Enhanced loss of retinoic acid network genes in Xenopus laevis achieves a tighter signal regulation

Retinoic acid (RA) is a major regulatory signal during embryogenesis produced from vitamin A (retinol) by an extensive, autoregulating metabolic and signaling network to prevent fluctuations that result in developmental malformations. Xenopus laevis is an allotetraploid hybrid frog species whose genome includes L (long) and S (short) chromosomes from the originating species. Evolutionarily, the X. laevis subgenomes have been losing either L or S homoeologs in about 43% of genes to generate singletons. In the RA network, out of the 47 genes, about 46% have lost one of the homoeologs, like the genome average. In contrast, RA metabolism genes from storage (retinyl esters) to retinaldehyde production exhibit enhanced gene loss with 75% singletons out of 28 genes. The effect of this gene loss on RA signaling autoregulation was studied. Employing transient RA manipulations, homoeolog gene pairs were identified in which one homeolog exhibits enhanced responses or looser regulation than the other, while in other pairs both homoeologs exhibit similar RA responses. CRISPR/Cas9 targeting of individual homoeologs to reduce their activity supports the hypothesis where the RA metabolic network gene loss results in tighter network regulation and more efficient RA robustness responses to overcome complex regulation conditions.

Breeding Polyploid Varieties of Acacia: Reproductive and Early Growth Characteristics of the Allotetraploid Hybrid (Acacia mangium × A. auriculiformis) in Comparison with Diploid Progenitors

Diploid clones of the hybrid acacia (Acacia mangium × A. auriculiformis) are widely planted in Vietnam because of their high productivity, adaptability, and commercial wood yields. Polyploid breeding offers possibilities for further enhancing hybrid vigor and generating new high value genotypes. In a field trial, we compared three diploid hybrid clones with their respective colchicine-induced tetraploid lines. Flowering and seed production of each cytotype were observed and open pollinated seed collected for determination of outcrossing rate and ploidy, inbreeding depression and marker inheritance in the progeny. Comparisons are also made with published characteristics of autotetraploids derived from A. mangium. Compared with their corresponding diploid cytotypes, the allotetraploids flowered slightly later but more intensely; produced the same number of seeds per pod but larger seeds; and showed a greatly reduced level of outcrossing (an average of 14% compared with 87%). Inbreeding depression for height growth was less for progeny from the allotetraploid lines (17%) than for those from the original diploids (33%). 96% of seeds from the allotetraploid clones were also tetraploid, but we observed triploids at low frequency at both the seed and field progeny stages. The segregation of the molecular markers in outcrossed allotetraploid progenies demonstrated both disomic and tetrasomic inheritance, indicating that the hybrid behaves as a segmental allotetraploid. Results suggest that an open pollinated breeding strategy is a practical option for improving polyploid acacia hybrids.

The Phylogenetic Position of Vincetoxicum pannonicum (Borhidi) Holub Supports the Species' Allopolyploid Hybrid Origin

The Pannonian endemic species <em>Vincetoxicum pannonicum </em>was described from specimens collected in Hungary and occurs at only few locations. It is considered “vulnerable” according to the International Red List. The chromosome set was reported to be tetraploid, and the species was hypothesized to be an allotetraploid hybrid of the Balkan species <em>V. fuscatum </em>and the Adriatic species <em>hirundinaria </em>subsp. <em>adriaticum. </em>We investigated the origin of <em>V. pannonicum </em>using molecular phylogenetic methods by separately analyzing the multicopy nuclear ribosomal internal transcribed spacer (nrITS) and the plastid-encoded <em>trn</em>H-<em>psb</em>A DNA regions and by evaluating discrepancies between the produced gene trees. Paralogs in the nrITS region clustered in two main groups, one of which was closest to <em>V. fuscatum</em>, and the other included <em>V. hirundinaria </em>subsp. <em>adriaticum</em>. According to <em>trn</em>H-<em>psb</em>A sequences, <em>V. pannonicum </em>and <em>V. hirundinaria </em>subsp. <em>adriaticum </em>formed a single group. Our results show that <em>V. pannonicum </em>diversified because of hybrid speciation, in which <em>V. fuscatum </em>was the pollen donor. We discovered a similar placement of <em>V. maeoticum</em>, which suggests a further hybridization event between <em>V. fuscatum </em>and a species of the <em>V. hirundinaria </em>group. Our genome-size estimate indicates almost sixfold larger genome size in <em>V. pannonicum </em>compared to the maternal diploid parent, suggesting hexaploidy; however, <em>V. pannonicum </em>is tetraploid. This may suggest cytological diploidization in the allopolyploid <em>V. pannonicum</em>. We observed substantial genetic distance between <em>V. hirundinaria </em>subsp. <em>adriaticum </em>and all other subspecies of <em>V. hirundinaria</em>, and we therefore propose that <em>V. adriaticum </em>should be regarded as a separate species.

Chimeras Link to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish

The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species and therefore it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs are benefit from the intervention of recombinases. In addition, TRs and TEs are linked not only with the recombinations, but also with the insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents which reduces the genomic shock effects and favors the evolutionary and adaptive capacity of the allotetraploidization. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.