Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblages

Spliceosomal introns in the diplomonad parasite Giardia duodenalis revisited

Complete reference genomes, including correct feature annotations, are a fundamental aspect of genomic biology. In the case of protozoan species such as Giardia duodenalis, a major human and animal parasite worldwide, accurate genome annotation can deepen our understanding of the evolution of parasitism and pathogenicity by identifying genes underlying key traits and clinically relevant cellular mechanisms, and by extension, the development of improved prevention strategies and treatments. This study used bioinformatics analyses of Giardia mRNA libraries to characterize known introns and identify new intron candidates, working towards completion of the G. duodenalis assemblage A strain 'WB' genome and further elucidating Giardia's gene expression. By using a set of experimentally validated positive control loci to calibrate our intron detection pipeline, we were able to detect evidence of previously missed candidate splice junctions directly from expressed transcript data. These intron candidates were further studied in silico using NMDS (non-metric multidimensional scaling) clustering to determine shared characteristics and their relative importance such as secondary structure, splicing efficiency and motif conservation, and thus to refine intron models. Results from this study identified 34 new intron candidates, with several potential introns showing evidence that secondary structure of the mRNA molecule might play a more significant role in splicing than previously reported eukaryotic splicing activity mediated by a reduced spliceosome present in G. duodenalis.

A chromosome-scale reference genome for Giardia intestinalis WB

Giardia intestinalis is a protist causing diarrhea in humans. The first G. intestinalis genome, from the WB isolate, was published more than ten years ago, and has been widely used as the reference genome for Giardia research. However, the genome is fragmented, thus hindering research at the chromosomal level. We re-sequenced the Giardia genome with Pacbio long-read sequencing technology and obtained a new reference genome, which was assembled into near-complete chromosomes with only four internal gaps at long repeats. This new genome is not only more complete but also better annotated at both structural and functional levels, providing more details about gene families, gene organizations and chromosomal structure. This near-complete reference genome will be a valuable resource for the Giardia community and protist research. It also showcases how a fragmented genome can be improved with long-read sequencing technology completed with optical maps.

Measurement(s)	DNA • sequence_assembly • sequence feature annotation
Technology Type(s)	DNA sequencing • sequence assembly process • sequence annotation
Sample Characteristic - Organism	Giardia intestinalis

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11695659

Sense-antisense gene overlap is probably a cause for retaining the few introns in Giardia genome and the implications

Background

It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive. Actually the reverse question -- how the few introns can be retained under the evolutionary selection pressure of intron loss -- is equally significant but was rarely studied, except that it was conjectured that the essential functions of some introns prevent their loss. The situation that extremely few (eight) spliceosome-mediated cis-spliced introns present in the relatively simple genome of Giardia lamblia provides an excellent opportunity to explore this question.

Results

Our investigation found three types of distribution patterns of the few introns in the intron-containing genes: ancient intron in ancient gene, later-evolved intron in ancient gene, and later-evolved intron in later-evolved gene, which can reflect to some extent the dynamic evolution of introns in Giardia. Without finding any special features or functional importance of these introns responsible for their retention, we noticed and experimentally verified that some intron-containing genes form sense-antisense gene pairs with transcribable genes on their complementary strands, and that the introns just reside in the overlapping regions.

Conclusions

In Giardia’s evolution, despite constant evolutionary selection pressure of intron loss, intron gain can still occur in both ancient and later-evolved genes, but only a few introns are retained; at least the evolutionary retention of some of the introns might not be due to the functional constraint of the introns themselves but the causes outside of introns, such as the constraints imposed by other genomic functional elements overlapping with the introns. These findings can not only provide some clues to find new genomic functional elements -- in the areas overlapping with introns, but suggest that “functional constraint” of introns may not be necessarily directly associated with intron loss and gain, and that the real functions are probably still outside of our current knowledge.

Reviewers

This article was reviewed by Mikhail Gelfand, Michael Gray, and Igor Rogozin.

Electronic supplementary material

The online version of this article (10.1186/s13062-018-0226-5) contains supplementary material, which is available to authorized users.

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites

The fornicata (fornicates) is a eukaryotic group known to consist of free-living and parasitic organisms. Genome datasets of two model fornicate parasites Giardia intestinalis and Spironucleus salmonicida are well annotated, so far. The nuclear genomes of G. intestinalis assemblages and S. salmonicida are small in terms of the genome size and simple in genome structure. However, an ancestral genomic structure and gene contents, from which genomes of the fornicate parasites have evolved, remains to be clarified. In order to understand genome evolution in fornicates, here, we present the draft genome sequence of a free-living fornicate, Kipferlia bialata, the divergence of which is earlier than those of the fornicate parasites, and compare it to the genomes of G. intestinalis and S. salmonicida. Our data show that the number of protein genes and introns in K. bialata genome are the most abundant in the genomes of three fornicates, reflecting an ancestral state of fornicate genome evolution. Evasion mechanisms of host immunity found in G. intestinalis and S. salmonicida are absent in the K. bialata genome, suggesting that the two parasites acquired the complex membrane surface proteins on the line leading to the common ancestor of G. intestinalis and S. salmonicida after the divergence from K. bialata. Furthermore, the mitochondrion related organelles (MROs) of K. bialata possess more complex suites of metabolic pathways than those in Giardia and in Spironucleus. In sum, our results unveil the process of reductive evolution which shaped the current genomes in two model fornicate parasites G. intestinalis and S. salmonicida.

Inhibición parcial de dos genes que codifican para proteínas spliceosomales en Giardia intestinalis

<p><strong>Introducción.</strong> <em>Giardia intestinalis</em> es un organismo tempranamente divergente en el que recientemente se demostró la presencia de intrones. La maquinaria responsable de la remoción de intrones en eucariotes superiores es el spliceosoma, conformado por 5 ribonucleoproteínas. Cada una tiene un ARN pequeño nuclear, un set de 7 proteínas Sm (B, D1, D2, D3, E, F y G) y varias proteínas específicas. En <em>G. intestinalis</em>, se han identificado los genes de algunas proteínas del spliceosoma por bioinformática. Aunque se asume que el spliceosoma es el responsable del splicing en el parásito, su caracterización bioquímica no ha sido realizada.</p><p><strong>Objetivo.</strong> Inhibir dos genes que codifican para proteínas del spliceosoma de <em>G. intestinalis</em> con el fin de determinar si esta inhibición afecta el crecimiento o la enquistación del parásito.</p><p><strong>Materiales y métodos.</strong> Se clonaron en un vector específico para <em>G. intestinalis</em> secuencias antisentido de los genes que codifican para las proteínas spliceosomales SmB y SmD3 del parásito. Posteriormente se transfectó <em>G. intestinalis</em> con los vectores recombinantes y se seleccionaron aquellos parásitos que lo incorporaron. Se confirmó la disminución del mensajero por PCR en tiempo real y se evaluó el crecimiento y la enquistación en parásitos silvestres y transfectados.</p><p><strong>Resultados.</strong> Se observó una disminución del 40% y 70% en el mARN de SmB y SmD3, respectivamente. El crecimiento y la enquistación no se vieron afectados en estos parásitos.</p><p><strong>Conclusión. </strong>La disminución de SmB y SmD3 no afectan el parásito, indicando que el spliceosoma sigue siendo funcional o que el splicing no es una función vital del parásito.</p>