Factors influencing gene family size variation among related species in a plant family

Abstract

the research plans; P.W. performed most of the analysis; B.M., N.P. and F.M. provided technical assistance to P.W.; P.W., M.L.-S., and S.-H.S. wrote the article. AbstractGene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, we used the Solanaceae family as a model to investigate differences in gene family size and the likely factors contributing to these differences. We found that genes in highly variable families have high turnover rate and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high-and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggests that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of oncefunctional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.

The round goby genome provides insights into mechanisms that may facilitate biological invasions

“…Custom HMM models for major NLR exons (FISNA-NACHT, and PRY-SPRY/ B30.2) were generated and utilized during this process (see Additional file 29 for hmm models). The majority of identified FISNA-NACHT exons contained frameshifts or a large insertion, indicating either pseudogenization, acquisition of new introns, problems with the assembly, or a combination of the three [228]. For subsequent phylogenetic analyses, only the 61 clearly intact NLRs were used.…”

Within and cross species predictions of plant specialized metabolism genes using transfer learning

“…The most recent duplication points for genes appearing to originate from multiple duplication nodes were defined by the highest-numbered node they belonged to (Figure S7). Pseudogenes in tomato were determined as in Wang et al (2018) where genomic regions with significant similarity to proteincoding genes but with premature stops/frameshifts and/or were truncated were treated as pseudogenes (64). Detailed methods and parsing scripts for different features can be found in: https://github.com/ShiuLab/SM-gene_prediction_Slycopersicum.…”

Read coverage as an indicator of misassembly in a short-read based genome assembly

“…Aside from gene annotations, we defined or obtained additional genome features including pseudogenes, transposable elements (TE), simple sequence repeat (SSR; stretch of DNA, 2 ~ 64bp, repeated >1 time and the repetitions are immediately adjacent to each other), and tandemly duplicated genes. Pseudogenes were defined as genomic regions with significant similarity to protein-coding genes had premature stops/frameshifts and/or were truncated as described in (27). Transposable element (TE) annotation was based on SGN ITAG2.4 release.…”

“…Minscore = 50, Maxperiod = 500 (28). Tandemly duplicated genes were identified using MCScanX-transposed (29), as described previously (27), where paralogs are directly adjacent to each other, or separated by…”