Chromosome-scale assembly of the bread wheat genome, Triticum aestivum, reveals over 5700 new genes

ABSTRACTBread wheat (Triticum aestivum) is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all 3 wheat subgenomes at chromosome scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 gigabases of genomic sequence. We earlier published an independent wheat assembly (Triticum 3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC 1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum 4.0, contains 15.07 gigabases of non-gap sequence anchored to chromosomes, which is 1.2 gigabases more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered more than 5700 new genes, all of them duplications in the Chinese Spring genome that are missing from the IWGSC assembly and annotation. The Triticum 4.0 assembly and annotations are freely available at www.ncbi.nlm.nih.gov/bioproject/PRJNA392179.

An Algorithmic Random Integer Generator Based on the Distribution of Prime Numbers

We talk about random when it is not possible to determine a pattern on the observed outcomes. A computer follows a sequence of fixed instructions to give any of its output, hence the difficulty of choosing numbers randomly from algorithmic approaches. However, some algorithms based on mathematical formulas like the Linear Congruential algorithm and the Lagged Fibonacci generator appear to produce "true" random sequences to anyone who does not know the secret initial input [1]. Up to now, we cannot rigorously answer the question on the randomness of prime numbers [2, page 1] and this highlights a connection between random number generator and the distribution of primes. From [3] and [4] one sees that it is quite naive to expect good random reproduction with prime numbers. We are, however, interested in the properties underlying the distribution of prime numbers, which emerge as sufficient or insufficient arguments to conclude a proof by contradiction which tends to show that prime numbers are not randomly distributed. To achieve this end, we use prime gap sequence variation. The algorithm that we produce makes possible to deduce, in the case of a binary choice, a uniform behavior in the individual consecutive occurrence of primes, and no uniformity trait when the occurrences are taken collectively.

An Algorithmic Random Integer Generator based on Prime Numbers Distribution

More than a philosophic thinking, we combine two researchers wishes on randomness reproduction and prime numbers distribution. Indeed, up to now we cannot rigorously answer the question on randomness of primes [6, page 1]. We then propose an example of algorithms that can be deduced by that connection. For this purpose, our main procedure uses prime gap sequence variation. An evaluation on randomness reproduction is made at the end for a conclusion about prime numbers distribution and its implications.

An empirical study of the gap sequences for Shell sort

We present an improved version of the Shell sort algorithm. Using the algorithm, we study various geometrical sequences and the performance of Shell sort. We demonstrate that neither number of assignments nor the number of comparisons is sufficient to properly evaluate Shell sort and pick the optimal gap sequence. We argue that one should count both operations, as well as measure actual running times.

Tree-ring study of a Late Holocene forest buried in the Ubuka Basin, southwestern Japan

Buried trees in the Ubuka Basin, southwestern Japan, were investigated to identify the wood species and to build tree-ring chronologies. A total of 65 trees were collected belonging to three species: Japanese cedar (Cryptomeria japonica, 63 trees), Japanese nutmeg tree (Torreya nucifera, one tree) and Hinoki cypress (Chamaecyparis obtusa, one tree). Crossdating of the individual ring-width series resulted in four independent tree-ring chronologies covering 605, 576, 507 and 395 years. The absolute ages of these chronologies were determined to be 3676, 4166, 4576 and 4876 cal BP by definite-gap sequence modeling of radiocarbon dates measured at a constant gap of 30 years. An extremely long, continuous chronology can probably be developed in the future by increasing the number of samples at this site.