fly genomes, which we make available as an online resource. We find that pseudogenes are lineage specific, much more so than protein-coding genes, reflecting the different remodeling processes marking each organism's genome evolution. The majority of human pseudogenes are processed, resulting from a retrotranspositional burst at the dawn of the primate lineage. This burst can be seen in the largely uniform distribution of pseudogenes across the genome, their preservation in areas with low recombination rates, and their preponderance in highly expressed gene families. In contrast, worm and fly pseudogenes tell a story of numerous duplication events. In worm, these duplications have been preserved through selective sweeps, so we see a large number of pseudogenes associated with highly duplicated families such as chemoreceptors. However, in fly, the large effective population size and high deletion rate resulted in a depletion of the pseudogene complement. Despite large variations between these species, we also find notable similarities. Overall, we identify a broad spectrum of biochemical activity for pseudogenes, with the majority in each organism exhibiting varying degrees of partial activity. In particular, we identify a consistent amount of transcription (∼15%) across all species, suggesting a uniform degradation process. Also, we see a uniform decay of pseudogene promoter activity relative to their coding counterparts and identify a number of pseudogenes with conserved upstream sequences and activity, hinting at potential regulatory roles.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations ...

متن کامل

Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple omic strategies, combining: Illumina and Pacific Biosciences Single-Mo...

متن کامل

Supporting Information for “The evolutionary history of Cys-tRNA formation”

Sequence information. The Institute for Genomic Research (TIGR), Joint Genome Institute (JGI), and NCBI genomic databases were searched for pseudogenes of SepRS and SepCysS using the tblastn program with a profiles composed of the known members of these protein families. These searches were carried out in the genomes of the euryarchaeal phyla that do not have proteins coding for the indirect pa...

متن کامل

Comparative analysis of processed pseudogenes in the mouse and human genomes.

Pseudogenes are important resources in evolutionary and comparative genomics because they provide molecular records of the ancient genes that existed in the genome millions of years ago. We have systematically identified approximately 5000 processed pseudogenes in the mouse genome, and estimated that approximately 60% are lineage specific, created after the mouse and human diverged. In both mou...

متن کامل

Evaluating Tolerance of Ground Covers Phyla nodiflora L. and Frankenia thymifolia Desf. to Simultaneous Salinity and Drought Stresses

A remarkable part of Iran is surrounded by arid and semi-arid areas, which are faced with drought and salinity stresses. Today, the management of salinity and drought stresses in the landscape, has a particular importance. In this study, the drought and salinity tolerance of Phyla and Frankenia were investigated, which consisted of 12 treatments (Four levels of salinity at 0.5, 3, 6 and 9 dS/m ...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Proceedings of the National Academy of Sciences of the United States of America

دوره 111 37  شماره 

صفحات  -

تاریخ انتشار 2014