Gene tree species tree reconciliation with gene conversion

Identification and functional characterization of piwi1 gene in sea cucumber, Apostichopus japonicas

The sea cucumber (Apostichopus japonicus) is an economically important mariculture species in Asia. However, the genetic breeding of sea cucumbers is difficult because the sexes cannot be identified by appearance. Therefore, studies on sex-related genes are helpful in revealing the mechanisms of sex determination and differentiation in sea cucumbers. P-element induced wimpy testis (piwi) is a germ cell marker involved in gametogenesis in vertebrates; however, the expression pattern and function during gametogenesis remain unclear in sea cucumbers. In this study, we identified a piwi homolog gene in A. japonicus (Ajpiwi1) and investigated its expression pattern, and function. Ajpiwi1 is a maternal factor and is ubiquitously expressed in adult tissues, including the ovary and testis. Ajpiwi1 expression is strong in early oocytes, spermatocytes, and spermatogonia; weak in mature oocytes; and undetected in spermatids and intra-gonadal somatic cells. The knockdown of Ajpiwi1 by RNA interference (RNAi) led to the downregulation of other conserved sex-related genes such as dmrt1, foxl2, and germ cell-less. Therefore, Ajpiwi1 might play a critical role during gametogenesis in A. japonicus. This study creates new possibilities for studying sex-related gene functions in the sea cucumber and builds a gene function research platform based on RNAi for the first time.

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

MOTIVATION

Species tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome. All common approaches in phylogenomic studies either reduce available data or are error-prone, and thus, scalable methods that do not discard data and have high accuracy on large heterogeneous datasets are needed.

RESULTS

We present FastMulRFS, a polynomial-time method for estimating species trees without knowledge of orthology. We prove that FastMulRFS is statistically consistent under a generic model of GDL when adversarial GDL does not occur. Our extensive simulation study shows that FastMulRFS matches the accuracy of MulRF (which tries to solve the same optimization problem) and has better accuracy than prior methods, including ASTRAL-multi (the only method to date that has been proven statistically consistent under GDL), while being much faster than both methods.

AVAILABILITY AND IMPEMENTATION

FastMulRFS is available on Github (https://github.com/ekmolloy/fastmulrfs).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms, including-but not limited to-speciation ([Formula: see text]), gene duplication ([Formula: see text]), gene loss ([Formula: see text]), and horizontal gene transfer ([Formula: see text]). The reconstruction of a gene tree representing the evolution of a gene family constrained by a species tree is an important problem in phylogenomics. However, unlike in the multispecies coalescent evolutionary model that considers only speciation and incomplete lineage sorting events, very little is known about the search space for gene family histories accounting for gene duplication, gene loss and horizontal gene transfer (the [Formula: see text]-model). In this work, we introduce the notion of evolutionary histories defined as a binary ordered rooted tree describing the evolution of a gene family, constrained by a species tree in the [Formula: see text]-model. We provide formal grammars describing the set of all evolutionary histories that are compatible with a given species tree, whether it is ranked or unranked. These grammars allow us, using either analytic combinatorics or dynamic programming, to efficiently compute the number of histories of a given size, and also to generate random histories of a given size under the uniform distribution. We apply these tools to obtain exact asymptotics for the number of gene family histories for two species trees, the rooted caterpillar and complete binary tree, as well as estimates of the range of the exponential growth factor of the number of histories for random species trees of size up to 25. Our results show that including horizontal gene transfers induce a dramatic increase of the number of evolutionary histories. We also show that, within ranked species trees, the number of evolutionary histories in the [Formula: see text]-model is almost independent of the species tree topology. These results establish firm foundations for the development of ensemble methods for the prediction of reconciliations.

Parameterized Algorithms in Bioinformatics: An Overview

Bioinformatics regularly poses new challenges to algorithm engineers and theoretical computer scientists. This work surveys recent developments of parameterized algorithms and complexity for important NP-hard problems in bioinformatics. We cover sequence assembly and analysis, genome comparison and completion, and haplotyping and phylogenetics. Aside from reporting the state of the art, we give challenges and open problems for each topic.