Paraphyly of bryophytes and close relationship of hornworts and vascular plants inferred from chloroplast rDNA spacers sequence analysis

Abstract

Phylogenetic analysis of nucleotide sequences of chloroplast rDNA internal transcribed spacer (cpITS) regions (cpITS2-4) of 14 species of liverworts, 4 species of hornworts, 20 species of mosses, 7 species of lycopods and 2 species of algae was carried out. Phylogenetic trees constructed by maximum parsimony, maximum likelihood and neighbour-joining methods indicated that bryophytes are not monophyletic. The cpITS data suggest that the hepatic lineage branches most deeply in the land plant topology and that mosses are monophyletic, forming the sister group of lycopods and hornworts. Within the mosses, a conspicuous deletion with distinct phylogenetic distribution was observed in the cpITS3 region. This deletion is absent in other land plants, including the enigmatic genus Takakia, and marks Takakia as an evolutionary lineage distinct from mosses. ÐåçþìåÏðîâåäåí ôèëîãåíåòè÷åñêèé àíàëèç íóêëåîòèäíûõ ïîñëåäîâàòåëüíîñòåé ñïåéñåðîâ õëîðîïëàñòíîé ðÄÍÊ (cpITS2-4) ó 14 âèäîâ ïå÷åíî÷íèêîâ, 4 âèäîâ àíòîöåðîòîâûõ, 20 âèäîâ ìõîâ, 7 âèäîâ ïëàóíîâèäíûõ è 2 âèäîâ õàðîâûõ âîäîðîñëåé. Ñîãëàñíî òîïîëîãèè ôèëîãåíåòè÷åñêèõ äåðåâüåâ, ðåêîíñòðóèðîâàííûõ ìåòîäàìè ìàêñèìàëüíîãî ïðàâäî-ïîäîáèÿ, áëèaeàéøåãî ñâÿçûâàíèÿ è ìàêñèìàëüíîé ýêîíîìèè, ìîõîîáðàçíûå íå ìîíîôèëåòè÷íû. Íà êëàäîãðàììàõ ñðåäè íàçåìíûõ ðàñòåíèé ïåðâûìè îòäåëÿþòñÿ âåòâè, âåäóùèå ê ïå÷åíî÷íèêàì. Ìõè ïðåäñòàþò êàê ìîíîôèëåòè÷åñêàÿ ãðóïïà, ñåñòðèíñêàÿ ê êëàäå, îáúåäèíÿþùåé ïëàóíîâèäíûå è àíòîöåðîòîâûå.  íóêëåîòèäíîé ïîñëåäî-âàòåëüíîñòè cpITS3 ó ìõîâ îáíàðóaeåíà ïðîòÿaeåííàÿ äåëåöèÿ, îòñóòñòâóþùàÿ ó îñòàëüíûõ íàçåìíûõ ðàñòåíèé, âêëþ÷àÿ Takakia.

The deepest divergences in land plants inferred from phylogenomic evidence

“…Hornworts have been strongly argued to be sister to all other land plants (14,15). On the other hand, several other studies hinted they could be sister to vascular plants (8)(9)(10)(11)(12)(13), and three recent analyses of cp-genome sequences and genomic structural characters are particularly noteworthy in this regard, because BS values supporting this relationship range from 82% to 100% (10, 12, 13). Our cp-genome matrices for the most part obtained the same results (Fig.…”

20,000 species and five key markers: The status of molecular bryophyte phylogenetics

“…700 nt of non-coding DNA plus the 4.5S, 5S, and trnR genes were spanned by the two amplicons. Length variation of the three spacers ranged between 62 and 238 nt in bryophytes (Samigullin et al 1998, no sequence lengths mentioned in Samigullin et al 2002). In contrast to the conserved 16 and 23S genes, the cpITS showed considerable length variability across bryophytes (Samigullin et al 2002) and vascular plants (Goremykin et al 1996), including several rather long but yet phylogenetically informative indels.…”

“…Length variation of the three spacers ranged between 62 and 238 nt in bryophytes (Samigullin et al 1998, no sequence lengths mentioned in Samigullin et al 2002). In contrast to the conserved 16 and 23S genes, the cpITS showed considerable length variability across bryophytes (Samigullin et al 2002) and vascular plants (Goremykin et al 1996), including several rather long but yet phylogenetically informative indels. However, findings such as the complete absence of cpITS2 in Riella and a markedly different cpITS2−4 sequence in Takakia than in all other bryophytes (Samigullin et al 2002) indicate that the phylogenetic utility of this region at higher taxonomic levels in bryophytes is limited.…”

“…Whereas the ITS1 and 2 of the nuclear rDNA became one of the most popular markers ( Fig. 2; see below), the respective plastid counterparts cpITS2 and 3 plus the 5S-trnR spacer ('cpITS4') were only used by Samigullin et al (1998Samigullin et al ( , 2002. They amplified the respective region in two parts, using two unnamed primers published by Goremykin et al (1996) for cpITS2−3 and newly designed primers (cpITS4F/cpITS4R) for cpITS4.…”

Sporoderm ultrastructure in Anthoceros agrestis Paton

“…Latest molecular data suggest that hornworts are sister group to vascular plants (Beckert et al, 1999, Samigullin et al, 2002Shaw & Renzaglia, 2004, Qui et al, 2006Troitsky et al, 2007;Stech et al, 2003), and that has aroused considerable interest to their morphology. Data on the spore morphology and ultrastructure are particularly pertinent because they allow comparisons with fossil material, including even the earliest land plants (Taylor, 2003;Taylor et al, 2011).…”