Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona, Valentina; Blom, Mozes P. K.; Xu, Luohao; Burri, Reto; Sullivan, Shawn; Bunikis, Ignas; Liachko, Ivan; Haryoko, Tri; Jønsson, Knud A.; Zhou, Qi; Irestedt, Martin; Suh, Alexander

doi:10.1111/1755-0998.13252

Cited by 118 publications

(156 citation statements)

References 159 publications

(302 reference statements)

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“…Moreover, the different coverage in different parts of ATF7IP2 suggests a divergence between the repeat units in their structure and composition. To reconstruct the exact structure and context of the ATF7IP2-derived repeat in the W chromosome of E. velox, its genomic DNA should be sequenced with a long-read technology, such as PacBio or Nanopore [69].…”

Section: Discussionmentioning

confidence: 99%

Amplified Fragments of an Autosome-Borne Gene Constitute a Significant Component of the W Sex Chromosome of Eremias velox (Reptilia, Lacertidae)

Lisachov

Andreyushkova

Davletshina

et al. 2021

Genes

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Heteromorphic W and Y sex chromosomes often experience gene loss and heterochromatinization, which is frequently viewed as their “degeneration”. However, the evolutionary trajectories of the heterochromosomes are in fact more complex since they may not only lose but also acquire new sequences. Previously, we found that the heterochromatic W chromosome of a lizard Eremias velox (Lacertidae) is decondensed and thus transcriptionally active during the lampbrush stage. To determine possible sources of this transcription, we sequenced DNA from a microdissected W chromosome sample and a total female DNA sample and analyzed the results of reference-based and de novo assembly. We found a new repetitive sequence, consisting of fragments of an autosomal protein-coding gene ATF7IP2, several SINE elements, and sequences of unknown origin. This repetitive element is distributed across the whole length of the W chromosome, except the centromeric region. Since it retained only 3 out of 10 original ATF7IP2 exons, it remains unclear whether it is able to produce a protein product. Subsequent studies are required to test the presence of this element in other species of Lacertidae and possible functionality. Our results provide further evidence for the view of W and Y chromosomes as not just “degraded” copies of Z and X chromosomes but independent genomic segments in which novel genetic elements may arise.

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Section: Discussionmentioning

confidence: 99%

Amplified Fragments of an Autosome-Borne Gene Constitute a Significant Component of the W Sex Chromosome of Eremias velox (Reptilia, Lacertidae)

Lisachov

Andreyushkova

Davletshina

et al. 2021

Genes

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“…Previous studies have highlighted the importance of genome assembly quality in repeat annotation, with higher sequencing depths and long read technologies critical for resolving TEs [35,36]. Our repeat analysis reveals significant variation in total TE content between genome assemblies (Table 1, Figure 1), however some of this variation is likely due to large differences in assembly quality rather than differential TE expansions or contractions in certain lineages.…”

Section: Resultsmentioning

confidence: 65%

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

Edwards

et al. 2021

Preprint

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Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they can be exapted as coding and regulatory elements, or can promote genetic rearrangement. In so doing TEs act as a source of genetic novelty, hence understanding TE evolution within lineages is key in understanding adaptation to their environment. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. The few broad scale studies in Squamata which have been conducted found both the diversity and total number of TEs differs significantly across the entire order. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if this pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~15-25 Mya and have since rapidly diversified into 6 amphibious, ~60 marine and ~100 terrestrial species which fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three transferred into the ancestral hydrophiine likely from marine species. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.

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“…It thus seems that some parts of each genome are missing from our sequencing reads. Transposons and repeat-rich genomic regions can contribute to gaps in genomic assemblies (Peona et al 2020). Some of these missing regions could also be GC-rich, a feature which is known to cause a sequencing-bias with Illumina technology (see for example , Botero-Castro et al 2017.…”

Section: Results and Discussion First Ostracod Reference Genomes And mentioning

confidence: 99%

First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes

Van

Anselmetti

Dumas

et al. 2020

Preprint

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SOstracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of non-marine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96%, and thus exceed the quality of several other published crustacean genomes obtained with similar techniques. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from non-marine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Cited by 118 publications

References 159 publications

Amplified Fragments of an Autosome-Borne Gene Constitute a Significant Component of the W Sex Chromosome of Eremias velox (Reptilia, Lacertidae)

Amplified Fragments of an Autosome-Borne Gene Constitute a Significant Component of the W Sex Chromosome of Eremias velox (Reptilia, Lacertidae)

Horizontal transposon transfer and its implications for the ancestral ecology of hydrophiine snakes

First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes

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